./BNW/0000775000076600007660000000000012133076605011622 5ustar abhatta3abhatta3./BNW/src/0000775000076600007660000000000012133077361012411 5ustar abhatta3abhatta3./BNW/src/print_structure/0000775000076600007660000000000012133051131015650 5ustar abhatta3abhatta3./BNW/src/print_structure/structure.c0000775000076600007660000000252312133041534020067 0ustar abhatta3abhatta3#include #include #include #include struct st{ char *name; double *data; }*st_tab; main(int argc,char *argv[]) { FILE *fp1,*fp2,*fp3; char line[2500]; int i,j,rd; double d,row; double thr=atof(argv[5]); fp1=fopen(argv[2],"r"); fp2=fopen(argv[3],"w"); fp3=fopen(argv[4],"w"); row=0.0; while(fgets(line,2500,fp1)!=NULL) row++; rd=(int)sqrt(row); printf("%d\n",rd); fclose(fp1); fp1=fopen(argv[1],"r"); st_tab=(struct st *)malloc(sizeof(struct st)*rd); for(i=0;ithr) fprintf(fp3,"1\t"); else fprintf(fp3,"0\t"); } fprintf(fp2,"\n"); fprintf(fp3,"\n"); } } ./BNW/src/example1/0000775000076600007660000000000012133077220014117 5ustar abhatta3abhatta3./BNW/src/example1/model_averaging_probabilities.txt0000664000076600007660000000117712133077220022721 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0.000000 0.032781 0.000000 1.000000 0.000000 0.000000 0.082576 0.000000 0.032781 0.000000 0.011504 0.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.018040 0.000000 0.107043 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.092149 0.000000 0.000000 0.000000 0.016134 0.120123 0.000000 1.000000 0.012820 0.395956 0.000000 0.000000 0.016574 0.000000 0.000000 0.000000 0.024600 0.032382 0.000000 0.000000 0.030586 0.000000 0.000000 0.000000 0.000000 0.160132 0.000000 0.000000 0.148572 0.089516 0.446511 0.032359 0.094787 0.000000 ./BNW/src/example1/banlist.txt0000664000076600007660000000001012121621012016272 0ustar abhatta3abhatta3From To ./BNW/src/example1/test_model_averaging_probabilities.txt0000664000076600007660000000117712133055616023765 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0.000000 0.032781 0.000000 1.000000 0.000000 0.000000 0.082576 0.000000 0.032781 0.000000 0.011504 0.000000 1.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.018040 0.000000 0.107043 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.092149 0.000000 0.000000 0.000000 0.016134 0.120123 0.000000 1.000000 0.012820 0.395956 0.000000 0.000000 0.016574 0.000000 0.000000 0.000000 0.024600 0.032382 0.000000 0.000000 0.030586 0.000000 0.000000 0.000000 0.000000 0.160132 0.000000 0.000000 0.148572 0.089516 0.446511 0.032359 0.094787 0.000000 ./BNW/src/example1/model_structure.txt0000664000076600007660000000027712133077220020106 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ./BNW/src/example1/whitelist.txt0000664000076600007660000000001012121621012016652 0ustar abhatta3abhatta3From To ./BNW/src/example1/test_model_structure.txt0000664000076600007660000000027712133055616021152 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ./BNW/src/example1/input.txt0000664000076600007660000002506312133055514016027 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 2 2 1 1 1 1 1 1 2 2 0.46259 1.2692 -1.3164 -0.44096 0.5929 -0.75422 1 1 -0.10011 -0.88834 1.6407 0.99972 0.31288 0.65602 1 1 -1.0533 -0.55296 1.2715 1.3686 -0.19153 0.37361 1 2 0.042371 0.13573 -0.72659 -0.66133 0.43157 -1.6715 1 2 -0.68686 -1.6152 -0.95019 -1.2239 0.12319 -0.79155 1 1 -0.4558 0.090877 0.94224 1.2354 -0.36356 0.34937 1 1 0.237 -0.49002 1.8939 1.4399 0.033059 1.3229 1 2 0.070265 0.22547 -1.4903 -0.069341 -0.16148 -0.01449 1 1 -0.69146 -0.43461 1.1501 0.21205 -0.18087 0.32746 1 1 0.31535 -0.9858 0.57816 0.35924 0.12866 1.0553 2 1 1.2718 0.39314 0.6669 0.90002 -0.30206 1.3376 1 1 1.1871 -0.45611 0.87227 0.31014 -0.092846 0.81278 2 1 -1.0168 -0.44286 1.6933 0.72968 0.038808 0.81906 2 2 -0.25313 0.52468 0.02823 -0.20984 -0.075809 -1.3591 1 2 -0.58108 -0.3967 -0.11925 -0.61288 0.46778 0.090941 1 2 -0.88043 -0.28187 -1.1645 -1.2543 -0.28951 -1.039 1 2 0.54121 0.24395 -1.0043 -1.4483 -0.19839 -2.5407 2 1 0.47375 1.1319 0.68553 1.035 0.44043 1.3011 2 1 0.57785 0.69093 1.5941 1.6735 0.19981 0.50708 1 2 -0.43989 0.0024131 -1.5405 -1.2304 -0.15382 -1.1058 2 1 0.38035 -0.063535 1.1606 1.3124 -0.38043 0.6277 1 2 0.70114 -0.41044 -0.39767 -1.5424 0.27477 -0.76183 1 1 -0.9406 -0.20526 1.3302 1.097 0.16006 1.2988 1 2 0.52122 0.064793 -0.031492 0.21696 -0.41979 -0.79123 1 2 -0.53387 -0.71043 -0.52344 -1.5584 -0.09538 -1.5781 1 1 0.49563 -0.58126 0.7747 1.274 0.19196 0.10624 2 2 1.1499 1.879 0.43595 0.73474 0.045381 -0.88645 1 2 0.40705 -0.37647 -0.19815 -1.5366 0.37167 -0.10553 2 2 0.62526 0.043371 -0.64449 -0.44076 -0.4318 -0.91807 1 1 -0.61788 -0.62414 0.3169 0.85091 -0.10135 0.79065 1 1 0.18491 -1.5226 1.1149 0.75046 0.25948 0.42431 2 2 0.86063 0.92883 -1.1584 -0.099858 -0.55095 -0.064129 1 2 -0.28946 0.0057533 -0.95703 -0.44018 0.084268 -0.23718 1 1 -0.073096 0.16452 1.4444 1.1452 0.46025 0.30452 1 1 0.15637 -0.73137 0.585 -0.046911 0.43881 1.2888 1 2 0.081142 -0.63691 -0.14883 0.66593 -0.13479 -0.22207 1 1 0.10876 -0.23383 1.8314 1.3282 0.4362 0.90139 1 2 -1.0582 -0.97152 -0.57118 -1.2617 0.17115 -0.060679 2 2 -0.47421 -0.56819 -0.38775 0.035215 0.51982 -1.6309 2 2 -0.10242 0.8127 0.41773 -1.1308 -0.30719 -0.80758 1 1 -0.083462 -0.4565 1.1556 0.3299 0.087362 0.31349 1 2 -0.98158 0.01727 -1.3281 -1.4474 0.54555 -0.10096 1 1 -0.80604 -0.19415 1.4986 1.3386 -0.16367 0.68271 1 1 0.80082 -0.57853 1.0716 0.94015 -0.54114 0.032172 2 2 2.0456 0.97954 -0.45536 -0.14332 -0.25819 -1.0833 1 1 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-0.6592 -2.1961 -0.013175 0.46007 1 2 -0.5254 0.0031225 -0.77758 0.8169 0.13224 -0.65572 2 1 0.24551 1.5078 0.10719 1.1454 0.70578 0.59051 1 2 0.29875 -0.11455 -1.0497 -0.77881 0.080708 -0.48337 1 1 -0.1047 0.011628 1.2504 0.41776 -0.20102 1.2252 1 2 0.44808 -0.8165 -0.080134 -0.49618 0.051011 -0.71722 2 1 2.0365 1.5592 1.3257 1.2472 -0.47899 0.10943 1 1 -0.16507 -0.66011 0.98739 0.58519 0.245 -0.43277 1 2 -0.028366 -0.16961 -1.3266 0.14248 -0.24634 -1.1154 2 1 0.92842 1.8842 1.3169 1.0358 -0.20988 0.88021 2 2 0.33158 0.32463 -0.50924 0.40233 0.54391 -0.24309 1 2 1.2555 0.1928 -0.487 0.048779 -0.23483 -1.477 2 1 0.75021 0.85943 -0.2323 0.10748 -0.68906 0.84276 2 2 0.6297 1.7397 -1.6136 -0.43268 -0.21442 -0.77462 2 1 0.53168 1.0807 1.0853 0.62304 0.44036 0.48087 1 2 -0.31256 -0.69771 -0.88556 -1.333 0.038614 -1.5744 1 2 -0.039695 -0.52447 0.91401 -0.93272 0.53434 -0.080746 2 1 -0.16596 0.56821 0.76008 0.45442 0.10286 0.6539 1 2 -0.4331 -0.89669 -1.3097 -1.2157 0.1065 -0.8512 1 2 -0.34708 -0.51457 -1.012 -0.39437 -0.55374 -1.144 2 2 0.024082 0.7128 -1.3702 -1.4492 -0.10228 -0.59071 1 2 -0.0037109 -0.68845 -0.649 -0.91581 0.066805 -0.98583 2 1 0.68706 0.067424 0.87139 0.7938 -0.099645 1.529 2 2 -0.31183 0.57814 -0.80815 -0.66724 -0.31919 -0.61319 1 2 -0.11153 -0.6246 -0.27979 -0.18363 0.83639 0.014919 2 2 0.20406 1.5838 -0.96334 -1.1228 -0.17808 -1.2123 2 2 -0.1134 0.63358 -0.53321 -0.84276 -0.27657 -0.36992 1 2 0.25517 0.67006 -0.1349 0.18275 0.40982 -0.62487 1 1 -1.2684 0.31042 0.91155 0.66143 0.2483 -0.12434 1 1 -0.97542 -0.85419 0.7663 0.16362 -0.18737 0.67266 1 2 -0.043882 -0.62746 -0.82816 -0.40626 -0.051048 -0.61297 1 1 0.59605 -0.45852 1.2962 0.78156 -0.48154 0.17778 2 2 -0.06266 1.1144 -0.80524 -0.3189 -0.16038 -0.96372 1 2 -1.1821 1.0798 -1.3407 -0.52643 0.12458 -0.7871 2 2 0.59446 0.89186 -0.97856 -0.64658 0.2712 -1.5538 1 2 0.15067 0.41827 -1.0487 -1.0551 0.19143 -1.4537 1 2 -1.073 0.022587 -1.7088 -1.3777 0.1964 -0.84025 2 1 0.20928 1.8026 1.2073 2.78 0.15131 0.3448 1 2 -1.1317 -0.6359 -0.70457 -1.676 -0.22886 -0.58769 1 1 -0.039428 -0.58746 0.56 0.7896 -0.052581 0.99511 1 2 0.55023 -0.20403 0.138 -0.70518 0.66927 -0.28861 2 2 0.57423 1.1886 0.092876 0.025677 -0.41099 -1.2858 2 2 -0.14179 1.5827 -0.94328 0.7703 -0.43967 -0.50448 2 2 0.14666 1.0492 -0.0030259 -0.62418 -0.087515 -0.048386./BNW/src/run.sh0000775000076600007660000000314412133057427013557 0ustar abhatta3abhatta3#!/bin/bash d=`dirname $0` #Name of the data directory data=$1 DIR="$d/$data/tmp" DIR_1="$d/$data/tmp/" mkdir -p $DIR #Arguments. User can modify these arguments. #Input data file name. input="$d/$data/input.txt" #Input banlist file ban="$d/$data/banlist.txt" #Input whitelist file white="$d/$data/whitelist.txt" #Max parents. We set the number of maximum parents to 4 maxparent=4 #k is the numbeer of structure considered in each step of k-best structure learning algorithm. We set the value of k=100 k=100 #Model averaging threshold. We set the model averaging threshold to 0.5 THR=0.5 echo "Dataset with number of variables:" head -1 $input|wc -w echo "Dataset with number of samples:" wc -l $input|cut -d' ' -f1 echo "Parameters are: max parent = $maxparent, k= $k and model averaging threshold = $THR" start_time1=`date +%s` #execute local score ./network_score $input $ban $white $maxparent $DIR end_time=`date +%s` echo "Local score execution time was `expr $end_time - $start_time1` s." start_time=`date +%s` #execute k-best structure learning sh $d/k-best/src/data2netk_poster.sh $input $DIR $k $maxparent end_time=`date +%s` echo "k-best parent total execution time was `expr $end_time - $start_time` s." start_time=`date +%s` #execute print structure ./structure $input $DIR/postProbEachEdge.txt $d/$data/model_averaging_probabilities.txt $d/$data/model_structure.txt $THR end_time1=`date +%s` echo "Preparing structure output file from model averaging matrix. Execution time was `expr $end_time1 - $start_time` s." echo "Total execution time was `expr $end_time1 - $start_time1` s." rm -r $DIR_1* rmdir $DIR ./BNW/src/build.sh0000775000076600007660000000026712124110004014032 0ustar abhatta3abhatta3#!/bin/bash gcc ./localscore/network_score.c ./localscore/libRmath.so -lm -o network_score gcc ./print_structure/structure.c -lm -o structure cd ./k-best/src/ sh buildk_poster.sh ./BNW/src/BNW_src_files.tar0000664000076600007660000002400012133077361015574 0ustar abhatta3abhatta3./BNW/src/example2/0000775000076600007660000000000012133076532014125 5ustar abhatta3abhatta3./BNW/src/example2/banlist.txt0000664000076600007660000000030412133056154016315 0ustar abhatta3abhatta3From To Geno1 Geno2 Geno2 Geno1 Trait5 Geno1 Trait5 Geno2 Trait5 Trait1 Trait5 Trait2 Trait5 Trait3 Trait5 Trait4 Trait6 Geno1 Trait6 Geno2 Trait6 Trait1 Trait6 Trait2 Trait6 Trait3 Trait6 Trait4 ./BNW/src/example2/test_model_averaging_probabilities.txt0000664000076600007660000000117712133056344023765 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0.000000 0.000000 0.013425 1.000000 0.000000 0.000000 0.138601 0.000000 0.000000 0.000000 0.052772 0.000000 1.000000 0.000000 0.006889 0.000000 0.000000 0.000000 0.000000 0.006712 0.070754 0.000000 0.192475 0.000000 0.000000 0.000000 0.993288 0.000000 0.010327 1.000000 0.152549 0.000000 0.000000 0.000000 0.075227 0.195153 0.000000 1.000000 0.049256 1.000000 0.000000 0.000000 0.071229 0.000000 0.000000 0.000000 0.057840 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.393439 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.116105 0.000000 ./BNW/src/example2/whitelist.txt0000664000076600007660000000004412133056266016702 0ustar abhatta3abhatta3From To Trait2 Trait4 Trait3 Trait6 ./BNW/src/example2/test_model_structure.txt0000664000076600007660000000027712133056344021152 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ./BNW/src/example2/input.txt0000664000076600007660000002506312133056032016024 0ustar abhatta3abhatta3Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 2 2 1 1 1 1 1 1 2 2 0.46259 1.2692 -1.3164 -0.44096 0.5929 -0.75422 1 1 -0.10011 -0.88834 1.6407 0.99972 0.31288 0.65602 1 1 -1.0533 -0.55296 1.2715 1.3686 -0.19153 0.37361 1 2 0.042371 0.13573 -0.72659 -0.66133 0.43157 -1.6715 1 2 -0.68686 -1.6152 -0.95019 -1.2239 0.12319 -0.79155 1 1 -0.4558 0.090877 0.94224 1.2354 -0.36356 0.34937 1 1 0.237 -0.49002 1.8939 1.4399 0.033059 1.3229 1 2 0.070265 0.22547 -1.4903 -0.069341 -0.16148 -0.01449 1 1 -0.69146 -0.43461 1.1501 0.21205 -0.18087 0.32746 1 1 0.31535 -0.9858 0.57816 0.35924 0.12866 1.0553 2 1 1.2718 0.39314 0.6669 0.90002 -0.30206 1.3376 1 1 1.1871 -0.45611 0.87227 0.31014 -0.092846 0.81278 2 1 -1.0168 -0.44286 1.6933 0.72968 0.038808 0.81906 2 2 -0.25313 0.52468 0.02823 -0.20984 -0.075809 -1.3591 1 2 -0.58108 -0.3967 -0.11925 -0.61288 0.46778 0.090941 1 2 -0.88043 -0.28187 -1.1645 -1.2543 -0.28951 -1.039 1 2 0.54121 0.24395 -1.0043 -1.4483 -0.19839 -2.5407 2 1 0.47375 1.1319 0.68553 1.035 0.44043 1.3011 2 1 0.57785 0.69093 1.5941 1.6735 0.19981 0.50708 1 2 -0.43989 0.0024131 -1.5405 -1.2304 -0.15382 -1.1058 2 1 0.38035 -0.063535 1.1606 1.3124 -0.38043 0.6277 1 2 0.70114 -0.41044 -0.39767 -1.5424 0.27477 -0.76183 1 1 -0.9406 -0.20526 1.3302 1.097 0.16006 1.2988 1 2 0.52122 0.064793 -0.031492 0.21696 -0.41979 -0.79123 1 2 -0.53387 -0.71043 -0.52344 -1.5584 -0.09538 -1.5781 1 1 0.49563 -0.58126 0.7747 1.274 0.19196 0.10624 2 2 1.1499 1.879 0.43595 0.73474 0.045381 -0.88645 1 2 0.40705 -0.37647 -0.19815 -1.5366 0.37167 -0.10553 2 2 0.62526 0.043371 -0.64449 -0.44076 -0.4318 -0.91807 1 1 -0.61788 -0.62414 0.3169 0.85091 -0.10135 0.79065 1 1 0.18491 -1.5226 1.1149 0.75046 0.25948 0.42431 2 2 0.86063 0.92883 -1.1584 -0.099858 -0.55095 -0.064129 1 2 -0.28946 0.0057533 -0.95703 -0.44018 0.084268 -0.23718 1 1 -0.073096 0.16452 1.4444 1.1452 0.46025 0.30452 1 1 0.15637 -0.73137 0.585 -0.046911 0.43881 1.2888 1 2 0.081142 -0.63691 -0.14883 0.66593 -0.13479 -0.22207 1 1 0.10876 -0.23383 1.8314 1.3282 0.4362 0.90139 1 2 -1.0582 -0.97152 -0.57118 -1.2617 0.17115 -0.060679 2 2 -0.47421 -0.56819 -0.38775 0.035215 0.51982 -1.6309 2 2 -0.10242 0.8127 0.41773 -1.1308 -0.30719 -0.80758 1 1 -0.083462 -0.4565 1.1556 0.3299 0.087362 0.31349 1 2 -0.98158 0.01727 -1.3281 -1.4474 0.54555 -0.10096 1 1 -0.80604 -0.19415 1.4986 1.3386 -0.16367 0.68271 1 1 0.80082 -0.57853 1.0716 0.94015 -0.54114 0.032172 2 2 2.0456 0.97954 -0.45536 -0.14332 -0.25819 -1.0833 1 1 -0.30148 0.20623 0.64194 0.76414 -0.59067 0.64326 1 1 -0.55625 -0.26957 1.8447 1.6568 -0.38077 0.58831 1 2 0.11898 0.80706 -0.025844 -0.57984 -0.23395 -1.1554 1 2 -0.095497 -1.0637 -0.92583 -0.57928 0.23695 -0.42992 2 2 0.066154 0.73037 -0.73622 -0.57047 0.39169 0.40928 1 1 0.81522 0.11381 0.68971 0.29219 0.037792 0.81502 1 1 -0.65356 -0.20182 0.92089 0.92298 -0.5417 0.49215 1 1 -0.90826 -0.10979 1.3847 0.75954 -0.20255 0.32975 1 2 -0.25671 -1.1903 -1.4241 -1.6058 -0.062549 -1.3981 2 2 -1.8038 -1.4801 -0.94121 -1.6244 0.4817 -0.0029469 1 2 0.12651 0.028719 -1.5818 -1.0266 0.19779 -0.36357 1 1 -1.0658 -0.58443 0.68956 0.35467 0.11177 1.5243 1 2 0.14729 -0.15111 -0.027639 -0.2899 0.11533 -0.60305 2 2 -0.76889 0.87161 -0.83556 -1.1777 -0.21878 -0.98527 2 2 0.12252 0.49068 -0.2557 -1.5816 0.25332 -0.78715 1 1 -0.40287 0.26456 0.62208 0.60909 0.36074 0.092703 2 1 -0.78301 1.4641 1.3162 1.9448 -0.10841 0.9618 1 2 -0.25018 -0.32797 -1.113 -1.6123 0.6272 -1.2718 2 1 0.15804 -0.18147 2.4571 0.59504 -0.34056 0.8691 2 1 -0.582 0.25738 1.4075 0.92251 -0.40889 0.66381 1 1 -0.26827 0.58632 0.51883 1.5745 -0.13818 1.0526 1 2 0.13453 0.18218 -0.51676 -0.54166 -0.36636 -1.206 2 1 1.1502 0.36164 1.9983 1.0809 0.11272 0.67683 1 2 0.27812 0.46559 -1.6109 -0.91039 0.3803 -0.71802 2 1 0.15292 0.61921 0.71009 1.3063 -0.35819 0.8661 1 2 0.19902 0.48986 -1.4026 -0.8495 0.47158 0.0622 2 1 0.4838 1.1096 1.4392 1.1438 0.34739 0.084004 1 1 -0.63609 -0.35105 0.63581 1.1939 -0.062938 0.91353 1 2 0.64203 -0.5095 -1.7792 -0.88803 0.43482 -0.66314 1 1 -0.18434 -0.48157 0.69942 0.56942 -0.019967 0.50506 1 1 0.10168 -1.0928 1.2144 0.28313 0.22159 0.54058 1 1 -0.18578 -0.45336 1.5468 0.99679 0.11821 1.0476 1 2 -0.60607 -1.1275 -0.90963 -0.69014 -0.33163 -1.2734 1 1 -0.35353 -0.42708 0.78989 0.14094 -0.056632 0.80598 1 1 -0.020221 -1.1235 1.9782 -0.041281 0.19857 1.2488 1 1 1.2346 -0.37121 1.3325 1.1237 -0.027458 1.0044 2 2 -0.54489 1.6812 -0.59836 -0.012441 0.41243 -0.58835 2 1 -0.029577 2.1707 1.3285 1.2109 0.29684 0.90646 2 2 0.70774 1.0606 -1.3996 -0.020914 -0.60955 -1.2187 2 1 0.07926 0.52862 1.3994 0.54549 0.55303 0.16155 1 1 0.041856 -0.92023 0.87269 -0.66601 -0.15945 0.1004 1 2 0.17665 0.31945 -1.7756 -0.60442 0.020525 -1.0625 1 1 -0.090238 -0.65111 0.56993 -0.4117 -0.19486 -0.18849 1 2 0.059166 -0.47194 -0.69068 -0.41022 0.25867 -0.057175 1 2 0.10473 0.66887 0.082035 -0.55975 -0.28439 -1.468 1 1 -0.20937 -0.36621 0.09609 0.28164 0.24673 -0.11107 1 2 -1.2678 0.22369 -0.42201 -0.70103 0.075915 -1.3347 1 2 -0.35467 0.11166 -0.42144 -0.095223 -0.29936 -0.68322 2 2 0.84875 1.24 -0.81217 0.084034 -0.32224 -1.6241 2 1 -0.45939 1.3208 0.97993 1.2991 -0.015791 1.487 1 2 -0.42254 -0.57928 -0.58529 -2.2375 0.51999 -0.79909 2 1 0.32092 -0.13796 0.67098 0.24639 -0.36066 -0.032948 1 2 -1.2408 -0.94836 0.026276 -0.37981 -0.02237 -0.38777 2 2 0.20959 2.1466 -1.7027 -1.3169 -0.16515 -1.046 2 2 -0.10482 1.3773 -1.2998 -0.014223 0.34065 -0.35362 1 2 -0.6188 -1.2477 -0.62084 0.27682 0.1674 -0.8918 1 1 -0.97246 -0.73017 1.3843 1.5549 0.1067 0.85754 1 1 0.74567 -0.032694 1.1153 0.97318 -0.0033905 0.85059 2 2 0.29324 -0.090608 -0.4945 -1.0484 -0.14987 -1.0141 2 1 -0.86818 0.44948 1.8531 0.51896 -0.021141 1.8486 1 2 0.362 -0.29749 -0.66525 0.21709 -0.15594 -1.4087 1 2 -0.17675 0.36465 -0.45423 -1.262 0.22968 -1.246 1 2 -0.34633 -0.16067 -1.2216 -1.3019 -0.040891 -1.2935 1 2 0.44608 -0.57732 0.25606 -1.1664 0.54705 -0.19859 1 2 0.45398 -0.55214 -0.33433 -0.085418 -0.10094 -0.48509 1 2 0.12407 0.022419 -1.0312 -0.47727 0.20924 -1.2961 1 1 -0.76644 -1.1794 1.2345 0.84756 0.1532 0.77648 1 2 -0.10329 -0.53768 -0.67677 -0.58708 -0.014634 -0.036347 1 1 0.2378 0.15372 0.49652 0.29193 0.19047 1.152 1 2 0.024605 -0.38937 -0.89907 -0.42106 0.16921 -0.80893 1 2 0.28812 0.26265 -0.94234 -0.88527 -0.49803 0.48254 1 1 0.85086 0.11783 1.5014 1.2382 0.24441 1.3649 2 2 0.86172 0.14894 -0.4846 -1.3488 -0.41844 -1.1372 1 2 0.67971 -0.27488 -0.50687 -0.79153 -0.093399 -1.391 1 1 -0.91977 -0.66099 0.5801 0.46587 -0.2263 1.43 1 2 0.88213 -0.48674 -0.42406 -1.2762 0.28981 -1.0813 2 1 -0.36583 0.51518 1.4491 1.4995 -0.073755 1.1218 1 1 -0.54006 -0.59443 0.81263 0.65809 -0.15621 1.2508 2 2 1.2125 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0.011628 1.2504 0.41776 -0.20102 1.2252 1 2 0.44808 -0.8165 -0.080134 -0.49618 0.051011 -0.71722 2 1 2.0365 1.5592 1.3257 1.2472 -0.47899 0.10943 1 1 -0.16507 -0.66011 0.98739 0.58519 0.245 -0.43277 1 2 -0.028366 -0.16961 -1.3266 0.14248 -0.24634 -1.1154 2 1 0.92842 1.8842 1.3169 1.0358 -0.20988 0.88021 2 2 0.33158 0.32463 -0.50924 0.40233 0.54391 -0.24309 1 2 1.2555 0.1928 -0.487 0.048779 -0.23483 -1.477 2 1 0.75021 0.85943 -0.2323 0.10748 -0.68906 0.84276 2 2 0.6297 1.7397 -1.6136 -0.43268 -0.21442 -0.77462 2 1 0.53168 1.0807 1.0853 0.62304 0.44036 0.48087 1 2 -0.31256 -0.69771 -0.88556 -1.333 0.038614 -1.5744 1 2 -0.039695 -0.52447 0.91401 -0.93272 0.53434 -0.080746 2 1 -0.16596 0.56821 0.76008 0.45442 0.10286 0.6539 1 2 -0.4331 -0.89669 -1.3097 -1.2157 0.1065 -0.8512 1 2 -0.34708 -0.51457 -1.012 -0.39437 -0.55374 -1.144 2 2 0.024082 0.7128 -1.3702 -1.4492 -0.10228 -0.59071 1 2 -0.0037109 -0.68845 -0.649 -0.91581 0.066805 -0.98583 2 1 0.68706 0.067424 0.87139 0.7938 -0.099645 1.529 2 2 -0.31183 0.57814 -0.80815 -0.66724 -0.31919 -0.61319 1 2 -0.11153 -0.6246 -0.27979 -0.18363 0.83639 0.014919 2 2 0.20406 1.5838 -0.96334 -1.1228 -0.17808 -1.2123 2 2 -0.1134 0.63358 -0.53321 -0.84276 -0.27657 -0.36992 1 2 0.25517 0.67006 -0.1349 0.18275 0.40982 -0.62487 1 1 -1.2684 0.31042 0.91155 0.66143 0.2483 -0.12434 1 1 -0.97542 -0.85419 0.7663 0.16362 -0.18737 0.67266 1 2 -0.043882 -0.62746 -0.82816 -0.40626 -0.051048 -0.61297 1 1 0.59605 -0.45852 1.2962 0.78156 -0.48154 0.17778 2 2 -0.06266 1.1144 -0.80524 -0.3189 -0.16038 -0.96372 1 2 -1.1821 1.0798 -1.3407 -0.52643 0.12458 -0.7871 2 2 0.59446 0.89186 -0.97856 -0.64658 0.2712 -1.5538 1 2 0.15067 0.41827 -1.0487 -1.0551 0.19143 -1.4537 1 2 -1.073 0.022587 -1.7088 -1.3777 0.1964 -0.84025 2 1 0.20928 1.8026 1.2073 2.78 0.15131 0.3448 1 2 -1.1317 -0.6359 -0.70457 -1.676 -0.22886 -0.58769 1 1 -0.039428 -0.58746 0.56 0.7896 -0.052581 0.99511 1 2 0.55023 -0.20403 0.138 -0.70518 0.66927 -0.28861 2 2 0.57423 1.1886 0.092876 0.025677 -0.41099 -1.2858 2 2 -0.14179 1.5827 -0.94328 0.7703 -0.43967 -0.50448 2 2 0.14666 1.0492 -0.0030259 -0.62418 -0.087515 -0.048386./BNW/src/k-best/0000775000076600007660000000000012133051130013560 5ustar abhatta3abhatta3./BNW/src/k-best/src/0000775000076600007660000000000012133077177014372 5ustar abhatta3abhatta3./BNW/src/k-best/src/Engine.h0000775000076600007660000015450411740177362015764 0ustar abhatta3abhatta3#ifndef ENGINE_H #define ENGINE_H #include #include #include"Arguments.h" #include"Model.h" #include #include #define MARK 9.0e99 // Substitutes la += log(1+exp(lb-la)) <=> a = a + b. #define LOGADD(la,lb) if(la>8e99||lb-la>100) la=lb;else la+=log(1+exp(lb-la)); #define LOG_ZERO -1.0e101 using namespace std; #include"UpdateHR.h" //---------------- // Fast Möbius transform routines. void sub_fumt(int j, int d, int S, int overlap, double *t, double *s, int n, int k){ if (d < n && overlap < k){ sub_fumt(j, d+1, S, overlap, t, s, n, k); S |= (1 << d); overlap += (d >= j+1); sub_fumt(j, d+1, S, overlap, t, s, n, k); } else{ //base case: //since s[S] = MARK initially, and the following 3 cases, s[S] must be assigned some score (neither MARK nor undecided) s[S] = MARK; //jinS: j is in S int jinS = ((S >> j) & 1); if (overlap + jinS <= k) s[S] = t[S]; //if (jinS) LOGADD(s[S], t[S - (1 << j)]); if (jinS) logAdd_New(s[S], t[S - (1 << j)]); } } // Fast upward Möbius transform: // s(S) := \sum_{T \subseteq S : |T| \leq k} t(T). void fumt(double *t, double *s, int n, int k){ double *tmp, *sprev = new double[1 << n]; for (int T = 0; T < (1<log_lcp(0, T)<num_layers(); h ++){ int *Vh, *Vu, *Vl; int nh, nu, nl; model->layer(h, &Vh, &nh); model->upper_layers(h, &Vu, &nu); model->lower_layers(h, &Vl, &nl); cerr<<"Layer "<num_layers(); //Arguments::option == 0 means the rebel method with new Dirichlet hyper-param (see sub_beta) if(Arguments::option == 0){ compute_edge_probabilities(0); } //Arguments::option == 1 means the forward method else if(Arguments::option == 1){ compute_edge_probabilities_forward(0); } //Arguments::option == 2 means the backward method else if(Arguments::option == 2){ compute_edge_probabilities_backward(0); } //Arguments::option == 3 means the mix method in the UAI paper else if(Arguments::option == 3){ compute_edge_probabilities_mixIndegree(0); //compute_edge_probabilities_mixIndegreeNoLog(0); } //Arguments::option == 4 means the computation used in top-k else if(Arguments::option == 4){ compute_edge_probabilities_top_k(0); } //Arguments::option == 5 means the computation required for in and out features else if(Arguments::option == 5){ //For In_Out features compute_edge_probabilities_in_out_features(0); } } // Computes probabilities for edges pointing to the h-th layer. void compute_edge_probabilities(int h){ cerr<<"\nREBEL Method:" << endl; cerr<<" Compute edge probabilities for Layer "<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); beta = new double*[nh]; alpha = new double*[nh]; k = model->max_indegree(); cerr<<" . "<makeADTree(); } for (int j = 0; j < nh; j ++){ beta[j] = new double[1 << nh]; //int i = Vh[j]; compute_beta(j, Vh, nh, Vu, nu); } //If Arguments::ADtree == 1, then delete the whole tree if(Arguments::ADtree == 1){ model->freeADTree(); } gettimeofday(&endTime, &myTimeZone); betaTime = (endTime.tv_sec - startTime.tv_sec) + (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ; cerr<<" . Tables beta are now ready."<print_edge_prob( cout, Vh[i], Vh[j], exp(log_prob - gb[(1<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); beta = new double*[nh]; alpha = new double*[nh]; betaNume = new double*[nh]; alphaNume = new double*[nh]; k = model->max_indegree(); cerr<<" . "<print_edge_prob(cout, Vh[vv], Vh[uu], exp(gfNume[(1<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); //If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first if(Arguments::ADtree == 1){ model->makeADTree(); } beta = new double*[nh]; alpha = new double*[nh]; betaNume = new double*[nh]; alphaNume = new double*[nh]; k = model->max_indegree(); cerr<<" . "<print_edge_prob(cout, Vh[vv], Vh[uu], exp(hFuncNume[(1<freeADTree(); } delete [] hFunc; //it better to move the following line inside the double for loop delete [] hFuncNume; for (int j = 0; j < nh; j ++){ delete [] beta[j]; delete [] betaNume[j]; delete [] alpha[j]; delete [] alphaNume[j]; } delete [] beta; delete [] betaNume; delete [] alpha; delete [] alphaNume; cerr<<" Edge probabilities now computed."<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); //If Arguments::ADtree == 1, user wants to use ADtree, then make the whole tree first if(Arguments::ADtree == 1){ model->makeADTree(); } beta = new double*[nh]; alpha = new double*[nh]; betaNume = new double*[nh]; alphaNume = new double*[nh]; k = model->max_indegree(); cerr<<" . "<print_edge_prob(cout, Vh[vv], Vh[uu], exp(RRFuncNume[(1<freeADTree(); } delete [] RRFunc; //it better to move the following line inside the double for loop delete [] RRFuncNume; for (int j = 0; j < nh; j ++){ delete [] beta[j]; delete [] betaNume[j]; delete [] alpha[j]; delete [] alphaNume[j]; } delete [] beta; delete [] betaNume; delete [] alpha; delete [] alphaNume; cerr<<" Edge probabilities now computed."<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); beta = new double*[nh]; alpha = new double*[nh]; betaInOut = new double*[nh]; alphaInOut = new double*[nh]; k = model->max_indegree(); cerr<<" . "<makeADTree(); } for (int j = 0; j < nh; j ++){ beta[j] = new double[1 << nh]; compute_beta(j, Vh, nh, Vu, nu); alpha[j] = new double[1 << nh]; compute_alpha(j, Vh, nh); cerr<<" . Tables beta and alpha computed for node "<print_edge_prob(cout, Vh[vv], Vh[uu], exp(RRFuncNume[(1<freeADTree(); } delete [] RRFunc; delete [] RRFuncInOut; delete [] inFeatureEdges; delete [] outFeatureEdges; for (int j = 0; j < nh; j ++){ delete [] beta[j]; delete [] betaInOut[j]; delete [] alpha[j]; delete [] alphaInOut[j]; } delete [] beta; delete [] betaInOut; delete [] alpha; delete [] alphaInOut; cerr<<" Poster probabilities now computed."<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); beta = new double*[nh]; alpha = new double*[nh]; //betaNume = new double*[nh]; //alphaNume = new double*[nh]; k = model->max_indegree(); cerr<<" . "<makeADTree(); } for (int j = 0; j < nh; j ++){ beta[j] = new double[1 << nh]; //cerr<<" Start compute_beta for node "<freeADTree(); } RRFunc = new double[1 << nh]; cerr<<"\n Compute_RR_Fast(): "<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); //Step 1(a) (b) beta = new double*[nh]; alpha = new double*[nh]; k = model->max_indegree(); cerr<<" . "<makeADTree(); } else{ //cout << "Arguments::ADtree == 0" << endl; } for (int j = 0; j < nh; j ++){ beta[j] = new double[1 << nh]; //int i = Vh[j]; compute_beta(j, Vh, nh, Vu, nu); //cerr<<" . Tables beta and alpha computed for node "<freeADTree(); } gettimeofday(&endTime, &myTimeZone); betaTime = (endTime.tv_sec - startTime.tv_sec) + (endTime.tv_usec - startTime.tv_usec) / 1000000.0 ; cerr<<" . Tables beta have been computed" << endl; //HR: Add for Top-k inside void compute_edge_probabilities_mixIndegree(int h) //HR: Use the Poster tool to compute the local scores for all the families of each variable (without max-indegree // restriction). So for each of n variables, there are 2^(n-1) family scores. write_family_scores_to_files(nh); //step 1(b) gettimeofday(&startTime, &myTimeZone); for (int j = 0; j < nh; j ++){ alpha[j] = new double[1 << nh]; compute_alpha(j, Vh, nh); //cerr<<" . Tables beta and alpha computed for node "<>v) & 1){ Gfb[U] = LOG_ZERO; } else{ //Gfb[U] = hFunc[U] + KFunc[v][U]; if(KFunc[v][U] == LOG_ZERO){ Gfb[U] = LOG_ZERO; } //note that KFunc[v][U] == 0 is possible else if(KFunc[v][U] <= 0){ Gfb[U] = hFunc[U] + KFunc[v][U]; } else{ //Now if Gfb[U] > 0, then Gfb[U] Gfb[U] = -(hFunc[U] - KFunc[v][U]); } //cerr<<" j = "<print_edge_prob( cout, Vh[i], Vh[v], exp(log_prob_nume - RRFunc[(1<layer(h, &Vh, &nh); model->upper_layers(h-1, &Vu, &nu); //Step 1(a) (b) beta = new double*[nh]; alpha = new double*[nh]; k = model->max_indegree(); cerr<<" . "<>v) & 1){ //Gfb[U] = LOG_ZERO; //Gfb[U] = 0; Gfb[U] = LOG_ZERO;// } else{ //Gfb[U] = hFunc[U] + KFunc[v][U]; if(KFunc[v][U] == LOG_ZERO){ Gfb[U] = exp(hFunc[U]); } else if (KFunc[v][U] > 0){ Gfb[U] = - exp(hFunc[U] - KFunc[v][U]); } else{ Gfb[U] = exp(hFunc[U] + KFunc[v][U]); } // if(Gfb[U] == 0){ Gfb[U] = LOG_ZERO; } else{ Gfb[U] = log(Gfb[U]); } // //cerr<<" j = "<print_edge_prob( cout, Vh[i], Vh[v], exp(log_prob_nume - RRFunc[(1<log_prior(i, S, d) + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d); } else{ lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d); } } else if(Arguments::option >= 1) { //lb = 0 + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = 0 + model->log_lcpHR(i, S, d); } else{ lb = 0 + model->log_lcpHR_ADtree(i, S, d); } } //LOGADD(b[T], lb); logAdd_New(b[T], lb); // if (d < k){ for (int j = jprev + 1; j < nu; j ++){ if (Vu[j] != i){ S[d] = Vu[j]; if (j < nh) { sub_beta(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j)); } else{ sub_beta(j, nh, b, d+1, S, i, Vu, nu, T); } } } } } void sub_betaNume(int jprev, int nh, double *b, int d, int *S, int i, int *Vu, int nu, int T, int uu, int vv){ //cerr<<" S:"; print_nodes(cerr, S, d); //cerr<<"; T:"; print_nodes(cerr, T, Vu, nu); cerr<log_prior(i, S, d) + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d); } else{ lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d); } } else if(Arguments::option >= 1) { //HR: for 1 prior for q(G_i) and new Dirichlet hyper-param //lb = 0 + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = 0 + model->log_lcpHR(i, S, d); } else{ lb = 0 + model->log_lcpHR_ADtree(i, S, d); } } //double lb = model->log_prior(i, S, d) + model->log_lcp(i, S, d); //double lb = 0 + model->log_lcpHR(i, S, d); //LOGADD(b[T], lb); logAdd_New(b[T], lb); } else{ //how to set? 0-no, MARK-no; log(0) = -inf = LOG_ZERO //LOGADD(b[T], LOG_ZERO); double tempLogB = LOG_ZERO; logAdd_New(b[T], tempLogB); } if (d < k){ for (int j = jprev + 1; j < nu; j ++){ if (Vu[j] != i){ S[d] = Vu[j]; if (j < nh) { sub_betaNume(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j), uu, vv); } else{ sub_betaNume(j, nh, b, d+1, S, i, Vu, nu, T, uu, vv); } } } } } void getInOutFeatures(int no_vars){ for(int i = 0; i < no_vars; i++){ inFeatureEdges[i] = 0; } for(int i = 0; i < no_vars; i++){ outFeatureEdges[i] = 0; } FILE * fpIn = fopen(Arguments::inFeasFileName, "r"); int fromNode; int toNode; //char c; //int i=0; while(!feof(fpIn)){ fromNode = -1; toNode = -1; //c = -1; fscanf(fpIn,"%d->%d\n",&fromNode, &toNode); //cout << "fromNode = "<< fromNode << endl; //cout << "toNode = "<< toNode << endl; //To guard against toNode == -1 if(toNode == -1){ break; } else{ inFeatureEdges[toNode] += (1 << fromNode); } } fclose(fpIn); // for(int i = 0; i < no_vars; i++){ // cout << "inFeatureEdges[" << i << "] " << inFeatureEdges[i] << endl; // } FILE *fp2 = fopen(Arguments::outFeasFileName, "r"); while(!feof(fp2)){ fromNode = -1; toNode = -1; fscanf(fp2,"%d->%d\n",&fromNode, &toNode); //cout << "fromNode = "<< fromNode << endl; //cout << "toNode = "<< toNode << endl; if(toNode == -1){ break; } else{ outFeatureEdges[toNode] += (1 << fromNode); } } fclose(fp2); // for(int i = 0; i < no_vars; i++){ // cout << "outFeatureEdges[" << i << "] " << outFeatureEdges[i] << endl; // } } //end of getInOutFeatures void sub_betaInOut(int jprev, int nh, double *b, int d, int *S, int i, int *Vu, int nu, int T){ // cerr<< "Start sub_betaInOut()" << endl; // cerr<<" S:"; print_nodes(cerr, S, d); // cerr<<" T: " << T << endl; // cerr<<" d: " << d << endl; //cerr<<"; T:"; print_nodes(cerr, T, Vu, nu); cerr<log_prior(i, S, d) + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = model->log_prior(i, S, d) + model->log_lcpHR(i, S, d); } else{ lb = model->log_prior(i, S, d) + model->log_lcpHR_ADtree(i, S, d); } } else if(Arguments::option >= 1) { //HR: for 1 prior for q(G_i) and new Dirichlet hyper-param //cerr << "start: double lb = 0 + model->log_lcpHR(i, S, d)" << endl; //lb = 0 + model->log_lcpHR(i, S, d); if(Arguments::ADtree == 0){ lb = 0 + model->log_lcpHR(i, S, d); } else{ lb = 0 + model->log_lcpHR_ADtree(i, S, d); } //cerr << "end: double lb = 0 + model->log_lcpHR(i, S, d)" << endl; } //LOGADD(b[T], lb); logAdd_New(b[T], lb); } else{ //LOGADD(b[T], LOG_ZERO); double tempLogB = LOG_ZERO; logAdd_New(b[T], tempLogB); } if (d < k){ for (int j = jprev + 1; j < nu; j ++){ if (Vu[j] != i){ S[d] = Vu[j]; if (j < nh) { sub_betaInOut(j, nh, b, d+1, S, i, Vu, nu, T | (1 << j)); } else{ sub_betaInOut(j, nh, b, d+1, S, i, Vu, nu, T); } } } } } //end of sub_betaInOut void sub_init(int d, int S, double *a, double value, int ones, int nh){ //cerr<<" d: "<>= 1; J <<= 1; } if (S == 0) gf[0] = 0; else gf[S] = sum; } } void sub_gfNume(int d, int nh, int S){ if (d < nh){ sub_gfNume(d+1, nh, S); sub_gfNume(d+1, nh, S | (1 << d)); } else { double sum = MARK; int T = S, J = 1; for (int j = 0; j < nh; j ++){ if (T & 1){ // Now S - J is a subset of S. double w = alphaNume[j][S - J] + gfNume[S - J]; //LOGADD(sum, w); logAdd_New(sum, w); } T >>= 1; J <<= 1; } if (S == 0) gfNume[0] = 0; else gfNume[S] = sum; } } void compute_g_backward(int nh){ sub_gb(0, nh, 0); } void sub_gb(int d, int nh, int S){ if (d < nh){ sub_gb(d+1, nh, S); sub_gb(d+1, nh, S | (1 << d)); } else { double sum = MARK; int T = S, J = 1, complS = (1 << nh) - 1 - S; for (int j = 0; j < nh; j ++){ if (T & 1){ // Now S - J is a subset of S. double w = alpha[j][complS] + gb[S - J]; //LOGADD(sum, w); logAdd_New(sum, w); } T >>= 1; J <<= 1; } if (S == 0) gb[0] = 0; else gb[S] = sum; } } double eval_edge(int i, int j, double *a, double *b, int nh, int k){ int T = 1 << i; return sub_eval_edge(-1, 1, T, i, j, a, b, nh, k); } double sub_eval_edge( int tprev, int d, int T, int i, int j, double *a, double *b, int nh, int k){ //cerr<<" T:"; print_set(cerr, T); //cerr<<": "< 0 "; sumRes = - ( Beta_j[T] - Gamma[T] ); } return sumRes; } //if T < k, can add more //double sum = Gamma[T] + Beta_j[T]; double sum; if(Beta_j[T] == MARK){ cerr<<"\n**** Beta_j[T] == MARK "; } if(Gamma[T] == LOG_ZERO){ sum = LOG_ZERO; } else if(Gamma[T] <= 0){ sum = Beta_j[T] + Gamma[T]; } else{ cerr<<"\n**** Gamma[T] > 0 "; sum = - ( Beta_j[T] - Gamma[T] ); } for (int t = tprev + 1; t < nh; t ++){ if (t == i || t == j) continue; int Tnext = T | (1 << t); double w = sub_eval_edge_mixIndegree(t, d+1, Tnext, i, j, Gamma, Beta_j, nh, k); logAddComp(sum, w); } return sum; } double eval_edge_mixIndegreeNoLog(int i, int j, double * Gamma, double * Beta_j, int nh, int k){ int T = 1 << i; return sub_eval_edge_mixIndegreeNoLog(-1, 1, T, i, j, Gamma, Beta_j, nh, k); } double sub_eval_edge_mixIndegreeNoLog( int tprev, int d, int T, int i, int j, double * Gamma, double * Beta_j, int nh, int k){ //cerr<<" T:"; print_set(cerr, T); //cerr<<": "< 0){ product_res = exp(Beta_j[T] + log(Gamma[T])); } else{ product_res = - exp(Beta_j[T] + log(-Gamma[T])); } } return product_res; } //if T < k, can add more //double sum = Gamma[T] * exp(Beta_j[T]); double sum; double product_res; //if Beta_j[T] has not been initialized if(Beta_j[T] == MARK){ cerr<<"***Beta_j[T] has not been initialized" << endl; product_res = 0; } else{ if(Gamma[T] == 0){ product_res = exp(Beta_j[T]); } else if(Gamma[T] > 0){ product_res = exp(Beta_j[T] + log(Gamma[T])); } else{ product_res = - exp(Beta_j[T] + log(-Gamma[T])); } } sum = product_res; for (int t = tprev + 1; t < nh; t ++){ if (t == i || t == j) continue; int Tnext = T | (1 << t); double w = sub_eval_edge_mixIndegreeNoLog(t, d+1, Tnext, i, j, Gamma, Beta_j, nh, k); //LOGADD(sum, w); sum += w; } return sum; } Model *model; double **alpha, **beta; double **alphaNume, **betaNume; double *gf, *gb; double *gfNume; int k; double **alphaInOut, **betaInOut; int * inFeatureEdges; int * outFeatureEdges; }; #endif ./BNW/src/k-best/src/cfg.h0000775000076600007660000000032511740177362015305 0ustar abhatta3abhatta3#ifndef __CFG_H_ #define __CFG_H_ #define MAX_NOF_VARS (32) #define LARGEST_SET(NOF_VARS) ((NOF_VARS)==MAX_NOF_VARS?(varset_t)~0:(1U<<(NOF_VARS))-1) typedef unsigned int varset_t; typedef double score_t; #endif ./BNW/src/k-best/src/get_kbest_parents.cc0000775000076600007660000001257411740177362020420 0ustar abhatta3abhatta3//HR: formetted only, no code change #include #include #include #include "cfg.h" #include #include #include #include #define EPSILON 0.001 #include "files.h" using namespace std; int h; //class for bparents //HR:F //HR: (variable set, score) pair //This class is to store the best parent set and the corresponding score class score_network{ public: score_t scores; varset_t bsps; score_network(score_t a,varset_t b){ scores=a; bsps=b; } score_network(){ scores=bsps=0; } friend int operator<(score_network s1,score_network s2); friend int operator==(score_network s1,score_network s2); friend int operator>(score_network s1,score_network s2); friend bool same_obj(score_network s1, score_network s2); }; //HR:F /*================================================================*/ void print_queue(list* v){ list::iterator iter; for(iter=v->begin();iter!=v->end();iter++){ cout<<" "<<(*iter).bsps<<","<<(*iter).scores; } } //HR:F /*================================================================*/ int operator<(score_network s1,score_network s2){ if(fabs(s1.scores-s2.scores)(score_network s1,score_network s2){ if(fabs(s1.scores-s2.scores)s2.scores); } int operator==(score_network s1,score_network s2){ return(fabs(s1.scores-s2.scores)* v,score_network s, int k){ list::iterator it; if( s < v->back()){ v->push_back(s); } else{ for(it=v->begin();it!=v->end();it++){ if(same_obj(s,*it)){ break; } else if(s>(*it)){ v->insert(it,s); break; } } } if(v->size()>k){ v->pop_back(); } } /*================================================================*/ void get_best_parents(int nof_vars, char* dirname, int k){ varset_t nof_parsets = 1U<<(nof_vars-1); int i; // cout< v[nof_parsets]; list::iterator it; score_network s; string str; char str1[40]; //HR: For each var for(i=0;iscores), sizeof(double), 1, fout); fwrite(&(it->bsps),sizeof(unsigned int),1,fout); //print_queue(&v[j]); //printf("\n"); //fprintf(fout,"\n"); } fwrite(&sentinel,sizeof(double),1,fout); v[j].clear(); } //printf("\n"); fclose(fout); }// endfor(i=0;i int nof_lines(char* filename); char* create_fn(char* dirname, int i, char* ext); FILE* open_file(char* dirname, int i, char* ext, char* mode); FILE** open_files(int nof_vars, char* dirname, char* ext, char* mode); void free_files(int nof_vars, FILE** files); #endif ./BNW/src/k-best/src/get_kbest_parents0000775000076600007660000006123612133077176020032 0ustar abhatta3abhatta3ELF>° @@`4@8@@@@@@ÀÀ@@@@`/`/ 00`0`ô0 0000`00`ÀÀ@@DDPåtd$$@$@Qåtd/lib64/ld-linux-x86-64.so.2GNUGNUôxPZcƒÂ…“Y|Øe2Hž¡!9ò‹(EÕL˜ CyIk¶¤í£  o´„Œñ$÷'_Íé®3 ’s»÷~Ð 4`B @i3`Z€ @libstdc++.so.6__gmon_start___Jv_RegisterClassespthread_cancel_ZNSt8ios_base4InitD1Ev__gxx_personality_v0_ZNKSs5c_strEv_Znwm__cxa_rethrow_ZNSs6appendEPKc_ZNSs6assignEPKc_ZdlPv__cxa_begin_catch_ZNSt15_List_node_base6unhookEv_ZNSsC1Ev_ZNSt15_List_node_base4hookEPS___cxa_end_catch_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc_ZNSsD1Ev_ZSt4cout_ZSt17__throw_bad_allocv_ZNSt8ios_base4InitC1Ev_ZNSolsEd_ZNSolsEjlibm.so.6libgcc_s.so.1_Unwind_Resumelibc.so.6sprintffopen__cxa_atexitfclosestderrfwritefreadatoi__libc_start_mainGCC_3.0GLIBC_2.2.5CXXABI_1.3GLIBCXX_3.4 P&y 6ß ui >Ó¯kJt)’Uð1`3` 4`2`2` 2`(2`02`82`@2` H2` P2` X2` `2`h2` p2`x2`€2`ˆ2`2`˜2` 2`¨2`°2`¸2`À2`È2`Ð2`Ø2`!à2`è2`Hƒìè èšèeHƒÄÃÿ5& ÿ%& @ÿ%& héàÿÿÿÿ%& héÐÿÿÿÿ% & héÀÿÿÿÿ%& hé°ÿÿÿÿ%ú% hé ÿÿÿÿ%ò% héÿÿÿÿ%ê% hé€ÿÿÿÿ%â% hépÿÿÿÿ%Ú% hé`ÿÿÿÿ%Ò% h éPÿÿÿÿ%Ê% h é@ÿÿÿÿ%Â% h é0ÿÿÿÿ%º% h é ÿÿÿÿ%²% h éÿÿÿÿ%ª% héÿÿÿÿ%¢% héðþÿÿÿ%š% héàþÿÿÿ%’% héÐþÿÿÿ%Š% héÀþÿÿÿ%‚% hé°þÿÿÿ%z% hé þÿÿÿ%r% héþÿÿÿ%j% hé€þÿÿÿ%b% hépþÿÿÿ%Z% hé`þÿÿÿ%R% héPþÿÿÿ%J% hé@þÿÿÿ%B% hé0þÿÿ1íI‰Ñ^H‰âHƒäðPTIÇÀ "@HÇÁ°"@HÇÇÀ@è—þÿÿôHƒìH‹ $ H…ÀtÿÐHƒÄÃUH‰åSHƒì€=& uK» 0`H‹& Hë0`HÁûHƒëH9Øs$fDHƒÀH‰Ý% ÿÅ0`H‹Ï% H9ØrâÆ»% HƒÄ[ÉÃfff.„Hƒ=°! 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0ustar abhatta3abhatta3#include #include #include //#include "varpar.h" #include #include #include #include #include #include "cfg.h" #include #include //HR //#define EPSILON 0.001 #define EPSILON 0.00001 //HR: Add for hash_set #if __GNUC__ < 3 && __GNUC__ >= 2 && __GNUC_MINOR__ >= 95 # include # include # define gnu_namespace std #elif __GNUC__ >= 3 # include # if __GNUC_MINOR__ == 0 # include # define gnu_namespace std # else # include # define gnu_namespace __gnu_cxx # endif #else # include # include # define gnu_namespace std #endif using namespace gnu_namespace; #include // using namespace std; #define MARK 9e99 #define LOG_ZERO -1e101 //HR: add from UpdateHR.h to deal with the problem in sum = 0 in comp_post() //call by reference to the original value //the log sum result is stored in logA #define epsilon 1.0e5 bool logSpecValEquals(double logX, double logSpecVal){ return (logX >= logSpecVal - epsilon && logX <= logSpecVal + epsilon); } void logAddComp(double & logA, double & logB){ //if(logA == MARK){ if(logSpecValEquals(logA, MARK)){ logA = logB; } //else if (logA == LOG_ZERO){ else if (logSpecValEquals(logA, LOG_ZERO)){ logA = logB; } //else if(logB == MARK){ else if(logSpecValEquals(logB, MARK)){ logA = logA; } //else if(logB == LOG_ZERO){ else if(logSpecValEquals(logB, LOG_ZERO)){ logA = logA; } //Neither logA nor logB is MARK/LOG_ZERO else{ //1 if(logA < 0 && logB < 0 ){ //1.1 //Gaurd logB-logA <= 100 to avoid that exp(logB-logA) go to inf if(logB - logA <= 100 ){ logA = logA + log( 1 + exp(logB-logA) ); } //1.2 //if logB - logA > 100, then logB > 100 + logA so that B is much bigger than A (B > e^100 * A) // So (A + B) almost = B else{ //logA = logB; //The following is the real formula,; but it is almost same as //logA = logB; logA = logB + log( exp(logA - logB) + 1); } } //2 else if(logA > 0 && logB > 0){ //always make exp(.): . > 0 if(-logB + logA <= 100){ //2.1 logA = -( -logA + log( 1 + exp(-logB+logA) ) ); } else{ //2.2 logA = -( -logB + log( 1 + exp(-logA+logB) ) ); } } //3 else if(logA < 0 && logB > 0){ //3.1 if(logA + logB > 0){ if(logA + logB <= 100){ //3.1.2 logA = -logB + log( exp(logA + logB) - 1 ); } else{ //3.1.1 logA = logA + log( 1 - exp(-logB-logA) ); } } //3.2 else if(logA + logB < 0){ if(-logA - logB <= 100){ //3.2.2 logA = -( logA + log( exp(-logB-logA) - 1) ); } else{ //3.2.1 logA = - ( -logB + log(1 - exp(logA+logB) ) ); } } //3.3 else{ logA = LOG_ZERO; } } //4 else if(logA > 0 && logB < 0){ //4.1 if(logA + logB > 0){ if(logA + logB <= 100){ //4.1.2 logA = -logA + log( exp(logB+logA) - 1); } else{ //4.1.1 logA = logB + log( 1 - exp(-logA-logB) ); } } //4.2 else if(logA + logB < 0){ if(-logA-logB <= 100){ //4.2.2 logA = -( logB + log( exp(-logA-logB) - 1) ); } else{ //4.2.1 logA = -( -logA + log(1 - exp(logB+logA)) ); } } //4.3 else{ logA = LOG_ZERO; } } } } // end of void logAddComp(double & logA, double & logB)c //HR: Note: The whole program supposes that max no. of vars = 32 and hardcord 32 //Convert the parent set to the appropriate variable set //HR:F varset_t parset2varset(int v, varset_t set){ varset_t sinkleton = 1U<(net_set s1,net_set s2); friend bool same_obj(net_set s1, net_set s2, int nof_vars); }; //HR:F /*================================================================*/ int operator<(net_set s1,net_set s2){ if(fabs(s1.score-s2.score)(net_set s1,net_set s2){ if(fabs(s1.score-s2.score)s2.score); } int operator==(net_set s1,net_set s2){ return(fabs(s1.score-s2.score)* v,net_set s, int k, int nof_vars){ list::iterator it; //HR: can improve its time //first check whether v->size() > 0 && s < v->back() //see Lav's comment bool flag=false; //HR: Refined // if( (v->size() > 0) && (s < v->back()) ){ v->push_back(s); flag=true; } else{ // for(it=v->begin();it!=v->end();it++){ if(same_obj(s,*it,nof_vars)){ // cout<<"Same object so not inserted!!!!!!!!!!!!!"<(*it)){ // cout<<"score of s:"<insert(it,s); flag=true; break; } } } if(flag==false){ v->push_back(s); } if(v->size()>k){ v->pop_back(); } //v->unique(); } /*================================================================*/ //class for bparents //HR:F //HR: (variable set, score) pair class score_network{ public: score_t scores; varset_t vset; friend int operator<(score_network s1,score_network s2); friend int operator==(score_network s1,score_network s2); friend int operator>(score_network s1,score_network s2); friend bool same_obj(score_network s1, score_network s2); }; //HR:F int operator<(score_network s1,score_network s2){ if(fabs(s1.scores-s2.scores)(score_network s1,score_network s2){ if(fabs(s1.scores-s2.scores)s2.scores); } int operator==(score_network s1,score_network s2){ return(fabs(s1.scores-s2.scores)* v,score_network s, int k) { list::iterator it; if( s < v->back()) { v->push_back(s); } else { for(it=v->begin();it!=v->end();it++) { // if(same_obj(s,*it)) // { // break; // } // else if(s>(*it)) { v->insert(it,s); break; } } } if(v->size()>k) { v->pop_back(); } } /*================================================================*/ //class for node //HR:F class node{ public: int ip; int in; score_t score; node(int x, int y, score_t z){ ip=x; in=y; score=z; } friend int operator<(node s1,node s2); friend int operator==(node s1,node s2); friend int operator>(node s1,node s2); friend bool same_obj(node s1, node s2); }; /*================================================================*/ int operator<(node s1,node s2){ if(fabs(s1.score-s2.score)(node s1,node s2){ if(fabs(s1.score-s2.score)s2.score); } int operator==(node s1,node s2){ return(fabs(s1.score-s2.score) v[],int size,int nof_vars){ list::iterator iter; for(int j=0;j* v){ vector::iterator iter; for(iter=v->begin();iter!=v->end();iter++){ cout<<"bparents "<<(*iter).vset<<","<<(*iter).scores<<" ,, "; } } void print_queue(list* v){ list::iterator iter; cout<<"fringe"<begin();iter!=v->end();iter++){ cout<<" ip "<<(*iter).ip<<", in "<<(*iter).in<<" score "<<(*iter).score; } } void print_queue(vector* v,int nof_vars){ vector::iterator iter; for(iter=v->begin();iter!=v->end();iter++){ // cout<<" "<<(*iter).bsps<<","<<(*iter).scores; cout<<"bnets "<<" Score:"<<(*iter).score<<" net "<* v,int nof_vars){ list::iterator iter; for(iter=v->begin();iter!=v->end();iter++){ // cout<<" "<<(*iter).bsps<<","<<(*iter).scores; cout<<"kbnet "<<" Score:"<<(*iter).score<<" net "<* v,node s, int k){ list::iterator it; //HR: test //bool sameObj = false; //bool inserted = false; // //if( s < v->back()){ same if( (v->size() == 0) || (s < v->back())){ v->push_back(s); } else{ for(it=v->begin();it!=v->end();it++){ //comment it out will give the different answer. Because Lav's original is wrong, it will still insert the same object. It will eventually pop the correct end > k // if(same_obj(s, *it)){ break; // sameObj = true; // cout << "s: "; // print_node(s); // cout << "*it: "; // print_node(*it); // cout << endl; // print_queue(v); } else{ // if(s>(*it)){ v->insert(it,s); //inserted = true; break; } } } //HR: test // if(sameObj == true && inserted == true){ // cout << "Error: sameObj == true && inserted = true" << endl; // cout << "s: "; // print_node(s); // print_queue(v); // } } if(v->size()>k){ //cout << "\n\nv->size()>k happens, v->pop_back()\n" << endl; v->pop_back(); } // cout<<"Inserted:"< struct hash { hash hasher_ns; size_t operator()(const net_set* ns) const { return hasher_ns((unsigned) roundl(- ns->score*10)); // wrong hash function?? } }; //end of struct } //end of namespace struct eqNetScore{ bool operator()(const net_set* ns1, const net_set* ns2) const{ return same_obj(*ns1, *ns2); } }; typedef hash_set, eqNetScore> NetScoreHashSet; NetScoreHashSet knets; //HR: Add void print_nsHashSet(NetScoreHashSet nsHSet, int nof_vars){ for(NetScoreHashSet::iterator it = nsHSet.begin(); it != nsHSet.end(); it++){ print_netscore(**it, nof_vars); } } // //=====================================================================================// /*================================================================*/ //HR:F //HR: call gettopk(&bnets,&bparents,&kbnetscore[varset],k,sink,nof_vars); void gettopk(vector* bnets, vector* bparents, list* kbnet, int k, varset_t sink,int nof_vars){ int h; int ipmax=bparents->size(); // cout<<"ipmax: "<size(); // cout<<"inmax: "< fringe; //HR: different from Algo4, here start from 0 vs. 1 node n(0,0,(bparents->at(0)).scores + (bnets->at(0)).score); insert_vec(&fringe,n,k); // print_queue(&fringe); // scanf("%d",&h); NetScoreHashSet::iterator iter1; while(!fringe.empty()){ // cout<<"Fringe not empty"<size())at(in)).net[j]; // cout<<"Net w j"<at(ip)).vset); //cout<<"net w sinkleton"<back()).score)>EPSILON)&&(score>(kbnet->back().score))){ // cout<<"score>kbnetback's score"<at(in)).net[j]; // cout<<"Net w j"<at(ip)).vset; //cout<<"net w sinkleton"<back(); //Lav insert_vec(kbnet,*netwP,k,nof_vars); //cout<<"After inserting"<at(ip+1)).scores + (bnets->at(in)).score); //cout<<"after child"<at(ip)).scores + (bnets->at(in+1)).score); //may add hash_set generated check here insert_vec(&fringe,child,k); //cout<<"Fringe after inserting"<* kbnet, int k,int nof_vars){ list::iterator it; //int j=0; //each it is one of k best for(it=kbnet->begin();it!=kbnet->end();it++){ for(int p=0;p kbnetscore[],char* dirname,int k,int nof_vars) { string str; list::iterator it; char str1[10]; int j=0; //HR: each it is the one of the k best for(it=kbnetscore[(1U<<(nof_vars))-1].begin();it!=kbnetscore[(1U<<(nof_vars))-1].end();it++){ str.assign(dirname); str.append("/"); sprintf(str1,"%d",j++); str.append(str1); str.append("net"); FILE* netf=fopen(str.c_str(),"w"); fprintf(netf,"%f \n",(*it).score); // cout<<(*it).score< kbnetscore[],char* dirname,int k,int nof_vars){ // string str; list::iterator it; int j=0; for(j=0;j<((1U<* kbnet, int k, char* dirname, int nof_vars){ //cout << "Start comp_postExact_compl()" << endl; //long double Sum=0.0; //double logSum = LOG_ZERO; list::iterator it; //HR: assume k < 5000 long double postExact[5000]; string str; char str1[32]; //cout << "dirname = " << dirname << endl; str.assign(dirname); str.append("/"); str.append("exactPD.txt"); //str.assign("exactPD.txt"); FILE *fp; fp=fopen(str.c_str(),"r"); double exactPD = 0.0; if(!feof(fp)){ char c; fscanf(fp, "%lf", &exactPD); fscanf(fp,"%c",&c); } fclose(fp); //printf("exactPD = %18.8f\n", exactPD); str.assign(dirname); str.append("/netpostExact"); fp=fopen(str.c_str(),"w"); //for each it of k best networks // for(it=kbnet->begin();it!=kbnet->end();it++){ // //HR: change it // //sum+=exp((*it).score); // logAddComp(logSum, (*it).score); //HR // } // cout << "logSum: " << logSum << endl; //HR // printf("logSum = %18.6f\n", logSum); // // // long double Sum = exp(logSum); //HR // cout << "Sum: " << exp(logSum) << endl; //HR // int i=0; //for each it of k best networks, compute equation (4) //each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network for(it=kbnet->begin();it!=kbnet->end();it++){ //post[i]=(exp((*it).score))/sum; //double logScore = (*it).score; //LOGMINUS_NEW(logScore, logSum) postExact[i]=exp( (*it).score - exactPD ); // fprintf(fp,"%Lg\n",postExact[i]); i++; } fclose(fp); //Start the update //define and init long double postProbExact[nof_vars][nof_vars]; for(int i = 0; i < nof_vars; i++){ for (int j = 0; j < nof_vars; j++){ postProbExact[i][j] = 0.0; } } int listSize = kbnet->size(); int num1 = -1; int num2 = -1; //HR: for each j of k best networks, j >=1 for(int j=0; j " << i << " \t" << postProbExact[j][i] << endl; } } } //end void comp_postExact_compl() //HR: Add //HR: Update from comp_post //Compute each edge out of nof_vars * nof_vars, instead of just the best network void comp_post_compl(list* kbnet, int k, char* dirname, int nof_vars){ //long double Sum=0.0; double logSum = LOG_ZERO; list::iterator it; //HR: assume k < 5000 long double post[5000]; string str; char str1[32]; str.assign(dirname); str.append("/netpost"); FILE *fp=fopen(str.c_str(),"w"); //for each it of k best networks for(it=kbnet->begin();it!=kbnet->end();it++){ //HR: change it //sum+=exp((*it).score); logAddComp(logSum, (*it).score); //HR } //cout << "logSum: " << logSum << endl; //HR //printf("logSum = %18.6f\n", logSum); // long double Sum = exp(logSum); //HR //cout << "Sum: " << exp(logSum) << endl; //HR // int i=0; //for each it of k best networks, compute equation (4) //each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network for(it=kbnet->begin();it!=kbnet->end();it++){ //post[i]=(exp((*it).score))/sum; //double logScore = (*it).score; //LOGMINUS_NEW(logScore, logSum) post[i]=exp( (*it).score - logSum ); // fprintf(fp,"%Lg\n",post[i]); i++; } fclose(fp); //Start the update //define and init long double postProb[nof_vars][nof_vars]; for(int i = 0; i < nof_vars; i++){ for (int j = 0; j < nof_vars; j++){ postProb[i][j] = 0.0; } } int listSize = kbnet->size(); int num1 = -1; int num2 = -1; //HR: for each j of k best networks, j >=1 for(int j=0; j " << i << " \t" << postProb[j][i] << endl; } } } //Computation of posterior probabilities - This function's call has been commented. Remove the commenting slashes if the posterior probability needs to be computed. //HR: call comp_post(&kbnetscore[nof_combs-1],k,dirname); void comp_post(list* kbnet, int k, char* dirname){ //long double Sum=0.0; double logSum = LOG_ZERO; list::iterator it; long double post[5000]; string str; char str1[32]; str.assign(dirname); str.append("/netpost"); FILE *fp=fopen(str.c_str(),"w"); //for each it of k best networks for(it=kbnet->begin();it!=kbnet->end();it++){ //HR: change it //sum+=exp((*it).score); logAddComp(logSum, (*it).score); //HR } cout << "logSum: " << logSum << endl; //HR // long double Sum = exp(logSum); //HR cout << "Sum: " << exp(logSum) << endl; //HR // int i=0; //for each it of k best networks, compute equation (4) //each post[i] ( 0 <= i <= k - 1). repre post prob for i'th best network for(it=kbnet->begin();it!=kbnet->end();it++){ //post[i]=(exp((*it).score))/sum; //double logScore = (*it).score; //LOGMINUS_NEW(logScore, logSum) post[i]=exp( (*it).score - logSum ); // fprintf(fp,"%Lg\n",post[i]); i++; } fclose(fp); ifstream indata; int n=0; int num[50][2]; int num1,num2; // char f[50][20]; long double postf[50]; str.assign(dirname); str.append("/"); str.append("arc0"); fp=fopen(str.c_str(),"r"); // fp=fopen(str.c_str(),"r"); i=0; while(!feof(fp)){ char c; //HR: for parent fscanf(fp,"%d",&num[i][0]); //HR: for var fscanf(fp,"%d",&num[i][1]); fscanf(fp,"%c",&c); //indata>>num[i][1]; //HR: // cout<<"HIIIII"<=1 for(j=1;j>num1; // indata>>num2; //HR: // cout< kbnetscore[nof_combs]" << endl; //cerr << "before list kbnetscore[nof_combs]" << endl; //HR: net_set is the (net, score) pair //HR: have not yet set each list kbnetscore[W] the size k list kbnetscore[nof_combs]; //cerr << "after list kbnetscore[nof_combs]" << endl; //cout << "after list kbnetscore[nof_combs]" << endl; list::iterator it; vector bnets; //HR: score_network is (variable set, score) pair score_network s; vector bparents; //HR: Add hash_set knets here; global may be better so that gettopk 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0ustar abhatta3abhatta3#ifndef ARGUMENTS_H #define ARGUMENTS_H #include #include using namespace std; class Arguments { public: static char* datafile; static char* layeringfile; static char* maxindegree; static char* model; static char* task; static char* maxnumrecords; //HR: Add for in_out features static char* inFeasFileName; static char* outFeasFileName; // //HR: Add for in_out features static int option; // //HR: Add for ADtree option static int ADtree; // //HR: Add for Topk dir option static char* directoryName; // static void init(int argc, char **args){ for(int i = 1; i < argc; i ++){ if(args[i][0]=='-' && args[i][1]=='d' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::datafile = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='l' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::layeringfile = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='m' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::maxindegree = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='u' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::maxnumrecords = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='M' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::model = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='T' && args[i][2]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::task = args[j]; j ++; } } //HR: Add for in_out feature else if(args[i][0]=='-' && args[i][1]=='i' && args[i][2]=='n' && args[i][3]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::inFeasFileName = args[j]; j ++; } } else if(args[i][0]=='-' && args[i][1]=='o' && args[i][2]=='u' && args[i][3]=='t' && args[i][4]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::outFeasFileName = args[j]; j ++; } } // //HR: Add for in_out feature else if(args[i][0]=='-' && args[i][1]=='o' && args[i][2]=='p' && args[i][3]=='t' && args[i][4]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::option = atoi(args[j]); j ++; } } // //HR: Add for ADtree feature else if(args[i][0]=='-' && args[i][1]=='a' && args[i][2]=='d' && args[i][3]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::ADtree = atoi(args[j]); j ++; } } // //HR: Add for Topk dir else if(args[i][0]=='-' && args[i][1]=='d' && args[i][2]=='i' && args[i][3]=='r' && args[i][4]=='\0'){ int j = i + 1; while (j < argc && args[j][0]!='-') { Arguments::directoryName = args[j]; j++; } } // } print_arguments(stderr); } static void print_arguments(FILE *f){ fprintf(f, " -d Data file:\n"); fprintf(f, " %62s\n", Arguments::datafile); //fprintf(f, " -l Layering file:\n"); //fprintf(f, " %62s\n", Arguments::layeringfile); fprintf(f, " -m Maximum indegree:\n"); fprintf(f, " %62s\n", Arguments::maxindegree); fprintf(f, " -u Maximum number of data records read:\n"); fprintf(f, " %62s\n", Arguments::maxnumrecords); //fprintf(f, " -M Model:\n"); //fprintf(f, " %62s\n", Arguments::model); //fprintf(f, " -T Task (Infer=I, Generate=G):\n"); //fprintf(f, " %62s\n", Arguments::task); //HR: Add for in_out fprintf(f, " -opt Option:\n"); fprintf(f, " %62d\n", Arguments::option); if(Arguments::option == 5){ fprintf(f, " -in In_Feature File:\n"); fprintf(f, " %62s\n", Arguments::inFeasFileName); fprintf(f, " -out Out_Feature File:\n"); fprintf(f, " %62s\n", Arguments::outFeasFileName); } // //HR: Add for ADtree fprintf(f, " -ad ADtree:\n"); fprintf(f, " %62d\n", Arguments::ADtree); // //HR: Add for Topk dir fprintf(f, " -dir directory name:\n"); fprintf(f, " %62s\n", Arguments::directoryName); // } }; char* Arguments::datafile = "testdata.dat"; char* Arguments::layeringfile = "%"; char* Arguments::maxindegree = "3"; char* Arguments::model = "M"; char* Arguments::task = "I"; char* Arguments::maxnumrecords = "999999"; //HR: For test //char* Arguments::datafile = "cases/iris.idt"; //char* Arguments::layeringfile = "%"; //char* Arguments::maxindegree = "4"; //char* Arguments::model = "M"; //char* Arguments::task = "I"; //char* Arguments::maxnumrecords = "150"; //HR: Add for in_out char* Arguments::inFeasFileName = "inFeature.txt"; char* Arguments::outFeasFileName = "outFeature.txt"; int Arguments::option = 5; //HR: Add for ADtree int Arguments::ADtree = 0; //HR: Add for Topk dir option char* Arguments::directoryName = "./"; // #endif ./BNW/src/k-best/src/files.o0000775000076600007660000000722012116447154015655 0ustar abhatta3abhatta3ELF>h@@ 1ɾgffff„‰øÁÿƒÁ÷îÁú)ú‰×uí‰ÈÃf.„AUI‰õATUS‰ûHƒì…ÿ~!I‰ô1í„I‹<$ƒÅIƒÄè9ëìHƒÄL‰ï[]A\A]éf.„H‰\$ØH‰l$à1ÛL‰d$èL‰l$ðA‰ôL‰t$øHƒì(H‰ýI‰ÕèD‰áI‰Æ¾gfff„‰ÈÁùƒÃ÷îÁú)ʉÑuíL‰ïHcÛèI|HßèM‰èH‰ÃD‰áH‰êH‰Ç¾1ÀèH‰ØH‹l$H‹$L‹d$L‹l$L‹t$ HƒÄ(Ãf.„U¾S1ÛHƒìèH‰Åëf„ƒø ”À¶ÀÃH‰ïèƒøÿuèH‰ïè‰ØHƒÄ[]ÀAWI‰÷AVI‰ÖAUATUSHƒì(‰|$ HcÿH‰L$HÁçè‹T$ H‰D$…ÒŽ½I‰Å1í»gfff@L‰ÿE1äè‰îH‰Á„‰ðÁþAƒÄ÷ëÁú)ò‰ÖuìL‰÷H‰ $McäèH‹ $H|Lçè‰éI‰ÄH‰ÇM‰ðL‰ú¾1Àè‰éM‰ðL‰ú¾L‰ç1ÀèH‹t$L‰çƒÅèL‰çH‰$èH‹$I‰EIƒÅ9l$ QÿÿÿH‹D$HƒÄ([]A\A]A^A_ÃDH‰\$ÐH‰l$؉õL‰d$àL‰l$èI‰ÔL‰t$ðL‰|$øHƒì8I‰ÎI‰ý1Ûè‰éI‰Ç¾gffff‰ÈÁùƒÃ÷îÁú)ʉÑuíL‰çHcÛèI|HßèM‰àH‰Ã‰éL‰êH‰Ç¾1ÀèM‰à‰éL‰êH‰ß¾1ÀèL‰öH‰ßèH‰ßH‰ÅèH‰èH‹\$H‹l$L‹d$L‹l$ L‹t$(L‹|$0HƒÄ8Ã%s/%d%srGCC: (GNU) 4.4.6 20120305 (Red Hat 4.4.6-4)zRx &40FBEŒA †A(ƒF0i(D ABB h¦L†ƒMŒI0Žƒ$ŒIA†FƒF yAAD´ BEŽE B(ŒA0†A8ƒD`ì8A0A(B BBB$üØL†ƒMŒN@Ž°.symtab.strtab.shstrtab.rela.text.data.bss.rodata.str1.1.comment.note.GNU-stack.rela.eh_frame @h0 Ð &¨,¨12¨ @0²-Iß^à Y h¨  ¸ vñÿ &0F&+€¦5<CK0IU[a€ lØfiles.cnof_digitsfree_filesfclosefreecreate_fnstrlenmallocsprintfnof_linesfopenfgetcopen_filesopen_file\ üÿÿÿÿÿÿÿ©üÿÿÿÿÿÿÿÚüÿÿÿÿÿÿÿçüÿÿÿÿÿÿÿû üÿÿÿÿÿÿÿ2 >üÿÿÿÿÿÿÿ_üÿÿÿÿÿÿÿl üÿÿÿÿÿÿÿ¥üÿÿÿÿÿÿÿÏüÿÿÿÿÿÿÿÿüÿÿÿÿÿÿÿüÿÿÿÿÿÿÿ# *üÿÿÿÿÿÿÿ7 AüÿÿÿÿÿÿÿQüÿÿÿÿÿÿÿ] üÿÿÿÿÿÿÿÀüÿÿÿÿÿÿÿêüÿÿÿÿÿÿÿ÷üÿÿÿÿÿÿÿ  üÿÿÿÿÿÿÿ! (üÿÿÿÿÿÿÿ3üÿÿÿÿÿÿÿ> üÿÿÿÿÿÿÿr üÿÿÿÿÿÿÿ 40l€0¸€./BNW/src/k-best/src/varpar.o0000775000076600007660000000252012116447154016044 0ustar abhatta3abhatta3ELF>H@@ ‰ù¸ÓàHÿ‰Ê÷Ò!ò!Î ðÃfD‰ù¸ÓàPÿ‰Ð÷Ð!ð!ÖÑè ðÃGCC: (GNU) 4.4.6 20120305 (Red Hat 4.4.6-4)zRx 0.symtab.strtab.shstrtab.text.data.bss.comment.note.GNU-stack.rela.eh_frame@9!|'|,0|-5©J°@E 0 ðTð  ø&ñÿ  varpar.cparset2varsetvarset2parset 4 ./BNW/src/k-best/src/data2netk_poster.sh0000775000076600007660000000220312121616716020172 0ustar abhatta3abhatta3#!/bin/bash binpath=`dirname $0` if [ $# -ne 4 ]; then echo Usage: data2net.sh datafile resultdir k 1>&2 exit 1 fi datafile=$1; shift #score=$1; shift rdir=$1; shift k=$1;shift n=$1;shift nof_vars=`head -1 $datafile|wc -w` #echo "The number of variables is $nof_vars." #HR: if [ "$n" -eq 0 ] then maxindegree=`expr $nof_vars - 1` else maxindegree=$n fi #maxindegree=`expr $nof_vars - 1` #echo "maxindegree is $maxindegree." #HR: nof_instances=`cat $datafile | wc -l` #delete the header and type nof_instances=`expr $nof_instances - 2` #echo "The number of instances is $nof_instances." START=$(date +%s%N) $binpath/get_kbest_parents $nof_vars ${rdir} $k #HR END=$(date +%s%N) #DIFF=$(( $END - $START )) DIFF2=$(( $END - $START )) #echo "get_kbest_parents is done." #echo "get_kbest_parents took $DIFF2 n-seconds." START=$(date +%s%N) $binpath/get_kbest_nets $nof_vars ${rdir} $k #HR END=$(date +%s%N) #DIFF=$(( $END - $START )) DIFF3=$(( $END - $START )) #echo "get_kbest_nets is done." #echo "get_kbest_nets took $DIFF3 n-seconds." DIFF=`expr $DIFF1 + $DIFF2 + $DIFF3` #echo "The total process took $DIFF n-seconds." ./BNW/src/localscore/0000775000076600007660000000000012133051131014522 5ustar abhatta3abhatta3./BNW/src/localscore/Linpack.h0000775000076600007660000001054612074111132016267 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1997 Robert Gentleman and Ross Ihaka * Copyright (C) 1999-2002 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* C declarations of double-precision LINPACK Fortran subroutines included in R, and some others. Those which are listed as part of R are in the API */ #ifndef R_LINPACK_H_ #define R_LINPACK_H_ #include /* for F77_... */ #include #ifdef __cplusplus extern "C" { #endif /* Double Precision Linpack */ extern void F77_NAME(dchdc)(double*, int*, int*, double*, int*, int*, int*); extern void F77_NAME(dpbfa)(double*, int*, int*, int*, int*); extern void F77_NAME(dpbsl)(double*, int*, int*, int*, double*); extern void F77_NAME(dpoco)(double*, int*, int*, double*, double*, int*); extern void F77_NAME(dpodi)(double*, int*, int*, double*, int*); extern void F77_NAME(dpofa)(double*, int*, int*, int*); extern void F77_NAME(dposl)(double*, int*, int*, double*); extern void F77_NAME(dqrdc)(double*, int*, int*, int*, double*, int*, double*, int*); extern void F77_NAME(dqrsl)(double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*); extern void F77_NAME(dsvdc)(double*, int*, int*, int*, double*, double*, double*, int*, double*, int*, double*, int*, int*); extern void F77_NAME(dtrco)(double*, int*, int*, double*, double*, int*); extern void F77_NAME(dtrsl)(double*, int*, int*, double*, int*, int*); /* The following routines are listed as they have always been declared here, but they are not currently included in R */ extern void F77_NAME(dchdc)(double*, int*, int*, double*, int*, int*, int*); extern void F77_NAME(dchdd)(double*, int*, int*, double*, double*, int*, int*, double*, double*, double*, double*, int*); extern void F77_NAME(dchex)(double*, int*, int*, int*, int*, double*, int*, int*, double*, double*, int*); extern void F77_NAME(dchud)(double*, int*, int*, double*, double*, int*, int*, double*, double*, double*, double*); extern void F77_NAME(dgbco)(double*, int*, int*, int*, int*, int*, double*, double*); extern void F77_NAME(dgbdi)(double*, int*, int*, int*, int*, int*, double*); extern void F77_NAME(dgbfa)(double*, int*, int*, int*, int*, int*, int*); extern void F77_NAME(dgbsl)(double*, int*, int*, int*, int*, int*, double*, int*); extern void F77_NAME(dgeco)(double*, int*, int*, int*, double*, double*); extern void F77_NAME(dgedi)(double*, int*, int*, int*, double*, double*, int*); extern void F77_NAME(dgefa)(double*, int*, int*, int*, int*); extern void F77_NAME(dgesl)(double*, int*, int*, int*, double*, int*); extern void F77_NAME(dgtsl)(int*, double*, double*, double*, double*, int*); extern void F77_NAME(dpbco)(double*, int*, int*, int*, double*, double*, int*); extern void F77_NAME(dpbdi)(double*, int*, int*, int*, double*); extern void F77_NAME(dppco)(double*, int*, double*, double*, int*); extern void F77_NAME(dppdi)(double*, int*, double*, int*); extern void F77_NAME(dppfa)(double*, int*, int*); extern void F77_NAME(dppsl)(double*, int*, double*); extern void F77_NAME(dptsl)(int*, double*, double*, double*); extern void F77_NAME(dsico)(double*, int*, int*, int*, double*, double*); extern void F77_NAME(dsidi)(double*, int*, int*, int*, double*, int*, double*, int*); extern void F77_NAME(dsifa)(double*, int*, int*, int*, int*); extern void F77_NAME(dsisl)(double*, int*, int*, int*, double*); extern void F77_NAME(dspco)(double*, int*, int*, double*, double*); extern void F77_NAME(dspdi)(double*, int*, int*, double*, int*, double*, int*); extern void F77_NAME(dspfa)(double*, int*, int*, int*); extern void F77_NAME(dspsl)(double*, int*, int*, double*); #ifdef __cplusplus } #endif #endif /* R_LINPACK_H_ */ ./BNW/src/localscore/modified_postc.c0000775000076600007660000001112112113462034017663 0ustar abhatta3abhatta3/* -*- Mode: C -*- * postc.c --- Posterior for continuous node with continuous parents * Author : Claus Dethlefsen * Created On : Tue Mar 12 06:44:35 2002 * Last Modified By: Claus Dethlefsen * Last Modified On: Wed Jun 04 11:56:51 2003 * Update Count : 227 * Status : Unknown, Use with caution! */ /* ## ## Copyright (C) 2002 Susanne Gammelgaard Bøttcher, Claus Dethlefsen ## ## This program is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ###################################################################### */ #include "R.h" #include "Rmath.h" #include "matrix.h" #include "modified_matrix.c" void postc(double *mu, double *tau, double *rho, double *phi, double *loglik, double *y, double *z, int *n, int *d) { int i,j,ii,jj; double logscale,logk,mscore; double **mtau, **mmu, **tauinv=0; double **zero, **zi, **ziy; double **oldtau, **oldmu; //temp pointers double **tm1,**tm2,**tm3,**tm4,**mm1,**sm1,**sm2,**tt1,**tt2; /* allocate space for matrices */ mtau = dmatrix(1,*d,1,*d); oldtau = dmatrix(1,*d,1,*d); zi = dmatrix(1,*d,1,1); ziy = dmatrix(1,*d,1,1); mmu = dmatrix(1,*d,1,1); oldmu = dmatrix(1,*d,1,1); zero = dmatrix(1,*d,1,1); tauinv = dmatrix(1,*d,1,*d); /* copy arguments into the matrices */ asmatrix(mu,mmu,*d,1); asmatrix(tau,mtau,*d,*d); /* show input */ for(i = 1; i <= *n; i++) { for (ii=1; ii<=*d; ii++) { for (jj=1; jj<=*d; jj++) { tauinv[ii][jj] = mtau[ii][jj]; } } invers(tauinv, *d, zero, 1); for (j=1; j<=*d; j++) { zi[j][1] = z[j-1+(i-1)*(*d)]; } //define once tt1=transp(zi,*d,1); tm1=matmult(tauinv,zi,*d,*d,1); tm2=matmult(tt1,tm1,1,*d,1); logscale = log(*phi) + log1p(tm2[1][1]); free_dmatrix(tm1,1,*d,1,*d); free_dmatrix(tm2,1,1,1,*d); logk = lgammafn( 0.5*(1.0+*rho) ) - lgammafn(*rho*0.5); logk -= 0.5*(logscale + log(M_PI)); tm1=matmult(tt1,mmu,1,*d,1); mscore = logk - 0.5*(*rho+1)*log1p((y[i-1] - tm1[1][1])*(y[i-1] - tm1[1][1])/exp(logscale)); *loglik += mscore; free_dmatrix(tm1,1,1,1,1); for (ii=1; ii<=*d; ii++) { for (jj=1; jj<=*d; jj++) { oldtau[ii][jj] = mtau[ii][jj]; } } for (jj=1; jj<=*d; jj++) { oldmu[jj][1] = mmu[jj][1]; } tm1=matmult(zi,tt1,*d,1,*d); sm1=matsum(mtau,tm1,*d,*d); free_dmatrix(mtau,1,*d,1,*d); mtau = sm1; free_dmatrix(tm1,1,*d,1,*d); for (ii=1; ii<=*d; ii++) { for (jj=1; jj<=*d; jj++) { tauinv[ii][jj] = mtau[ii][jj]; } } invers(tauinv, *d, zero, 1); for (j=1;j<=*d;j++) ziy[j][1] = zi[j][1]*y[i-1]; tm1=matmult(oldtau,mmu,*d,*d,1); sm2=matsum(tm1,ziy,*d,1); free_dmatrix(mmu,1,*d,1,1); mmu=matmult(tauinv,sm2,*d,*d,1); free_dmatrix(tm1,1,*d,1,*d); free_dmatrix(sm2,1,*d,1,1); (*rho)++; tm1=matmult(tt1,mmu,1,*d,1); mm1=matminus(oldmu,mmu,*d,1); tt2=transp(mm1,*d,1); tm3=matmult(oldtau,oldmu,*d,*d,1); tm4=matmult(tt2,tm3,1,*d,1); (*phi) += (y[i-1]-tm1[1][1])*y[i-1] + tm4[1][1]; free_dmatrix(tm1,1,1,1,*d); free_dmatrix(mm1,1,*d,1,1); free_dmatrix(tt2,1,1,1,*d); free_dmatrix(tm3,1,*d,1,*d); free_dmatrix(tm4,1,1,1,*d); free_dmatrix(tt1,1,1,1,*d); } free_dmatrix(mtau,1,*d,1,*d); free_dmatrix(zi,1,*d,1,1); free_dmatrix(ziy,1,*d,1,1); free_dmatrix(mmu,1,*d,1,1); free_dmatrix(zero,1,*d,1,1); free_dmatrix(tauinv,1,*d,1,*d); free_dmatrix(oldtau,1,*d,1,*d); free_dmatrix(oldmu,1,*d,1,1); } ./BNW/src/localscore/MathThreads.h0000775000076600007660000000220112074111132017077 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2000, 2001 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Experimental: included by src/library/stats/src/distance.c */ #ifndef R_EXT_MATHTHREADS_H_ #define R_EXT_MATHTHREADS_H_ #ifdef __cplusplus extern "C" { #endif #include LibExtern int R_num_math_threads; LibExtern int R_max_num_math_threads; #ifdef __cplusplus } #endif #endif /* R_EXT_MATHTHREADS_H_ */ ./BNW/src/localscore/libextern.h0000775000076600007660000000300512074111132016672 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001, 2004 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API on Windows */ /* don't disallow including this one more than once */ /* This is intended to be called from other header files, so not callable from C++ */ #undef LibExtern #undef LibImport #undef LibExport /* Don't try to include CYGWIN here: decorating some symbols breaks the auto-export that it relies on, even if R_DLL_BUILD were set. */ #ifdef WIN32 /* WIN32 as does not depend on config.h */ #define LibImport __declspec(dllimport) #define LibExport __declspec(dllexport) #else #define LibImport #define LibExport #endif #ifdef __MAIN__ #define LibExtern LibExport #define extern #elif defined(R_DLL_BUILD) #define LibExtern extern #else #define LibExtern extern LibImport #endif ./BNW/src/localscore/Riconv.h0000775000076600007660000000245212074111132016143 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2005 the R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Interface to R's platform-independent implementation of iconv. Part of the API. */ #ifndef R_ICONV_H #define R_ICONV_H #ifdef __cplusplus extern "C" { #endif /* from sysutils.c */ #undef Riconv_open #undef Riconv #undef Riconv_close void * Riconv_open (const char* tocode, const char* fromcode); size_t Riconv (void * cd, const char **inbuf, size_t *inbytesleft, char **outbuf, size_t *outbytesleft); int Riconv_close (void * cd); #ifdef __cplusplus } #endif #endif /* R_ICONV_H */ ./BNW/src/localscore/Rmath.h0000775000076600007660000004050012074112342015756 0ustar abhatta3abhatta3/* -*- C -*- * Mathlib : A C Library of Special Functions * Copyright (C) 1998-2011 The R Core Team * Copyright (C) 2004 The R Foundation * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * * Rmath.h should contain ALL headers from R's C code in `src/nmath' ------- such that ``the Math library'' can be used by simply ``#include '' and nothing else. It is part of the API and supports 'standalone Rmath'. */ #ifndef RMATH_H #define RMATH_H /* Note that on some systems we need to include math.h before the defines below, to avoid redefining ftrunc */ #ifndef NO_C_HEADERS # include #endif /*-- Mathlib as part of R -- define this for standalone : */ /* #undef MATHLIB_STANDALONE */ #define R_VERSION_STRING "2.15.2" #ifndef HAVE_EXPM1 # define HAVE_EXPM1 1 #endif #ifndef HAVE_HYPOT # define HAVE_HYPOT 1 #endif #ifndef HAVE_LOG1P # define HAVE_LOG1P 1 #endif #ifndef HAVE_WORKING_LOG1P # define HAVE_WORKING_LOG1P 1 #endif #if defined(HAVE_LOG1P) && !defined(HAVE_WORKING_LOG1P) /* remap to avoid problems with getting the right entry point */ double Rlog1p(double); #define log1p Rlog1p #endif /* Undo SGI Madness */ #ifdef ftrunc # undef ftrunc #endif #ifdef qexp # undef qexp #endif #ifdef qgamma # undef qgamma #endif /* ----- The following constants and entry points are part of the R API ---- */ /* 30 Decimal-place constants */ /* Computed with bc -l (scale=32; proper round) */ /* SVID & X/Open Constants */ /* Names from Solaris math.h */ #ifndef M_E #define M_E 2.718281828459045235360287471353 /* e */ #endif #ifndef M_LOG2E #define M_LOG2E 1.442695040888963407359924681002 /* log2(e) */ #endif #ifndef M_LOG10E #define M_LOG10E 0.434294481903251827651128918917 /* log10(e) */ #endif #ifndef M_LN2 #define M_LN2 0.693147180559945309417232121458 /* ln(2) */ #endif #ifndef M_LN10 #define M_LN10 2.302585092994045684017991454684 /* ln(10) */ #endif #ifndef M_PI #define M_PI 3.141592653589793238462643383280 /* pi */ #endif #ifndef M_2PI #define M_2PI 6.283185307179586476925286766559 /* 2*pi */ #endif #ifndef M_PI_2 #define M_PI_2 1.570796326794896619231321691640 /* pi/2 */ #endif #ifndef M_PI_4 #define M_PI_4 0.785398163397448309615660845820 /* pi/4 */ #endif #ifndef M_1_PI #define M_1_PI 0.318309886183790671537767526745 /* 1/pi */ #endif #ifndef M_2_PI #define M_2_PI 0.636619772367581343075535053490 /* 2/pi */ #endif #ifndef M_2_SQRTPI #define M_2_SQRTPI 1.128379167095512573896158903122 /* 2/sqrt(pi) */ #endif #ifndef M_SQRT2 #define M_SQRT2 1.414213562373095048801688724210 /* sqrt(2) */ #endif #ifndef M_SQRT1_2 #define M_SQRT1_2 0.707106781186547524400844362105 /* 1/sqrt(2) */ #endif /* R-Specific Constants */ #ifndef M_SQRT_3 #define M_SQRT_3 1.732050807568877293527446341506 /* sqrt(3) */ #endif #ifndef M_SQRT_32 #define M_SQRT_32 5.656854249492380195206754896838 /* sqrt(32) */ #endif #ifndef M_LOG10_2 #define M_LOG10_2 0.301029995663981195213738894724 /* log10(2) */ #endif #ifndef M_SQRT_PI #define M_SQRT_PI 1.772453850905516027298167483341 /* sqrt(pi) */ #endif #ifndef M_1_SQRT_2PI #define M_1_SQRT_2PI 0.398942280401432677939946059934 /* 1/sqrt(2pi) */ #endif #ifndef M_SQRT_2dPI #define M_SQRT_2dPI 0.797884560802865355879892119869 /* sqrt(2/pi) */ #endif #ifndef M_LN_SQRT_PI #define M_LN_SQRT_PI 0.572364942924700087071713675677 /* log(sqrt(pi)) == log(pi)/2 */ #endif #ifndef M_LN_SQRT_2PI #define M_LN_SQRT_2PI 0.918938533204672741780329736406 /* log(sqrt(2*pi)) == log(2*pi)/2 */ #endif #ifndef M_LN_SQRT_PId2 #define M_LN_SQRT_PId2 0.225791352644727432363097614947 /* log(sqrt(pi/2)) */ #endif #ifdef MATHLIB_STANDALONE # ifndef R_EXT_BOOLEAN_H_ /* "copy-paste" R_ext/Boolean.h if not already included: */ #define R_EXT_BOOLEAN_H_ #undef FALSE #undef TRUE typedef enum { FALSE = 0, TRUE } Rboolean; # endif #else # include "Boolean.h" #endif #ifndef MATHLIB_STANDALONE #define bessel_i Rf_bessel_i #define bessel_j Rf_bessel_j #define bessel_k Rf_bessel_k #define bessel_y Rf_bessel_y #define bessel_i_ex Rf_bessel_i_ex #define bessel_j_ex Rf_bessel_j_ex #define bessel_k_ex Rf_bessel_k_ex #define bessel_y_ex Rf_bessel_y_ex #define beta Rf_beta #define choose Rf_choose #define dbeta Rf_dbeta #define dbinom Rf_dbinom #define dcauchy Rf_dcauchy #define dchisq Rf_dchisq #define dexp Rf_dexp #define df Rf_df #define dgamma Rf_dgamma #define dgeom Rf_dgeom #define dhyper Rf_dhyper #define digamma Rf_digamma #define dlnorm Rf_dlnorm #define dlogis Rf_dlogis #define dnbeta Rf_dnbeta #define dnbinom Rf_dnbinom #define dnchisq Rf_dnchisq #define dnf Rf_dnf #define dnorm4 Rf_dnorm4 #define dnt Rf_dnt #define dpois Rf_dpois #define dpsifn Rf_dpsifn #define dsignrank Rf_dsignrank #define dt Rf_dt #define dtukey Rf_dtukey #define dunif Rf_dunif #define dweibull Rf_dweibull #define dwilcox Rf_dwilcox #define fmax2 Rf_fmax2 #define fmin2 Rf_fmin2 #define fprec Rf_fprec #define fround Rf_fround #define ftrunc Rf_ftrunc #define fsign Rf_fsign #define gammafn Rf_gammafn #define imax2 Rf_imax2 #define imin2 Rf_imin2 #define lbeta Rf_lbeta #define lchoose Rf_lchoose #define lgammafn Rf_lgammafn #define lgammafn_sign Rf_lgammafn_sign #define lgamma1p Rf_lgamma1p #define log1pmx Rf_log1pmx #define logspace_add Rf_logspace_add #define logspace_sub Rf_logspace_sub #define pbeta Rf_pbeta #define pbeta_raw Rf_pbeta_raw #define pbinom Rf_pbinom #define pcauchy Rf_pcauchy #define pchisq Rf_pchisq #define pentagamma Rf_pentagamma #define pexp Rf_pexp #define pf Rf_pf #define pgamma Rf_pgamma #define pgeom Rf_pgeom #define phyper Rf_phyper #define plnorm Rf_plnorm #define plogis Rf_plogis #define pnbeta Rf_pnbeta #define pnbinom Rf_pnbinom #define pnchisq Rf_pnchisq #define pnf Rf_pnf #define pnorm5 Rf_pnorm5 #define pnorm_both Rf_pnorm_both #define pnt Rf_pnt #define ppois Rf_ppois #define psignrank Rf_psignrank #define psigamma Rf_psigamma #define pt Rf_pt #define ptukey Rf_ptukey #define punif Rf_punif #define pythag Rf_pythag #define pweibull Rf_pweibull #define pwilcox Rf_pwilcox #define qbeta Rf_qbeta #define qbinom Rf_qbinom #define qcauchy Rf_qcauchy #define qchisq Rf_qchisq #define qchisq_appr Rf_qchisq_appr #define qexp Rf_qexp #define qf Rf_qf #define qgamma Rf_qgamma #define qgeom Rf_qgeom #define qhyper Rf_qhyper #define qlnorm Rf_qlnorm #define qlogis Rf_qlogis #define qnbeta Rf_qnbeta #define qnbinom Rf_qnbinom #define qnchisq Rf_qnchisq #define qnf Rf_qnf #define qnorm5 Rf_qnorm5 #define qnt Rf_qnt #define qpois Rf_qpois #define qsignrank Rf_qsignrank #define qt Rf_qt #define qtukey Rf_qtukey #define qunif Rf_qunif #define qweibull Rf_qweibull #define qwilcox Rf_qwilcox #define rbeta Rf_rbeta #define rbinom Rf_rbinom #define rcauchy Rf_rcauchy #define rchisq Rf_rchisq #define rexp Rf_rexp #define rf Rf_rf #define rgamma Rf_rgamma #define rgeom Rf_rgeom #define rhyper Rf_rhyper #define rlnorm Rf_rlnorm #define rlogis Rf_rlogis #define rnbeta Rf_rnbeta #define rnbinom Rf_rnbinom #define rnchisq Rf_rnchisq #define rnf Rf_rnf #define rnorm Rf_rnorm #define rnt Rf_rnt #define rpois Rf_rpois #define rsignrank Rf_rsignrank #define rt Rf_rt #define rtukey Rf_rtukey #define runif Rf_runif #define rweibull Rf_rweibull #define rwilcox Rf_rwilcox #define sign Rf_sign #define tetragamma Rf_tetragamma #define trigamma Rf_trigamma #endif #define rround fround #define prec fprec #undef trunc #define trunc ftrunc #ifdef __cplusplus extern "C" { #endif /* R's versions with !R_FINITE checks */ double R_pow(double x, double y); double R_pow_di(double, int); /* Random Number Generators */ double norm_rand(void); double unif_rand(void); double exp_rand(void); #ifdef MATHLIB_STANDALONE void set_seed(unsigned int, unsigned int); void get_seed(unsigned int *, unsigned int *); #endif /* Normal Distribution */ #define pnorm pnorm5 #define qnorm qnorm5 #define dnorm dnorm4 double dnorm(double, double, double, int); double pnorm(double, double, double, int, int); double qnorm(double, double, double, int, int); double rnorm(double, double); void pnorm_both(double, double *, double *, int, int);/* both tails */ /* Uniform Distribution */ double dunif(double, double, double, int); double punif(double, double, double, int, int); double qunif(double, double, double, int, int); double runif(double, double); /* Gamma Distribution */ double dgamma(double, double, double, int); double pgamma(double, double, double, int, int); double qgamma(double, double, double, int, int); double rgamma(double, double); double log1pmx(double); double log1pexp(double); // <-- ../nmath/plogis.c double lgamma1p(double); double logspace_add(double, double); double logspace_sub(double, double); /* Beta Distribution */ double dbeta(double, double, double, int); double pbeta(double, double, double, int, int); double qbeta(double, double, double, int, int); double rbeta(double, double); /* Lognormal Distribution */ double dlnorm(double, double, double, int); double plnorm(double, double, double, int, int); double qlnorm(double, double, double, int, int); double rlnorm(double, double); /* Chi-squared Distribution */ double dchisq(double, double, int); double pchisq(double, double, int, int); double qchisq(double, double, int, int); double rchisq(double); /* Non-central Chi-squared Distribution */ double dnchisq(double, double, double, int); double pnchisq(double, double, double, int, int); double qnchisq(double, double, double, int, int); double rnchisq(double, double); /* F Distibution */ double df(double, double, double, int); double pf(double, double, double, int, int); double qf(double, double, double, int, int); double rf(double, double); /* Student t Distibution */ double dt(double, double, int); double pt(double, double, int, int); double qt(double, double, int, int); double rt(double); /* Binomial Distribution */ double dbinom(double, double, double, int); double pbinom(double, double, double, int, int); double qbinom(double, double, double, int, int); double rbinom(double, double); /* Multnomial Distribution */ void rmultinom(int, double*, int, int*); /* Cauchy Distribution */ double dcauchy(double, double, double, int); double pcauchy(double, double, double, int, int); double qcauchy(double, double, double, int, int); double rcauchy(double, double); /* Exponential Distribution */ double dexp(double, double, int); double pexp(double, double, int, int); double qexp(double, double, int, int); double rexp(double); /* Geometric Distribution */ double dgeom(double, double, int); double pgeom(double, double, int, int); double qgeom(double, double, int, int); double rgeom(double); /* Hypergeometric Distibution */ double dhyper(double, double, double, double, int); double phyper(double, double, double, double, int, int); double qhyper(double, double, double, double, int, int); double rhyper(double, double, double); /* Negative Binomial Distribution */ double dnbinom(double, double, double, int); double pnbinom(double, double, double, int, int); double qnbinom(double, double, double, int, int); double rnbinom(double, double); double dnbinom_mu(double, double, double, int); double pnbinom_mu(double, double, double, int, int); double qnbinom_mu(double, double, double, int, int); double rnbinom_mu(double, double); /* Poisson Distribution */ double dpois(double, double, int); double ppois(double, double, int, int); double qpois(double, double, int, int); double rpois(double); /* Weibull Distribution */ double dweibull(double, double, double, int); double pweibull(double, double, double, int, int); double qweibull(double, double, double, int, int); double rweibull(double, double); /* Logistic Distribution */ double dlogis(double, double, double, int); double plogis(double, double, double, int, int); double qlogis(double, double, double, int, int); double rlogis(double, double); /* Non-central Beta Distribution */ double dnbeta(double, double, double, double, int); double pnbeta(double, double, double, double, int, int); double qnbeta(double, double, double, double, int, int); double rnbeta(double, double, double); /* Non-central F Distribution */ double dnf(double, double, double, double, int); double pnf(double, double, double, double, int, int); double qnf(double, double, double, double, int, int); /* Non-central Student t Distribution */ double dnt(double, double, double, int); double pnt(double, double, double, int, int); double qnt(double, double, double, int, int); /* Studentized Range Distribution */ double ptukey(double, double, double, double, int, int); double qtukey(double, double, double, double, int, int); /* Wilcoxon Rank Sum Distribution */ double dwilcox(double, double, double, int); double pwilcox(double, double, double, int, int); double qwilcox(double, double, double, int, int); double rwilcox(double, double); /* Wilcoxon Signed Rank Distribution */ double dsignrank(double, double, int); double psignrank(double, double, int, int); double qsignrank(double, double, int, int); double rsignrank(double); /* Gamma and Related Functions */ double gammafn(double); double lgammafn(double); double lgammafn_sign(double, int*); void dpsifn(double, int, int, int, double*, int*, int*); double psigamma(double, double); double digamma(double); double trigamma(double); double tetragamma(double); double pentagamma(double); double beta(double, double); double lbeta(double, double); double choose(double, double); double lchoose(double, double); /* Bessel Functions */ double bessel_i(double, double, double); double bessel_j(double, double); double bessel_k(double, double, double); double bessel_y(double, double); double bessel_i_ex(double, double, double, double *); double bessel_j_ex(double, double, double *); double bessel_k_ex(double, double, double, double *); double bessel_y_ex(double, double, double *); /* General Support Functions */ #ifndef HAVE_HYPOT double hypot(double, double); #endif double pythag(double, double); #ifndef HAVE_EXPM1 double expm1(double); /* = exp(x)-1 {care for small x} */ #endif #ifndef HAVE_LOG1P double log1p(double); /* = log(1+x) {care for small x} */ #endif int imax2(int, int); int imin2(int, int); double fmax2(double, double); double fmin2(double, double); double sign(double); double fprec(double, double); double fround(double, double); double fsign(double, double); double ftrunc(double); double log1pmx(double); /* Accurate log(1+x) - x, {care for small x} */ double lgamma1p(double);/* accurate log(gamma(x+1)), small x (0 < x < 0.5) */ /* Compute the log of a sum or difference from logs of terms, i.e., * * log (exp (logx) + exp (logy)) * or log (exp (logx) - exp (logy)) * * without causing overflows or throwing away too much accuracy: */ double logspace_add(double logx, double logy); double logspace_sub(double logx, double logy); /* ----------------- Private part of the header file ------------------- */ /* old-R Compatibility */ #ifdef OLD_RMATH_COMPAT # define snorm norm_rand # define sunif unif_rand # define sexp exp_rand #endif #if defined(MATHLIB_STANDALONE) && !defined(MATHLIB_PRIVATE_H) /* second is defined by nmath.h */ /* If isnan is a macro, as C99 specifies, the C++ math header will undefine it. This happens on OS X */ # ifdef __cplusplus int R_isnancpp(double); /* in mlutils.c */ # define ISNAN(x) R_isnancpp(x) # else # define ISNAN(x) (isnan(x)!=0) # endif # define R_FINITE(x) R_finite(x) int R_finite(double); # ifdef WIN32 /* not Win32 as no config information */ # ifdef RMATH_DLL # define R_EXTERN extern __declspec(dllimport) # else # define R_EXTERN extern # endif R_EXTERN double NA_REAL; R_EXTERN double R_PosInf; R_EXTERN double R_NegInf; R_EXTERN int N01_kind; # undef R_EXTERN #else extern int N01_kind; # endif #endif /* MATHLIB_STANDALONE */ #ifdef __cplusplus } #endif #endif /* RMATH_H */ ./BNW/src/localscore/Complex.h0000775000076600007660000000201412074111132016304 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2001 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_COMPLEX_H #define R_COMPLEX_H #ifdef __cplusplus extern "C" { #endif typedef struct { double r; double i; } Rcomplex; #ifdef __cplusplus } #endif #endif /* R_COMPLEX_H */ ./BNW/src/localscore/libRmath.so0000775000076600007660000061711012043550044016647 0ustar abhatta3abhatta3ELF>`/@ˆ@8@$$ ((#(#\Ø XX#X#  $$Påtd¨å¨å¨åLLQåtdGNU׌ÙV¶ÈU@Ð!›{RXÍÓFƒ# œ‘4h‰8€ <˜¨ @8ˆ¤ ,H ‚ 2$à 04â7ÞAa  Œ)L 88YH£À‚‚€¥ _ E&GG °B@T /È )@àJ&x#$%&')0358;=>?BCEFGIJKMNORVWYZ\]^`bcdfhjkmopstuwxz|}~€‚ƒ„†ˆ‹Ž“•˜™›žŸ ¡£¥¨ª«­®°³¸¹º»¼ŸTi}R¤æ÷Í1Ó6ò©X>ë(“ÆÂ+^5¾2’"Là2]ø$4xþÜjˆ ‚¢‡\¿ºœR}Ÿu~»Kø¹ñì‡mhŽwY·bcÍìËãsùyYC°3å ù+¢ˆ S FŸ¬ÜšcT«Ëž³üþ:ö ¹¡‰”|ëjˆ ?ƒV`õsÙ~ú¸éwNùwYâÃœ|[ Î:ýï#)yYðÉJ:J±.Ž8¢ˆ ¬ê<<`§â•í<<`ì<<`I@ì™NÇôw~§:%hI —>ùµŸÒÃU tX<(ù5Ç] û<<`=yYxÒIý2²cE™»ôàUr­Ð؇L{¢ò{#5rö¡šG3‹/QÔ…:9ÐÁøKyYÙqXÍ¥?¼oS3:MCÖ>ZøîR9ãí_DP|ÿ+·.h3K3¯kMôó½Ž<]yY Ç%hß««2r·óŠ l[±!;Š%“lìùGœçI8 £IÎ] »ã’|H ëeɼêÓïlΡøû2Ž¯HÛ=7®‚dŸ¨ºô^ó• •öˆ <ù€¤¬[|¦~¨õKVi÷¢•|iS&hç#&-KsÉ{” @)C‹Ö6F + pÇÿèâ‰yõ"_xDöU+’·{?FÐÊÄ €¡ˆ  B\' Õ £ €¦T à0¶ ¡%© °"qÚ ­)Æ °7¤- àc! 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Arg. out of range? bessel_i(%g,nu=%g): precision lost in result (†@jø@-Cëâ6?€à7yÃQC\Âõ(\ù?úTÏk‰| Èë…óÌá€à7yÃACZb××çtiÛ@cºÿ/Û@cºÿ?J_besselbessel_jbessel_j allocation errorbessel_j(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range? bessel_j(%g,nu=%g): precision lost in result ð?ð?@@8@^@€†@°³@°ã@&A€¯KA¨ƒAüŒ¼AÀŒ2÷A(;L4B€uwsB€uw³BØìî7ôBsÊì¾6Ch0¹{CZA¾³áÀC Ƶé;(DlðYaRwNDΤø5Ãå•Dš{zhRlàD9@ƒÈÉm0_ä?P@@`@1@*@€F@€D@€E@€@@=@?@-DTû!@ Àj„ÑBDµ_¿ƒÈÉm0_ä¿À?V瞯Ò‰تãÇ>ÿ³ÿ *?c?UUUUUUÅ?EH:B@”9ÀµµLÆR’j@ÕÓ®€…ƒÀ²z`¢%kz@ø â˃&ß¿Õ‰0_²(*@‡"KÁ}YÀÝQ1(wºu@†C¾Ï$é6?®»“Ïu=@ ó>Yq@d=Q"ÐÚ’@Lj°1Ô•¥@òÞz#{çª@ÖŸ‹ˆCE¡@ EK‚#â@©«N¸Çé?ëÌ—g4@")Q”¶c@m¸Or^Å€@šrä#Œ@a.¯d׆@ûSÂà“©l@ÓSb¦Qê?Ûù~j¼ †@›>O¼Ööÿ€®»“Ïu=@©«N¸Çé?ÓSb¦Qê?²T°­½?†C¾Ï$é6?»½×Ùß|Û=ÿÿÿÿÿÿïÐ?ûËîÉÃêD@®Gázn@Q6Ô3Eˆé?¬­Ø_vJ@ÐDØðô @DúíëÀ9@ðHPÜ,@b¡Ö4ï¸@Å °rhAE@ýöuàœ)g@‘í|?5¾"@4@ÁV ‡³õ?ª‚QI U@bessel_ybessel_y allocation errorbessel_y(%g): ncalc (=%ld) != nb (=%ld); alpha=%g. Arg. out of range? bessel_y(%g,nu=%g): precision lost in result ÄNÙ¿›` »€PØ?Ý’R»¯)`#h«;'bÓ <ÿê§ÎùEÛÕI¹ÑÈa¾'Ïù3­¾Á™A”\ÚÔ¾,mç ?¢ß]ÙÖT?WùŒÃô[?v¶ ¬³¿RUK„+Ò¿Y>L!öí?„×—A+øO W>ƒÈÉm0_Ô?3@ @ÄNÙ¿›` »€PØ?Ý’R»Y>L!öí?-DTû!ù?0@0C-DTû!ù¿^8U)zj/@.Àæ…S•¢§æ¿'k' (%.2f) must be integer, rounded to %.0fH¯¼šò×z>>@norm_rand(): invalid N01_kind: %d  ýýÿ0þýÿ`ÿýÿ£üýÿÿýÿØüýÿ çÃÔ¤?œA2Ó¬"¤? ÔE§:¤?´­E[¤?§˜½K-„¤?Ιž¶¤?Õ}¾5Éò¤?:‰ÎS™9¥?óóSÚê‹¥?¿“?­Üê¥?ÞmbqÍW¦?ú?MNiÔ¦?¶¯,f¾b§?È»<V¨?,ÐY¿¨?ñ­8j¿”©?}qq–Šª?Ètl-a§«?mwͳ«ó¬?'>-õâz®?LøkÓT&°?ÀÁjn}?±?\ç=䘲?çJ-)±J´?ú7ÜR{¶?sovRük¹?¼¡:gU•½?yß!ÁùÁ?Þd Œ«€Ç?ñâ†)ÛÑ?>Dþôúnæ?9ÇF%I?Z˜fÛåb?©×¬M o?•ÿ!á¡Fv?‡-ç™1á|?\9* µÕ?$âóX…?rpe`O‰?f÷äa¡ÖŒ?¼„ØÓíp?xkO¬–’?PëOEžâ”?]›tø÷[—?Ǭj‹c š?ƒêQ~sûœ?™Ó†?š ?.óëÁƒê¡?!¾1ãñ£? 륭:@¦?P0Qcç¨?ÄAßitÿ«?ˆöÒÈ©¯?þ¬àT÷ ²?$é?Å´?ÞÊ3«N9¸?WhÖ³¿¼?ü6ÄxÁ?‘J ]äùÅ?¤XÉ"Í?™-Yá&Õ?ŒÕ‹Fãµâ?hþ=4àÐ?B@¾„ Ï?™dßÌ?(‰ÛWÔË?}•—É?”AÿNÈ?ý›)c2Ç?£Å’8Æ?Ì L[Å?+ç{ü”Ä?³Áx¼âÃ?ßg@Ã?`³·ï¬Â?ÚæÆô„%Â?Ê—4ǨÁ?V‘c5Á?Áz’*@ÊÀ?Á6âÉnfÀ?ù§¯B% À?’¢mc¿?òÁ! ¿¾? àîQ$¾? Ì0’½?ÓŠÊáî½?2¤/)ㄼ?ÒH•r¼? ™«rã¤?iðŒðÕ´?Iô +&¾?ÊçËÁ"Ä?¡I‹:É?Yqo£\Î?0qšô­ÅÑ?Zä‚–dÔ?¸ó³G^ ×?Ã4w¾Ù? Äv|Ü?’ŸCÏHß?@Ð8±á?ßïa@@ˆâ? Ý!Å ä?ቢk•å?Ýd¯Ò8/ç?´Ø܇rØè?¿O˜‹“ê?5>8Dcì?VnX Lî?·—4Fë(ð?óªÎj=ñ?çÇ_ZÔgò?k{¡€­ó?ÇJ̳’õ?ßÞ5èK¯ö?…µ1v‹ø?î v¦Ðú?gÓÀÍý?B`åÐ";@@@B`åÐ";@æ‚'NJì?®[|ò?¦ñAqº@Š~ ]%ï?·–­¬¤@E?Ю’ï?K×­î?ßÞmwÌ/ä¿\³´JÎ-è??Oœ§ø‡¡?V6Ô3EˆÙ?•=  ǿ»‰xky)í?ìÝJ&°ñ?ÂW’Ú³Þ?B‡óCîë?Í129©?DJüdã¿ôøZKÇé?D A@>B[|ò?@òZMT«?ï9úþB.æ?RëÚ~2Þí?^5K ã¤ï?˜ º­óï?Ìãýù™þï?8ÜÝÿï?Á¡Ðÿüÿï?6æPÅÿÿï?Ýõûÿÿï?€,¿ÿÿÿï?ÙEüÿÿÿï?TÍÿÿÿÿï?€ýÿÿÿÿï?ãÿÿÿÿÿï?ÿÿÿÿÿÿï?ð?ï9úþB.æ? ** NON-convergence in pgamma()'s pd_lower_cf() f= %g. .Ÿ‡¢®B}ÔUUUUUUµ?ÇqÇql?È´ÚŽ&÷e¿Y¨_FÎ.¿Äòthÿ°I?8À9H`G?H{¹½sgC¿.Ÿ‡¢®B}ÔUUUUUUå?tåÉ:Wž¿4ÇV¥ãg?E´sÜ„Ò^?•/8ZTG¿÷A£š:F¿‡æš@Xý>?¦¦ÄL£Ô?vU>±?ƒ„}¬"•?òõÂO@~?0lÛêÖ­g?Ž¿ÂÅŠS?é–cøj³@?È/mÇÔ?-?ZÖ{?ï|½å?ëfîÜ€õ>C"ÎcÉËã>¬Jó9zYÒ>A•g·.Á>/²ÞL°>/ý<Ù&ž>Mzð³»vŒ>—Š¿Ë¦õz> “›i>¬>ß4ÇbX>ͭϬFG>­®G„JC6>ÃÒÿw¨U%>%y{> Á/+]±>àã«Ÿšöò=LC7£2Iâ=¦ÿÿÿÿÿï?0Žä.ÿ++À_@ u@^@  *?N@€Q@U@@Z@€a@@j@88c?ø“@Ô‘@0Ž@ø†@@z@  :? @†@à|@x’@…@€o@0›@È‹@`r@°¡@ð‚@\’@ÍÌÌÌÌÌì?›ò×ð?ËPÊÿÿï?8ï,6V‹×?(ÀµüÀUž @wS%%˜Å/?„ŒoC0?wˆ=¼^?ˆJDtßœW?úŽm[Œh€?ü!OõØT•??àÃVU¥?°rh‘í| @oƒÀÊ¡Ý?bX9´ÈÆ?ö(\ÂõÈ?ÓMbX9´?{®GázÄ?%•C *@Å1w-!?X9´Èvú?áz®Gáú?š™™™™™Ñ?X9´Èv¾¯?ú~j¼t“˜?1¬ZdÃ?b0…Ì•¿?:e$1÷Á?<É 9Â? ¥Š=IÅ?g¥ÿ›Í™É?ˆ¸9• Ð?‡¼Š1UUÕ?É@…,õÿæ¿pbeta_raw() -> bratio() gave error code %dqbeta¨þš¬QÑ? OäIÒu@þHVñ¦?»DõÖÀï?«ªªªªªê?ÀwºMhƒ’þÿÿÿÿÿï?ÀYóøÂn¥ÈªsVU¥? %8šÈqŒ?“‹1°Žãè?ï9úþB.†@ j C.ö?f„·!à@Q6Ô3EˆÙ?ÛˆPTŒô?­ðUh÷Ý?9,>™ä°?ç}}‘Bün?Ѻ G!?B„+¢Ë?”íSf®NÀ?zp=ØÄ–?‹ONü³JW?ƒÄmˆí†þ>Út%w —?›ŸìªED6@çÍÿ°ilm@¿Ik©‚½—@'¢ìŽU¹@£¦Ã•ä-Ò@†±|ž á@äoëã@a_Ó[9Ó@fÜÛúAˆÙ?¼¸5,Ä!@d× m`W@b¤«†)ª‚@ìa>}£@×È]Á0Àº@`ObS©Æ@ŽüÒ[9Ã@X_F—7‡k•å? <á”HŎа?ó÷´ÑËá@Þ²/4î™G@·…×Dç d@¸U~ÕÉ€Ž@qýy®@È­œRw Ä@ìÒÚ̾ºÑ@­‡;By8æ@Í;fž @X_ŽüÒ[9Ã@a_Ó[9Ó@°?Ï¢åER:c h"lxÂBÀh³êsµ• @h³êsµ• À h"lxÂB@Út%w —?ƒÄmˆí†þ>Ѻ G!?333333Û?…ëQ¸Ç?^’}o)š£@äE.kÒRà@ ·Ulð@*u›†>læ@çNÍØÑÊ@ÌÀ"]Ξ@nC‹ˆ¤`@uïžÙ @iK˜Ê~j´@v®±|EÜ@¾ôdª|1ã@fRÖÕr·Ô@ŸÈu.2µ@÷³Èý~y…@µn8(E@š™™™™™ù?鬷ÀZaI?gìElëD—?7\¸¹«òÎ?²uSÌSô?Ä=Ë. @j%b÷@›±ÊHw…@jRéýeÆö?ä9dh? >('ß¿ŒñA?¿«~z ?@ð”3õÂ?É…3ò’æ?3fRæxÒú?I¤F»ïl@“¿“ÖtûŠ>*àYÌÆnü>ESB\T?çN;A+›?ÏUR1ÙúÒ?E¤F¦Žü?P‡nêÚ@&å>Á±¡@Áøñ¿iâ<à¹@÷Fƒ>¿tcI,\ó>×Å—¼ÈI?*F2ùvŽ?ûC4ë†Á?×ÇOÓ1ã?ļÖBjAÐcAš™™™™™É?}Ô%­I²Tqtì¯ð?( þÿÿÿï?ÿÿÿÿÿÿïÿ‚vIhÂ%<=@Œµx¯Dê-™—q=Í;fž ö?˜ð?H@7Ô@€X@×£p= X@ W@ÍÌÌÌÌÌ@š™™™™™©?@333333Ó?333333ã?333333@B@ú7'{O^BÀbX9´È¶¿çû©ñÒMê?½¡çHÐPò?non-integer x = %f´¾dÈñgý?)\Âõ(°<€ÿÿÿÿÿï?Y@ÀÿÿÿßAÂõ(\@ffffffÀš™™™™™.@€4@ôýÔxé&Á?ä?óKUUUUÅ?€aÀÀX@€`@Ë@€MArbinom: probability sum should be 1, but is %g€?€%@@0øÿÿÿÿï?rhyper.c: afc(i), i=%d < 0 -- SHOULD NOT HAPPEN! ï9úþB.æ? *ú «ü?ù,’|§l @ÉyD bratio() gave error code %dð?ð?@@8@^@€†@°³@°ã@&AVŸ«­Ø_ò?Zd;ßOÝ?UUUUUU¥?’$I’$IÂ?À AñcÌ]»?ÍÌÌÌÌÌü?M„ O¯”å¿333333À"âæT2À?ϸg±¹Á?µñq·53Â?½0>q¥CÅ?14è•ü™É?hÄq…Ð?2@fffff¦@@›+¡†›„öˆÃ@Aòÿÿÿï?-ð?pntpnt{final}D@DþºL –@½¡çHÐPâ?Øí½ÎþæÛÝ¿?ptukey·´ÚÍ›?]&Á¢±ß¯?XÂœçN\¸?j8­+¯ç¿?¿<Êö%Ã?üuZ»ë¦Å?ÀàwŒ_Ç?üMèê?È?~xM&,©ï?°ùfõ9î?ƒä5@³ë?kr¤ÝE,è?¸èÕf¤Åã?r§Cš%PÝ?|3BæÊÒ?ù©vf½R¸?mê]'¨?aÎ+``»?-òXr}Ä?r«±æcÊ?µj%\ãÍ?%ðÔæ äÏ?.äØñhï?´ˆûO‡îì?6Øî £è?ùwÀOËâ?±¨ Š×?ä0öø¥À?IÀ>ÀjØ@‰@ˆ³@qtukeybíîÈ¿¼™'?$Ê?Fñg\KçÕ?Æ*’»tŸÔ?ˆEÚÖo?h_d>sº?Tð4°Ìþà?/½‰©Õâ?T÷Ìæn¹?¬­Ø_vOοlxz¥,Cì?•C‹ló¿‡ÙÎ÷Só? 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you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* This file was contributed by Ei-ji Nakama. * See also the comments in src/main/rlocale.c. * For use in R only. */ #ifndef R_LOCALE_H #define R_LOCALE_H #ifndef NO_C_HEADERS #include #include #include #endif #ifdef __cplusplus extern "C" { #endif extern const char *locale2charset(const char *); /* * Windows CJK * In Unicode, there is not a rule about character width. * A letter of breadth is used in a CJK (China, Japan, Korea, * Taiwan, Hong Kong, and Singapore) area, and there are a * letter and a standard (character width is not still prescribed) * of a cord in a country. * Letter width is a problem of a font, but it is a rule route * besides a alphanumeric character that use a breadth letter. * It is generally defined as a breadth letter for a font such * as Japanese. * - Win32 * Attempted explanation by BDR * The display widths of characters are not prescribed in Unicode. * Double-width characters are used in the CJK area: their width can * be font-specific, with different fonts in use in different parts * of the CJK area. The tables supplied in many OSes and by Marcus * Kuhn are not do not take the exact locale into account. The * tables supplied in rlocale_data.h allow different widths for * different parts of the CJK area, and also where needed different * widths on Windows. (The Windows differences are in zh_CN, and * apply to European characters.) * */ extern int Ri18n_wcwidth(wchar_t); extern int Ri18n_wcswidth (const wchar_t *, size_t); /* Mac OSX CJK and WindowXP(Japanese) * iswctypes of MacOSX calls isctypes. no i18n. * For example, iswprint of Windows does not accept a macron of * Japanese "a-ru" of R as a letter. * Therefore Japanese "Buraian.Ripuri-" of "Brian Ripley" is * shown of hex-string.:-) * We define alternatives to be used if * defined(Win32) || defined(__APPLE_CC__) || defined(_AIX) */ extern wctype_t Ri18n_wctype(const char *); extern int Ri18n_iswctype(wint_t, wctype_t); #ifndef IN_RLOCALE_C /* We want to avoid these redefinitions in rlocale.c itself */ #undef iswupper #undef iswlower #undef iswalpha #undef iswdigit #undef iswxdigit #undef iswspace #undef iswprint #undef iswgraph #undef iswblank #undef iswcntrl #undef iswpunct #undef iswalnum #undef wctype #undef iswctype #define iswupper(__x) Ri18n_iswctype(__x, Ri18n_wctype("upper")) #define iswlower(__x) Ri18n_iswctype(__x, Ri18n_wctype("lower")) #define iswalpha(__x) Ri18n_iswctype(__x, Ri18n_wctype("alpha")) #define iswdigit(__x) Ri18n_iswctype(__x, Ri18n_wctype("digit")) #define iswxdigit(__x) Ri18n_iswctype(__x, Ri18n_wctype("xdigit")) #define iswspace(__x) Ri18n_iswctype(__x, Ri18n_wctype("space")) #define iswprint(__x) Ri18n_iswctype(__x, Ri18n_wctype("print")) #define iswgraph(__x) Ri18n_iswctype(__x, Ri18n_wctype("graph")) #define iswblank(__x) Ri18n_iswctype(__x, Ri18n_wctype("blank")) #define iswcntrl(__x) Ri18n_iswctype(__x, Ri18n_wctype("cntrl")) #define iswpunct(__x) Ri18n_iswctype(__x, Ri18n_wctype("punct")) #define iswalnum(__x) Ri18n_iswctype(__x, Ri18n_wctype("alnum")) #define wctype(__x) Ri18n_wctype(__x) #define iswctype(__x,__y) Ri18n_iswctype(__x,__y) #endif #ifdef __cplusplus } #endif #endif /* R_LOCALE_H */ ./BNW/src/localscore/Constants.h0000775000076600007660000000276612074111132016667 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka * Copyright (C) 1998-2012 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_EXT_CONSTANTS_H_ #define R_EXT_CONSTANTS_H_ /* usually in math.h, but not with strict C99 compliance */ #ifndef M_PI #define M_PI 3.141592653589793238462643383279502884197169399375 #endif #ifndef STRICT_R_HEADERS #define PI M_PI #include /* Defines the rest, at least in C99 */ #define SINGLE_EPS FLT_EPSILON #define SINGLE_BASE FLT_RADIX #define SINGLE_XMIN FLT_MIN #define SINGLE_XMAX FLT_MAX #define DOUBLE_DIGITS DBL_MANT_DIG #define DOUBLE_EPS DBL_EPSILON #define DOUBLE_XMAX DBL_MAX #define DOUBLE_XMIN DBL_MIN #endif #endif /* R_EXT_CONSTANTS_H_ */ ./BNW/src/localscore/R-ftp-http.h0000775000076600007660000000374712074111132016660 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001-6 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Advertized entry points, for that part of libxml included in * the internet module. */ #ifndef R_FTP_HTTP_H_ #define R_FTP_HTTP_H_ #ifdef __cplusplus extern "C" { #endif void *R_HTTPOpen(const char *url); int R_HTTPRead(void *ctx, char *dest, int len); void R_HTTPClose(void *ctx); void *R_FTPOpen(const char *url); int R_FTPRead(void *ctx, char *dest, int len); void R_FTPClose(void *ctx); void * RxmlNanoHTTPOpen(const char *URL, char **contentType, const char *headers, int cacheOK); int RxmlNanoHTTPRead(void *ctx, void *dest, int len); void RxmlNanoHTTPClose(void *ctx); int RxmlNanoHTTPReturnCode(void *ctx); char * RxmlNanoHTTPStatusMsg(void *ctx); int RxmlNanoHTTPContentLength(void *ctx); char * RxmlNanoHTTPContentType(void *ctx); void RxmlNanoHTTPTimeout(int delay); void * RxmlNanoFTPOpen(const char *URL); int RxmlNanoFTPRead(void *ctx, void *dest, int len); int RxmlNanoFTPClose(void *ctx); void RxmlNanoFTPTimeout(int delay); int RxmlNanoFTPContentLength(void *ctx); void RxmlMessage(int level, const char *format, ...); /* not currently used */ void RxmlNanoFTPCleanup(void); void RxmlNanoHTTPCleanup(void); #ifdef __cplusplus } #endif #endif /* R_FTP_HTTP_H_ */ ./BNW/src/localscore/modified_matrix.c0000775000076600007660000001410312113242446020045 0ustar abhatta3abhatta3/* -*- Mode: C -*- * matrix.c --- Simple matrix functions for use with postc.c * Author : Claus Dethlefsen * Created On : Thu Mar 14 06:48:02 2002 * Last Modified By: Claus Dethlefsen * Last Modified On: Wed Jun 04 11:56:23 2003 * Update Count : 36 * Status : Ready */ /* ## ## Copyright (C) 2002 Susanne Gammelgaard Bøttcher, Claus Dethlefsen ## ## This program is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ###################################################################### */ #include "matrix.h" #include "R.h" #include "Rmath.h" int *ivector(int nl, int nh) { int *v; v=(int *) calloc((unsigned) (nh-nl+1)*sizeof(int),sizeof(int)); if ( v == NULL ){ //error("memory allocation failure in ivector()"); return(NULL); } return v-nl; } void free_ivector(int *v, int nl, int nh) { free((char*) (v+nl)); } double **dmatrix(int nrl, int nrh, int ncl, int nch) { int i; double **m; m=(double **) calloc((unsigned) (nrh-nrl+1)*sizeof(double*),sizeof(double*)); m -= nrl; for(i=nrl;i<=nrh;i++) { m[i]=(double *) calloc((unsigned) (nch-ncl+1)*sizeof(double),sizeof(double)); m[i] -= ncl; } return m; } void free_dmatrix(double **m, int nrl, int nrh, int ncl, int nch) { int i; for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } void printmat(double **mat, int nr, int nc) { int i,j; } void asmatrix(double *vek, double **mat, int nr, int nc) { int i,j; for (i=1; i<=nr; i++) { for (j=1; j<=nc; j++) { mat[i][j] = vek[j-1+(i-1)*nc]; } } } double** matcopy(double **mat, int nr, int nc) { /* copy mat[i][j] into nat[i][j] */ int i,j; double **nat; nat = dmatrix(1,nr,1,nc); /* Rprintf("(nr=%d,nc=%d)\n",nr,nc); Rprintf("(mat=%d)\n",mat); Rprintf("(mat[1][1]=%f)\n",mat[1][1]); */ for (i=1; i<=nr; i++) { for (j=1; j<=nc; j++) { nat[i][j] = mat[i][j]; } } return(nat); } double** matmult(double **a, double **b, int nra, int nca, int ncb) { double **c; int i,j,k; c = dmatrix(1,nra,1,ncb); for (i=1; i<=nra; i++) for (j=1; j<=ncb; j++) c[i][j] = 0.0; for (i=1; i<=nra; i++) for (k=1; k<=ncb; k++) for (j=1; j<=nca; j++) c[i][k] += a[i][j]*b[j][k]; return(c); } double** modified_matmult(double **a, double **b, int nra, int nca, int ncb) { double **c; int i,j,k; c = dmatrix(1,nra,1,ncb); for (i=1; i<=nra; i++) for (j=1; j<=ncb; j++) c[i][j] = 0.0; for (i=1; i<=nra; i++) for (k=1; k<=ncb; k++) for (j=1; j<=nca; j++) c[i][k] += a[i][j]*b[j][k]; for (i=1; i<=nra; i++) { for (j=1; j<=ncb; j++) printf("%lf\t",c[i][j]); printf("\n"); } return(c); } double** matsum(double **a, double **b, int nr, int nc) { double **c; int i,j; c = dmatrix(1,nr,1,nc); for (i=1; i<=nr; i++) for (j=1; j<=nc; j++) c[i][j] = a[i][j] + b[i][j]; return(c); } double** matminus(double **a, double **b, int nr, int nc) { double **c; int i,j; c = dmatrix(1,nr,1,nc); for (i=1; i<=nr; i++) for (j=1; j<=nc; j++) c[i][j] = a[i][j] - b[i][j]; return(c); } double** transp (double **a, int n, int m) { double **b; int i,j; b = dmatrix(1,m,1,n); for (i=1; i<=n; i++) for (j=1; j<=m; j++) b[j][i] = a[i][j]; return(b); } int invers(double **a, int n, double **b, int m) { int *indxc,*indxr,*ipiv; int i,icol=1,irow=1,j,k,l,ll; double big,dum,pivinv; // if( (indxc = ivector(1,n)) == NULL){ return(-1); } // if( (indxr = ivector(1,n)) == NULL){ return(-1); } // if( (ipiv = ivector(1,n)) == NULL){ return(-1); } if( (indxc=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); } if( (indxr=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); } if( (ipiv=(int *)calloc((unsigned)(n+1)*sizeof(int),sizeof(int))) == NULL){ return(-1); } for (j=1;j<=n;j++) ipiv[j]=0; for (i=1;i<=n;i++) { big=0.0; for (j=1;j<=n;j++) if (ipiv[j] != 1) for (k=1;k<=n;k++) { if (ipiv[k] == 0) { if (fabs(a[j][k]) >= big) { big=fabs(a[j][k]); irow=j; icol=k; } } else if (ipiv[k] > 1){ return(-1); } } ++(ipiv[icol]); if (irow != icol) { for (l=1;l<=n;l++){ double temp=a[irow][l]; a[irow][l]=a[icol][l]; a[icol][l]=temp; } for (l=1;l<=m;l++){ double temp=b[irow][l]; b[irow][l]=b[icol][l]; b[icol][l]=temp; } } indxr[i]=irow; indxc[i]=icol; if (a[icol][icol] == 0.0){ //error("Invers: Singular Matrix-2"); return(-1); } pivinv=1.0/a[icol][icol]; a[icol][icol]=1.0; for (l=1;l<=n;l++) a[icol][l] *= pivinv; for (l=1;l<=m;l++) b[icol][l] *= pivinv; for (ll=1;ll<=n;ll++) if (ll != icol) { dum=a[ll][icol]; a[ll][icol]=0.0; for (l=1;l<=n;l++) a[ll][l] -= a[icol][l]*dum; for (l=1;l<=m;l++) b[ll][l] -= b[icol][l]*dum; } } for (l=n;l>=1;l--) { if (indxr[l] != indxc[l]){ for (k=1;k<=n;k++){ double temp = a[k][indxr[l]]; a[k][indxr[l]] = a[k][indxc[l]]; a[k][indxc[l]] = temp; } } } free(indxc); free(indxr); free(ipiv); return(0); } ./BNW/src/localscore/network_score.c0000775000076600007660000013151312133057354017576 0ustar abhatta3abhatta3#include #include #include #define MATHLIB_STANDALONE 1 #include "matrix.h" #include "postc0.c" #include "modified_postc.c" // only line that has been changed in this code //#define OUT_DIR "./Result/" //WHERE BENE READ DATA FOR STRUCTURE LEARNING //change it to #define OUT_DIR "/var/www/html/compbio/BNW/bene-0.9-4/example/resdir/" for server. Also change from sprintf(line+9,"%d",i); to sprintf(line+52,"%d",i); struct white{ int n; int *list; }; struct ban{ int n; int *list; }; struct ndata{ int idx,type,score_i; char **ddata; char **label; //for descrete node int lindex; double *prob,*cdata,*post_alpha; double score_zeroparent; double *score; struct white wlist; struct ban blist; }; struct nd{ int num,nd,*discrete,nc,*continuous,row; double score; struct ndata *node; }; void get_next_seq(int *,int *,int); void learn_node(struct nd *); double learn_parent(struct nd *,int,int); double run_strtof (const char * input) //Convert string to double { double output; char * end; output = strtod (input, & end); if (end == input) { return 0.0; } else { return output; } } char* itoa(int val, int base){ //convert number to string static char buf[32] = {0}; int i = 30; for(; val && i ; --i, val /= base) buf[i] = "0123456789abcdef"[val % base]; return &buf[i+1]; } double standarizedata(double val,double mean,double std) { return (val-mean)/std; } double mean(double *a,int l) { int i; double m; m=0; for(i=0;i1) //discrete // fprintf(outfile,"%d\t",j); //else //continuous // fprintf(outfile,"%d\t",k); } banf=fopen (argv[2],"r"); //ban list file name whitef=fopen (argv[3],"r"); //white list file name //read banlist strcpy(nf,""); strcpy(nt,""); while (fgets (line,2500,banf)!=NULL){ fscanf(banf,"%s",nf); //node from fscanf(banf,"%s",nt); //node to for(i=0;inetwork.node[i].score_zeroparent) min_score=network.node[i].score_zeroparent; //fprintf(outfile,"%d\t0\t%lf\n",i+1,network.node[i].score_zeroparent); //printing score for zero parent } else { network.node[i].score[0]=1.0; //fprintf(outfile,"%d\t0\t0.0\n",i+1); } network.node[i].score_i=1; for(j=0;j> i) & 1; if(bit!=1) //check if the child itself is present in parent list { bit_count=0; //fprintf(outfile,"%d\t",i+1); for(l=0;l> l) & 1; if(bit==1) { //fprintf(outfile,"%d",l+1); bit_count++; } } if(network.node[i].type>1) //if discrete node checck if any continuous node is included in the parent list { flag=0; ban_flag=0; for(l=0;l> l) & 1; if(bit==1 && network.node[l].type==1) //check if continuous is parent of discrete { flag=1; break; } if(bit==1) { for(k=0;kMAX_PARENT) { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } else if(ban_flag==1) { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } else // calculate score if white list check get satisfied { if(network.node[i].wlist.n==0) { score_val=learn_parent(&network,i,j); if(min_score>score_val) min_score=score_val; //fprintf(outfile,"\t%lf\n",score_val); s_i=network.node[i].score_i; network.node[i].score[s_i]=score_val; network.node[i].score_i=s_i+1; } else if(bit_count> l) & 1; if(bit==1) { for(k=0;kscore_val) min_score=score_val; //fprintf(outfile,"\t%lf\n",score_val); s_i=network.node[i].score_i; network.node[i].score[s_i]=score_val; network.node[i].score_i=s_i+1; } else { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } } } } else //fill up data when continuous is parent of discrete { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } } else //if continuous node then learn the network with the parent set { ban_flag=0; for(l=0;l> l) & 1; if(bit==1) { for(k=0;kMAX_PARENT) { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } else if(ban_flag==1) { //fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } else { if(network.node[i].wlist.n==0) { score_val=learn_parent(&network,i,j); if(min_score>score_val) min_score=score_val; //fprintf(outfile,"\t%lf\n",score_val); s_i=network.node[i].score_i; network.node[i].score[s_i]=score_val; network.node[i].score_i=s_i+1; } else if(bit_count> l) & 1; if(bit==1) { for(k=0;kscore_val) min_score=score_val; //fprintf(outfile,"\t%lf\n",score_val); s_i=network.node[i].score_i; network.node[i].score[s_i]=score_val; network.node[i].score_i=s_i+1; } else { // fprintf(outfile,"\t0.0\n"); s_i=network.node[i].score_i; network.node[i].score[s_i]=1.0; network.node[i].score_i=s_i+1; } } } } } } } //print scores to separate files min_score*=10; inputFiles= (FILE **) malloc(network.num * sizeof(FILE*)); for(i=0;i1) nk*=network.node[i].type; } for(i=0;i1) { alpha=(double *)malloc(sizeof(double)*network.node[i].type); k=1; for(j=0;j1) k*=network.node[j].type; } N=0.0; n=0.0; for(j=0;j1) nk*=network.node[i].type; } //list of discrete snd continuous parents cn=0; ds=0; alpha_parent=0; alpha=2; k1=network.node[child].type; k2=1; //printf("%d\n",child); for(j=0;j> j) & 1; if(bit==1 && j!=child) { if(network.node[j].type>1) { discrete[ds]=j; //printf("discrete parent=%d\n",j); k1*=network.node[j].type; k2*=network.node[j].type; ds++; } else { continuous[cn]=j; //printf("continuous parent=%d\n",j); cn++; } } else if(j!=child) { alpha*=network.node[j].type; } } if(network.nd<=2) alpha=2; i=child; //i is the node with changes in its parrent nodes if(network.node[i].type>1 && cn==0) // no continuous node //prepare alpha and post alpha and then calculate local score { k=k1; postalpha=(double *)calloc(network.node[i].type,sizeof(double)); label=(char **)malloc(sizeof(char *)*(ds+1)); //label array a=(int *)calloc((ds+1),sizeof(int)); l_list=(int *)malloc(sizeof(int)*(ds+1)); for(j=0;j<=ds;j++) label[j]=(char *)malloc(sizeof(char)*100); for(j=0;j=0;j--){ a[j]+=1; if(a[j]==l[j]) a[j]=0; else break; } } } ./BNW/src/localscore/Arith.h0000775000076600007660000000526212074112226015761 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka * Copyright (C) 1998--2007 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_ARITH_H_ #define R_ARITH_H_ /* Only for use where config.h has not already been included */ #if defined(HAVE_GLIBC2) && !defined(_BSD_SOURCE) /* ensure that finite and isnan are declared */ # define _BSD_SOURCE 1 #endif #include "libextern.h" #ifdef __cplusplus extern "C" { #elif !defined(NO_C_HEADERS) /* needed for isnan and isfinite, neither of which are used under C++ */ # include #endif /* implementation of these : ../../main/arithmetic.c */ LibExtern double R_NaN; /* IEEE NaN */ LibExtern double R_PosInf; /* IEEE Inf */ LibExtern double R_NegInf; /* IEEE -Inf */ LibExtern double R_NaReal; /* NA_REAL: IEEE */ LibExtern int R_NaInt; /* NA_INTEGER:= INT_MIN currently */ #ifdef __MAIN__ #undef extern #undef LibExtern #endif #define NA_LOGICAL R_NaInt #define NA_INTEGER R_NaInt /* #define NA_FACTOR R_NaInt unused */ #define NA_REAL R_NaReal /* NA_STRING is a SEXP, so defined in Rinternals.h */ int R_IsNA(double); /* True for R's NA only */ int R_IsNaN(double); /* True for special NaN, *not* for NA */ int R_finite(double); /* True if none of NA, NaN, +/-Inf */ #define ISNA(x) R_IsNA(x) /* ISNAN(): True for *both* NA and NaN. NOTE: some systems do not return 1 for TRUE. Also note that C++ math headers specifically undefine isnan if it is a macro (it is on OS X and in C99), hence the workaround. This code also appears in Rmath.h */ #ifdef __cplusplus int R_isnancpp(double); /* in arithmetic.c */ # define ISNAN(x) R_isnancpp(x) #else # define ISNAN(x) (isnan(x)!=0) #endif /* The following is only defined inside R */ #ifdef HAVE_WORKING_ISFINITE /* isfinite is defined in according to C99 */ # define R_FINITE(x) isfinite(x) #else # define R_FINITE(x) R_finite(x) #endif #ifdef __cplusplus } #endif #endif /* R_ARITH_H_ */ ./BNW/src/localscore/Boolean.h0000775000076600007660000000207112074111132016257 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2000, 2001 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_EXT_BOOLEAN_H_ #define R_EXT_BOOLEAN_H_ #undef FALSE #undef TRUE #ifdef __cplusplus extern "C" { #endif typedef enum { FALSE = 0, TRUE /*, MAYBE */ } Rboolean; #ifdef __cplusplus } #endif #endif /* R_EXT_BOOLEAN_H_ */ ./BNW/src/localscore/Rdynload.h0000775000076600007660000000762612074111132016467 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001-12 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* C functions used to register compiled code in packages. Those needed for that purpose are part of the API. */ #ifndef R_EXT_DYNLOAD_H_ #define R_EXT_DYNLOAD_H_ #include /* called with a variable argument set */ typedef void * (*DL_FUNC)(); typedef unsigned int R_NativePrimitiveArgType; #define SINGLESXP 302 /* Don't have a single type for this. */ /* In the future, we will want to allow people register their own types and then refer to these in other contexts. Something like the Gtk type system may be appropriate. */ typedef unsigned int R_NativeObjectArgType; /* In the near future, we may support registering information about the arguments of native routines and whether they are used to return information. The hope is that we can minimize copying objects even further. Not currently in use. */ typedef enum {R_ARG_IN, R_ARG_OUT, R_ARG_IN_OUT, R_IRRELEVANT} R_NativeArgStyle; /* These are very similar to those in unix/dynload.c but we maintain them separately to give us more freedom to do some computations on the internal versions that are derived from these definitions. */ typedef struct { const char *name; DL_FUNC fun; int numArgs; R_NativePrimitiveArgType *types; R_NativeArgStyle *styles; } R_CMethodDef; typedef R_CMethodDef R_FortranMethodDef; typedef struct { const char *name; DL_FUNC fun; int numArgs; /* In the future, we will put types in here for the different arguments. We need a richer type system to do this effectively so that one can specify types for new classes. */ } R_CallMethodDef; typedef R_CallMethodDef R_ExternalMethodDef; typedef struct _DllInfo DllInfo; /* Currently ignore the graphics routines, accessible via .External.graphics() and .Call.graphics(). */ #ifdef __cplusplus extern "C" { #endif int R_registerRoutines(DllInfo *info, const R_CMethodDef * const croutines, const R_CallMethodDef * const callRoutines, const R_FortranMethodDef * const fortranRoutines, const R_ExternalMethodDef * const externalRoutines); Rboolean R_useDynamicSymbols(DllInfo *info, Rboolean value); DllInfo *R_getDllInfo(const char *name); /* to be used by applications embedding R to register their symbols that are not related to any dynamic module */ DllInfo *R_getEmbeddingDllInfo(void); typedef struct Rf_RegisteredNativeSymbol R_RegisteredNativeSymbol; typedef enum {R_ANY_SYM=0, R_C_SYM, R_CALL_SYM, R_FORTRAN_SYM, R_EXTERNAL_SYM} NativeSymbolType; DL_FUNC R_FindSymbol(char const *, char const *, R_RegisteredNativeSymbol *symbol); /* Experimental interface for exporting and importing functions from one package for use from C code in a package. The registration part probably ought to be integrated with the other registrations. The naming of these routines may be less than ideal. */ void R_RegisterCCallable(const char *package, const char *name, DL_FUNC fptr); DL_FUNC R_GetCCallable(const char *package, const char *name); #ifdef __cplusplus } #endif #endif /* R_EXT_DYNLOAD_H_ */ ./BNW/src/localscore/R.h0000775000076600007660000000353712074112210015107 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2000-2010 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ #ifndef R_R_H #define R_R_H #ifndef USING_R # define USING_R #endif #ifndef NO_C_HEADERS #include #include /* Used by several packages, remove in due course */ #include /* for INT_MAX */ #include #endif #include "Rconfig.h" #include "Arith.h" /* R_FINITE, ISNAN, ... */ #include "Boolean.h" /* Rboolean type */ #include "Complex.h" /* Rcomplex type */ #include "Constants.h" /* PI, DOUBLE_EPS, etc */ #include "Error.h" /* error and warning */ #include "Memory.h" /* R_alloc and S_alloc */ #include "Print.h" /* Rprintf etc */ #include "Random.h" /* RNG interface */ #include "Utils.h" /* sort routines et al */ #include "RS.h" /* for PROBLEM ... Calloc, Realloc, Free, Memcpy, F77_xxxx */ typedef double Sfloat; typedef int Sint; #define SINT_MAX INT_MAX #define SINT_MIN INT_MIN #ifdef __cplusplus extern "C" { #endif void R_FlushConsole(void); /* always declared, but only usable under Win32 and Aqua */ void R_ProcessEvents(void); #ifdef __cplusplus } #endif #endif /* !R_R_H */ ./BNW/src/localscore/Memory.h0000775000076600007660000000243412074111132016153 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2007 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * * * Memory Allocation (garbage collected) --- INCLUDING S compatibility --- */ /* Included by R.h: API */ #ifndef R_EXT_MEMORY_H_ #define R_EXT_MEMORY_H_ #ifndef NO_C_HEADERS # include /* for size_t */ #endif #ifdef __cplusplus extern "C" { #endif void* vmaxget(void); void vmaxset(const void *); void R_gc(void); char* R_alloc(size_t, int); char* S_alloc(long, int); char* S_realloc(char *, long, long, int); #ifdef __cplusplus } #endif #endif /* R_EXT_MEMORY_H_ */ ./BNW/src/localscore/GraphicsEngine.h0000775000076600007660000004406112074111132017573 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001-11 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Used by graphics.c, grid and by third-party graphics devices */ #ifndef R_GRAPHICSENGINE_H_ #define R_GRAPHICSENGINE_H_ #ifdef __cplusplus extern "C" { #endif /* * The current graphics engine (including graphics device) API version * MUST be integer * * This number should be bumped whenever there are changes to * GraphicsEngine.h or GraphicsDevice.h so that add-on packages * that compile against these headers (graphics systems such as * graphics and grid; graphics devices such as gtkDevice, RSvgDevice) * can detect any version mismatch. * * Version 1: Introduction of the version number. * Version 2: GEDevDesc *dd dropped from GEcontourLines(). * Version 3: R_GE_str2col() added to API. (r41887) * Version 4: UTF-8 text hooks, useRotatedTextInContour, * add newFrameConfirm() to NewDevDesc. * New API: GEaddDevice[2] GEgetDevice, GEkillDevice, * ndevNumber. (R 2.7.0) * Version 5: Clean up 1.4.0/2.0.0 changes! * Remove newDevStruct from GEDevDesc and NewDevDesc. * Remove asp, dot(), hold(), open() from NewDevDesc. * Move displayList, DLlastElt, savedSnapshot from * NewDevDesc to GEDevDesc. * Add 'ask' to GEDevDesc. (R 2.8.0) * Version 6: Add dev_Raster() and dev_Cap() (R 2.11.0) * Version 7: Change graphics event handling, adding eventEnv and eventHelper() * to DevDesc. (R 2.12.0) * Version 8: Add dev_Path() (R 2.12.0) * Version 9: Add dev_HoldFlush(), haveTrans*, haveRaster, * haveCapture, haveLocator. (R 2.14.0) */ #define R_GE_version 9 int R_GE_getVersion(void); void R_GE_checkVersionOrDie(int version); /* The graphics engine will only accept locations and dimensions * in native device coordinates, but it provides the following functions * for converting between a couple of simple alternative coordinate * systems and device coordinates: * DEVICE = native units of the device * NDC = Normalised device coordinates * INCHES = inches (!) * CM = centimetres (!!) */ typedef enum { GE_DEVICE = 0, /* native device coordinates (rasters) */ GE_NDC = 1, /* normalised device coordinates x=(0,1), y=(0,1) */ GE_INCHES = 2, GE_CM = 3 } GEUnit; #define MAX_GRAPHICS_SYSTEMS 24 typedef enum { /* In response to this event, the registered graphics system * should allocate and initialise the systemSpecific structure * * Should return R_NilValue on failure so that engine * can tidy up memory allocation */ GE_InitState = 0, /* This event gives the registered system a chance to undo * anything done in the initialisation. */ GE_FinaliseState = 1, /* This is sent by the graphics engine prior to initialising * the display list. It give the graphics system the chance * to squirrel away information it will need for redrawing the * the display list */ GE_SaveState = 2, /* This is sent by the graphics engine prior to replaying the * display list. It gives the graphics system the chance to * restore any information it saved on the GE_SaveState event */ GE_RestoreState = 6, /* Copy system state information to the current device. * This is used when copying graphics from one device to another * so all the graphics system needs to do is to copy across * the bits required for the display list to draw faithfully * on the new device. */ GE_CopyState = 3, /* Create a snapshot of the system state that is sufficient * for the current "image" to be reproduced */ GE_SaveSnapshotState = 4, /* Restore the system state that is saved by GE_SaveSnapshotState */ GE_RestoreSnapshotState = 5, /* When replaying the display list, the graphics engine * checks, after each replayed action, that the action * produced valid output. This is the graphics system's * chance to say that the output is crap (in which case the * graphics engine will abort the display list replay). */ GE_CheckPlot = 7, /* The device wants to scale the current pointsize * (for scaling an image) * This is not a nice general solution, but a quick fix for * the Windows device. */ GE_ScalePS = 8 } GEevent; /* * Some line end/join constants */ typedef enum { GE_ROUND_CAP = 1, GE_BUTT_CAP = 2, GE_SQUARE_CAP = 3 } R_GE_lineend; typedef enum { GE_ROUND_JOIN = 1, GE_MITRE_JOIN = 2, GE_BEVEL_JOIN = 3 } R_GE_linejoin; /* * A structure containing graphical parameters * * This is how graphical parameters are passed from graphics systems * to the graphics engine AND from the graphics engine to graphics * devices. * * Devices are not *required* to honour graphical parameters * (e.g., alpha transparency is going to be tough for some) */ typedef struct { /* * Colours * * NOTE: Alpha transparency included in col & fill */ int col; /* pen colour (lines, text, borders, ...) */ int fill; /* fill colour (for polygons, circles, rects, ...) */ double gamma; /* Gamma correction */ /* * Line characteristics */ double lwd; /* Line width (roughly number of pixels) */ int lty; /* Line type (solid, dashed, dotted, ...) */ R_GE_lineend lend; /* Line end */ R_GE_linejoin ljoin; /* line join */ double lmitre; /* line mitre */ /* * Text characteristics */ double cex; /* Character expansion (font size = fontsize*cex) */ double ps; /* Font size in points */ double lineheight; /* Line height (multiply by font size) */ int fontface; /* Font face (plain, italic, bold, ...) */ char fontfamily[201]; /* Font family */ } R_GE_gcontext; typedef R_GE_gcontext* pGEcontext; #include /* needed for DevDesc */ typedef struct _GEDevDesc GEDevDesc; typedef SEXP (* GEcallback)(GEevent, GEDevDesc *, SEXP); typedef struct { /* An array of information about each graphics system that * has registered with the graphics engine. * This is used to store graphics state for each graphics * system on each device. */ void *systemSpecific; /* * An array of function pointers, one per graphics system that * has registered with the graphics engine. * * system_Callback is called when the graphics engine wants * to give a graphics system the chance to play with its * device-specific information (stored in systemSpecific) * There are two parameters: an "event" to tell the graphics * system why the graphics engine has called this function, * and the systemSpecific pointer. The graphics engine * has to pass the systemSpecific pointer because only * the graphics engine will know what array index to use. */ GEcallback callback; } GESystemDesc; struct _GEDevDesc { /* * Stuff that the devices can see (and modify). * All detailed in GraphicsDevice.h */ pDevDesc dev; /* * Stuff about the device that only the graphics engine sees * (the devices don't see it). */ Rboolean displayListOn; /* toggle for display list status */ SEXP displayList; /* display list */ SEXP DLlastElt; /* A pointer to the end of the display list to avoid tranversing pairlists */ SEXP savedSnapshot; /* The last element of the display list * just prior to when the display list * was last initialised */ Rboolean dirty; /* Has the device received any output? */ Rboolean recordGraphics; /* Should a graphics call be stored * on the display list? * Set to FALSE by do_recordGraphics, * do_dotcallgr, and do_Externalgr * so that nested calls are not * recorded on the display list */ /* * Stuff about the device that only graphics systems see. * The graphics engine has no idea what is in here. * Used by graphics systems to store system state per device. */ GESystemDesc *gesd[MAX_GRAPHICS_SYSTEMS]; /* per-device setting for 'ask' (use NewFrameConfirm) */ Rboolean ask; }; typedef GEDevDesc* pGEDevDesc; /* functions from devices.c for use by graphics devices */ #define desc2GEDesc Rf_desc2GEDesc /* map DevDesc to enclosing GEDevDesc */ pGEDevDesc desc2GEDesc(pDevDesc dd); int GEdeviceNumber(pGEDevDesc); pGEDevDesc GEgetDevice(int); void GEaddDevice(pGEDevDesc); void GEaddDevice2(pGEDevDesc, const char *); void GEkillDevice(pGEDevDesc); pGEDevDesc GEcreateDevDesc(pDevDesc dev); void GEdestroyDevDesc(pGEDevDesc dd); void *GEsystemState(pGEDevDesc dd, int index); void GEregisterWithDevice(pGEDevDesc dd); void GEregisterSystem(GEcallback callback, int *systemRegisterIndex); void GEunregisterSystem(int registerIndex); SEXP GEhandleEvent(GEevent event, pDevDesc dev, SEXP data); #define fromDeviceX GEfromDeviceX #define toDeviceX GEtoDeviceX #define fromDeviceY GEfromDeviceY #define toDeviceY GEtoDeviceY #define fromDeviceWidth GEfromDeviceWidth #define toDeviceWidth GEtoDeviceWidth #define fromDeviceHeight GEfromDeviceHeight #define toDeviceHeight GEtoDeviceHeight double fromDeviceX(double value, GEUnit to, pGEDevDesc dd); double toDeviceX(double value, GEUnit from, pGEDevDesc dd); double fromDeviceY(double value, GEUnit to, pGEDevDesc dd); double toDeviceY(double value, GEUnit from, pGEDevDesc dd); double fromDeviceWidth(double value, GEUnit to, pGEDevDesc dd); double toDeviceWidth(double value, GEUnit from, pGEDevDesc dd); double fromDeviceHeight(double value, GEUnit to, pGEDevDesc dd); double toDeviceHeight(double value, GEUnit from, pGEDevDesc dd); /*------------------------------------------------------------------- * * COLOUR CODE is concerned with the internals of R colour representation * * From colors.c, used in par.c, grid/src/gpar.c */ #define RGBpar Rf_RGBpar #define RGBpar3 Rf_RGBpar3 #define col2name Rf_col2name #define name2col Rf_name2col /* Convert an element of a R colour specification (which might be a number or a string) into an internal colour specification. */ unsigned int RGBpar(SEXP, int); unsigned int RGBpar3(SEXP, int, unsigned int); /* Convert an internal colour specification to/from a colour name */ const char *col2name(unsigned int col); /* used in par.c, grid */ unsigned int name2col(const char *); /* used by plotmath.c */ /* Convert either a name or a #RRGGBB[AA] string to internal. Because people were using it, it also converts "1", "2" ... to a colour in the palette, and "0" to transparent white. */ unsigned int R_GE_str2col(const char *s); /* * Some Notes on Line Textures * * Line textures are stored as an array of 4-bit integers within * a single 32-bit word. These integers contain the lengths of * lines to be drawn with the pen alternately down and then up. * The device should try to arrange that these values are measured * in points if possible, although pixels is ok on most displays. * * If newlty contains a line texture description it is decoded * as follows: * * ndash = 0; * for(i=0 ; i<8 && newlty & 15 ; i++) { * dashlist[ndash++] = newlty & 15; * newlty = newlty>>4; * } * dashlist[0] = length of pen-down segment * dashlist[1] = length of pen-up segment * etc * * An integer containing a zero terminates the pattern. Hence * ndash in this code fragment gives the length of the texture * description. If a description contains an odd number of * elements it is replicated to create a pattern with an * even number of elements. (If this is a pain, do something * different its not crucial). * */ /*--- The basic numbered & names line types; Here device-independent: e.g. "dashed" == "44", "dotdash" == "1343" */ /* NB: was also in Rgraphics.h in R < 2.7.0 */ #define LTY_BLANK -1 #define LTY_SOLID 0 #define LTY_DASHED 4 + (4<<4) #define LTY_DOTTED 1 + (3<<4) #define LTY_DOTDASH 1 + (3<<4) + (4<<8) + (3<<12) #define LTY_LONGDASH 7 + (3<<4) #define LTY_TWODASH 2 + (2<<4) + (6<<8) + (2<<12) R_GE_lineend GE_LENDpar(SEXP value, int ind); SEXP GE_LENDget(R_GE_lineend lend); R_GE_linejoin GE_LJOINpar(SEXP value, int ind); SEXP GE_LJOINget(R_GE_linejoin ljoin); void GESetClip(double x1, double y1, double x2, double y2, pGEDevDesc dd); void GENewPage(const pGEcontext gc, pGEDevDesc dd); void GELine(double x1, double y1, double x2, double y2, const pGEcontext gc, pGEDevDesc dd); void GEPolyline(int n, double *x, double *y, const pGEcontext gc, pGEDevDesc dd); void GEPolygon(int n, double *x, double *y, const pGEcontext gc, pGEDevDesc dd); SEXP GEXspline(int n, double *x, double *y, double *s, Rboolean open, Rboolean repEnds, Rboolean draw, const pGEcontext gc, pGEDevDesc dd); void GECircle(double x, double y, double radius, const pGEcontext gc, pGEDevDesc dd); void GERect(double x0, double y0, double x1, double y1, const pGEcontext gc, pGEDevDesc dd); void GEPath(double *x, double *y, int npoly, int *nper, Rboolean winding, const pGEcontext gc, pGEDevDesc dd); void GERaster(unsigned int *raster, int w, int h, double x, double y, double width, double height, double angle, Rboolean interpolate, const pGEcontext gc, pGEDevDesc dd); SEXP GECap(pGEDevDesc dd); void GEText(double x, double y, const char * const str, cetype_t enc, double xc, double yc, double rot, const pGEcontext gc, pGEDevDesc dd); void GEMode(int mode, pGEDevDesc dd); void GESymbol(double x, double y, int pch, double size, const pGEcontext gc, pGEDevDesc dd); void GEPretty(double *lo, double *up, int *ndiv); void GEMetricInfo(int c, const pGEcontext gc, double *ascent, double *descent, double *width, pGEDevDesc dd); double GEStrWidth(const char *str, cetype_t enc, const pGEcontext gc, pGEDevDesc dd); double GEStrHeight(const char *str, cetype_t enc, const pGEcontext gc, pGEDevDesc dd); void GEStrMetric(const char *str, cetype_t enc, const pGEcontext gc, double *ascent, double *descent, double *width, pGEDevDesc dd); int GEstring_to_pch(SEXP pch); /*------------------------------------------------------------------- * * LINE TEXTURE CODE is concerned with the internals of R * line texture representation. */ unsigned int GE_LTYpar(SEXP, int); SEXP GE_LTYget(unsigned int); /* * Raster operations */ void R_GE_rasterScale(unsigned int *sraster, int sw, int sh, unsigned int *draster, int dw, int dh); void R_GE_rasterInterpolate(unsigned int *sraster, int sw, int sh, unsigned int *draster, int dw, int dh); void R_GE_rasterRotatedSize(int w, int h, double angle, int *wnew, int *hnew); void R_GE_rasterRotatedOffset(int w, int h, double angle, int botleft, double *xoff, double *yoff); void R_GE_rasterResizeForRotation(unsigned int *sraster, int w, int h, unsigned int *newRaster, int wnew, int hnew, const pGEcontext gc); void R_GE_rasterRotate(unsigned int *sraster, int w, int h, double angle, unsigned int *draster, const pGEcontext gc, Rboolean perPixelAlpha); /* * From plotmath.c */ double GEExpressionWidth(SEXP expr, const pGEcontext gc, pGEDevDesc dd); double GEExpressionHeight(SEXP expr, const pGEcontext gc, pGEDevDesc dd); void GEExpressionMetric(SEXP expr, const pGEcontext gc, double *ascent, double *descent, double *width, pGEDevDesc dd); void GEMathText(double x, double y, SEXP expr, double xc, double yc, double rot, const pGEcontext gc, pGEDevDesc dd); /* * (End from plotmath.c) */ /* * From plot3d.c : used in package clines */ SEXP GEcontourLines(double *x, int nx, double *y, int ny, double *z, double *levels, int nl); /* * (End from plot3d.c) */ /* * From vfonts.c */ double R_GE_VStrWidth(const char *s, cetype_t enc, const pGEcontext gc, pGEDevDesc dd); double R_GE_VStrHeight(const char *s, cetype_t enc, const pGEcontext gc, pGEDevDesc dd); void R_GE_VText(double x, double y, const char * const s, cetype_t enc, double x_justify, double y_justify, double rotation, const pGEcontext gc, pGEDevDesc dd); /* * (End from vfonts.c) */ /* Also in Graphics.h */ #define DEG2RAD 0.01745329251994329576 pGEDevDesc GEcurrentDevice(void); Rboolean GEdeviceDirty(pGEDevDesc dd); void GEdirtyDevice(pGEDevDesc dd); Rboolean GEcheckState(pGEDevDesc dd); Rboolean GErecording(SEXP call, pGEDevDesc dd); void GErecordGraphicOperation(SEXP op, SEXP args, pGEDevDesc dd); void GEinitDisplayList(pGEDevDesc dd); void GEplayDisplayList(pGEDevDesc dd); void GEcopyDisplayList(int fromDevice); SEXP GEcreateSnapshot(pGEDevDesc dd); void GEplaySnapshot(SEXP snapshot, pGEDevDesc dd); void GEonExit(void); void GEnullDevice(void); /* From ../../main/plot.c, used by ../../library/grid/src/grid.c */ #define CreateAtVector Rf_CreateAtVector SEXP CreateAtVector(double*, double*, int, Rboolean); /* From ../../main/graphics.c, used by ../../library/grDevices/src/axis_scales.c */ #define GAxisPars Rf_GAxisPars void GAxisPars(double *min, double *max, int *n, Rboolean log, int axis); #ifdef __cplusplus } #endif #endif /* R_GRAPHICSENGINE_ */ ./BNW/src/localscore/Rconfig.h0000775000076600007660000000063712074042704016305 0ustar abhatta3abhatta3/* Rconfig.h. Generated automatically */ #ifndef R_RCONFIG_H #define R_RCONFIG_H #ifndef R_CONFIG_H #define HAVE_F77_UNDERSCORE 1 #define IEEE_754 1 /* #undef WORDS_BIGENDIAN */ #define R_INLINE inline #define HAVE_VISIBILITY_ATTRIBUTE 1 #define SUPPORT_UTF8 1 #define SUPPORT_MBCS 1 #define ENABLE_NLS 1 /* #undef HAVE_AQUA */ #define SUPPORT_OPENMP 1 #endif /* not R_CONFIG_H */ #endif /* not R_RCONFIG_H */ ./BNW/src/localscore/PrtUtil.h0000775000076600007660000000443412074111132016310 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2012 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* * These functions are not part of the API. */ #ifndef PRTUTIL_H_ #define PRTUTIL_H_ #include #include #define formatLogical Rf_formatLogical #define formatInteger Rf_formatInteger #define formatReal Rf_formatReal #define formatComplex Rf_formatComplex #define EncodeLogical Rf_EncodeLogical #define EncodeInteger Rf_EncodeInteger #define EncodeReal Rf_EncodeReal #define EncodeComplex Rf_EncodeComplex #define VectorIndex Rf_VectorIndex #define printIntegerVector Rf_printIntegerVector #define printRealVector Rf_printRealVector #define printComplexVector Rf_printComplexVector #ifdef __cplusplus extern "C" { #endif /* Computation of printing formats */ void formatLogical(int *, int, int *); void formatInteger(int *, int, int *); void formatReal(double *, int, int *, int *, int *, int); void formatComplex(Rcomplex *, int, int *, int *, int *, int *, int *, int *, int); /* Formating of values */ const char *EncodeLogical(int, int); const char *EncodeInteger(int, int); const char *EncodeReal(double, int, int, int, char); const char *EncodeComplex(Rcomplex, int, int, int, int, int, int, char); /* Printing */ void VectorIndex(int, int); void printLogicalVector(int *, int, int); void printIntegerVector(int *, int, int); void printRealVector (double *, int, int); void printComplexVector(Rcomplex *,int, int); /* char *Rsprintf(char*, ...); */ #ifdef __cplusplus } #endif #endif /* PRTUTIL_H_ */ ./BNW/src/localscore/Utils.h0000775000076600007660000000710012074112272016004 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2005 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * * * Generally useful UTILITIES *NOT* relying on R internals (from Defn.h) */ /* Included by R.h: API */ #ifndef R_EXT_UTILS_H_ #define R_EXT_UTILS_H_ #include "Boolean.h" #include "Complex.h" #define revsort Rf_revsort #define iPsort Rf_iPsort #define rPsort Rf_rPsort #define cPsort Rf_cPsort #define IndexWidth Rf_IndexWidth #define setIVector Rf_setIVector #define setRVector Rf_setRVector #define StringFalse Rf_StringFalse #define StringTrue Rf_StringTrue #define isBlankString Rf_isBlankString #define hsv2rgb Rf_hsv2rgb #define rgb2hsv Rf_rgb2hsv #ifdef __cplusplus extern "C" { #endif /* ../../main/sort.c : */ void R_isort(int*, int); void R_rsort(double*, int); void R_csort(Rcomplex*, int); void rsort_with_index(double *, int *, int); void revsort(double*, int*, int);/* reverse; sort i[] alongside */ void iPsort(int*, int, int); void rPsort(double*, int, int); void cPsort(Rcomplex*, int, int); /* ../../main/qsort.c : */ void R_qsort (double *v, int i, int j); void R_qsort_I (double *v, int *I, int i, int j); void R_qsort_int (int *iv, int i, int j); void R_qsort_int_I(int *iv, int *I, int i, int j); #ifdef R_RS_H void F77_NAME(qsort4)(double *v, int *indx, int *ii, int *jj); void F77_NAME(qsort3)(double *v, int *ii, int *jj); #endif /* ../../main/printutils.c : */ int IndexWidth(int); /* ../../main/util.c and others : */ const char *R_ExpandFileName(const char *); void setIVector(int*, int, int); void setRVector(double*, int, double); Rboolean StringFalse(const char *); Rboolean StringTrue(const char *); Rboolean isBlankString(const char *); /* These two are guaranteed to use '.' as the decimal point, and to accept "NA". */ double R_atof(const char *str); double R_strtod(const char *c, char **end); char *R_tmpnam(const char *prefix, const char *tempdir); char *R_tmpnam2(const char *prefix, const char *tempdir, const char *fileext); void hsv2rgb(double h, double s, double v, double *r, double *g, double *b); void rgb2hsv(double r, double g, double b, double *h, double *s, double *v); void R_CheckUserInterrupt(void); void R_CheckStack(void); /* ../../appl/interv.c: also in Applic.h */ int findInterval(double *xt, int n, double x, Rboolean rightmost_closed, Rboolean all_inside, int ilo, int *mflag); #ifdef R_RS_H int F77_SUB(interv)(double *xt, int *n, double *x, Rboolean *rightmost_closed, Rboolean *all_inside, int *ilo, int *mflag); #endif void find_interv_vec(double *xt, int *n, double *x, int *nx, int *rightmost_closed, int *all_inside, int *indx); /* ../../appl/maxcol.c: also in Applic.h */ void R_max_col(double *matrix, int *nr, int *nc, int *maxes, int *ties_meth); #ifdef __cplusplus } #endif #endif /* R_EXT_UTILS_H_ */ ./BNW/src/localscore/matrix.h0000775000076600007660000000346412012442570016220 0ustar abhatta3abhatta3/* -*- Mode: C -*- * matrix.h --- * Author : Claus Dethlefsen * Created On : Thu Mar 14 06:47:52 2002 * Last Modified By: Claus Dethlefsen * Last Modified On: Tue May 07 09:39:46 2002 * Update Count : 22 * Status : Unknown, Use with caution! */ /* ## ## Copyright (C) 2002 Susanne Gammelgaard Bøttcher, Claus Dethlefsen ## ## This program is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ###################################################################### */ extern double ** dmatrix( int, int, int, int ); extern int * ivector( int, int ); extern void free_ivector( int *, int, int ); extern int invers(double **a, int n, double **b, int m); extern void printmat( double **, int, int); extern void asmatrix( double *, double **, int, int); extern double** matcopy(double **, int, int); extern double** matmult(double **,double **, int, int, int); extern double** matsum(double **a, double **b, int nr, int nc); extern double** matminus(double **a, double **b, int nr, int nc); extern double** transp (double **a, int n, int m); ./BNW/src/localscore/RStartup.h0000775000076600007660000000530512074111132016467 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1999-2010 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* C functions to be called from alternative front-ends. Part of the API for such front-ends but not for packages. */ #ifndef R_EXT_RSTARTUP_H_ #define R_EXT_RSTARTUP_H_ #include /* TRUE/FALSE */ #ifdef __cplusplus extern "C" { #endif #ifdef Win32 typedef int (*blah1) (const char *, char *, int, int); typedef void (*blah2) (const char *, int); typedef void (*blah3) (void); typedef void (*blah4) (const char *); /* Return value here is expected to be 1 for Yes, -1 for No and 0 for Cancel: symbolic constants in graphapp.h */ typedef int (*blah5) (const char *); typedef void (*blah6) (int); typedef void (*blah7) (const char *, int, int); typedef enum {RGui, RTerm, LinkDLL} UImode; #endif /* Startup Actions */ typedef enum { SA_NORESTORE,/* = 0 */ SA_RESTORE, SA_DEFAULT,/* was === SA_RESTORE */ SA_NOSAVE, SA_SAVE, SA_SAVEASK, SA_SUICIDE } SA_TYPE; typedef struct { Rboolean R_Quiet; Rboolean R_Slave; Rboolean R_Interactive; Rboolean R_Verbose; Rboolean LoadSiteFile; Rboolean LoadInitFile; Rboolean DebugInitFile; SA_TYPE RestoreAction; SA_TYPE SaveAction; size_t vsize; size_t nsize; size_t max_vsize; size_t max_nsize; size_t ppsize; int NoRenviron; #ifdef Win32 char *rhome; /* R_HOME */ char *home; /* HOME */ blah1 ReadConsole; blah2 WriteConsole; blah3 CallBack; blah4 ShowMessage; blah5 YesNoCancel; blah6 Busy; UImode CharacterMode; blah7 WriteConsoleEx; /* used only if WriteConsole is NULL */ #endif } structRstart; typedef structRstart *Rstart; void R_DefParams(Rstart); void R_SetParams(Rstart); void R_SetWin32(Rstart); void R_SizeFromEnv(Rstart); void R_common_command_line(int *, char **, Rstart); void R_set_command_line_arguments(int argc, char **argv); void setup_Rmainloop(void); // also in Rembedded.h #ifdef __cplusplus } #endif #endif ./BNW/src/localscore/Applic.h0000775000076600007660000002541712074111132016121 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2012 Robert Gentleman, Ross Ihaka * and the R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * * * Application Routines, typically implemented in ../appl/ * ---------------------------------------------- ======== */ /* This header file contains routines which are in the R API and ones which are not. Those which are not can be used only at the user's risk and may change or disappear in a future release of R. */ #ifndef R_APPLIC_H_ #define R_APPLIC_H_ #include #include /* F77_... */ #include #ifdef __cplusplus extern "C" { #endif /* Entry points in the R API */ /* appl/integrate.c */ typedef void integr_fn(double *x, int n, void *ex); /* vectorizing function f(x[1:n], ...) -> x[] {overwriting x[]}. */ void Rdqags(integr_fn f, void *ex, double *a, double *b, double *epsabs, double *epsrel, double *result, double *abserr, int *neval, int *ier, int *limit, int *lenw, int *last, int *iwork, double *work); void Rdqagi(integr_fn f, void *ex, double *bound, int *inf, double *epsabs, double *epsrel, double *result, double *abserr, int *neval, int *ier, int *limit, int *lenw, int *last, int *iwork, double *work); /* main/optim.c */ typedef double optimfn(int, double *, void *); typedef void optimgr(int, double *, double *, void *); void vmmin(int n, double *b, double *Fmin, optimfn fn, optimgr gr, int maxit, int trace, int *mask, double abstol, double reltol, int nREPORT, void *ex, int *fncount, int *grcount, int *fail); void nmmin(int n, double *Bvec, double *X, double *Fmin, optimfn fn, int *fail, double abstol, double intol, void *ex, double alpha, double bet, double gamm, int trace, int *fncount, int maxit); void cgmin(int n, double *Bvec, double *X, double *Fmin, optimfn fn, optimgr gr, int *fail, double abstol, double intol, void *ex, int type, int trace, int *fncount, int *grcount, int maxit); void lbfgsb(int n, int m, double *x, double *l, double *u, int *nbd, double *Fmin, optimfn fn, optimgr gr, int *fail, void *ex, double factr, double pgtol, int *fncount, int *grcount, int maxit, char *msg, int trace, int nREPORT); void samin(int n, double *pb, double *yb, optimfn fn, int maxit, int tmax, double ti, int trace, void *ex); /* Entry points NOT in the R API */ /* appl/bakslv.c : hidden */ void bakslv(double *, int *, int *, double *, int *, int *, double *, int *, int *); /* appl/binning.c : hidden */ void bincode (double *x, int *n, double *breaks, int *nb, int *code, int *right, int *include_border, int *naok); void bincount(double *x, int *n, double *breaks, int *nb, int *count, int *right, int *include_border, int *naok); /* appl/ch2inv.f */ void F77_NAME(ch2inv)(double *x, int *ldx, int *n, double *v, int *info); /* appl/chol.f Used in nlme */ void F77_NAME(chol)(double *a, int *lda, int *n, double *v, int *info); /* appl/cpoly.c : hidden */ void R_cpolyroot(double *opr, double *opi, int *degree, double *zeror, double *zeroi, Rboolean *fail); /* More `Complex Polynomial Utilities' could be exported: polyev(...) errev(...) cpoly_cauchy(...) cpoly_scale(...) cdivid(...) */ /* appl/cumsum.c : non-API, used in package DCluster */ void R_cumsum(double *, int *, double *, double *); /* appl/eigen.f */ int F77_NAME(cg)(int *nm, int *n, double *ar, double *ai, double *wr, double *wi, int *matz, double *zr, double *zi, double *fv1, double *fv2, double *fv3, int *ierr); int F77_NAME(ch)(int *nm, int *n, double *ar, double *ai, double *w, int *matz, double *zr, double *zi, double *fv1, double *fv2, double *fm1, int *ierr); int F77_NAME(rg)(int *nm, int *n, double *a, double *wr, double *wi, int *matz, double *z, int *iv1, double *fv1, int *ierr); /* used in nlme */ int F77_NAME(rs)(int *nm, int *n, double *a, double *w, int *matz, double *z, double *fv1, double *fv2, int *ierr); /* appl/fft.c */ /* NOTE: The following functions use GLOBAL (static) variables !! * ---- some of R-core think that this should be changed, * which will INEVITABLY extend the argument lists ...! */ /* non-API, but used by package RandomFields */ void fft_factor(int n, int *pmaxf, int *pmaxp); Rboolean fft_work(double *a, double *b, int nseg, int n, int nspn, /* TRUE: success */ int isn, double *work, int *iwork); /* appl/fmin.c : */ double Brent_fmin(double ax, double bx, double (*f)(double, void *), void *info, double tol); /* appl/interv.c: also in Utils.h */ /* used in packages gam and mda */ int F77_SUB(interv)(double *xt, int *n, double *x, Rboolean *rightmost_closed, Rboolean *all_inside, int *ilo, int *mflag); /* Non-API No longer used */ void find_interv_vec(double *xt, int *n, double *x, int *nx, int *rightmost_closed, int *all_inside, int *indx); /* API, used in package eco */ int findInterval(double *xt, int n, double x, Rboolean rightmost_closed, Rboolean all_inside, int ilo, int *mflag); /* appl/lbfgsb.c */ void setulb(int n, int m, double *x, double *l, double *u, int *nbd, double *f, double *g, double factr, double *pgtol, double *wa, int * iwa, char *task, int iprint, int *lsave, int *isave, double *dsave); /* appl/machar.c */ void machar(int *ibeta, int *it, int *irnd, int *ngrd, int *machep, int *negep, int *iexp, int *minexp, int *maxexp, double *eps, double *epsneg, double *xmin, double *xmax); /* appl/maxcol.c: also in Utils.h Used in package MNP */ void R_max_col(double *matrix, int *nr, int *nc, int *maxes, int *ties_meth); /* appl/pretty.c */ double R_pretty0(double *lo, double *up, int *ndiv, int min_n, double shrink_sml, double high_u_fact[], int eps_correction, int return_bounds); void R_pretty(double *lo, double *up, int *ndiv, int *min_n, double *shrink_sml, double *high_u_fact, int *eps_correction); /* appl/rcont.c: API prior to R 2.15.2 */ void rcont2(int *nrow, int *ncol, int *nrowt, int *ncolt, int *ntotal, double *fact, int *jwork, int *matrix); /* appl/rowsum.c */ void R_rowsum(int *dim, double *na_x, double *x, double *group); /* appl/stem.c */ Rboolean stemleaf(double *x, int *n, double *scale, int *width, double *atom); /* appl/strsignif.c */ void str_signif(char *x, int *n, const char **type, int *width, int *digits, const char **format, const char **flag, char **result); /* appl/tabulate.c : non-API, used in package ape, phangorn, pcaPA */ void R_tabulate(int *x, int *n, int *nbin, int *ans); /* appl/uncmin.c : */ /* type of pointer to the target and gradient functions */ typedef void (*fcn_p)(int, double *, double *, void *); /* type of pointer to the hessian functions */ typedef void (*d2fcn_p)(int, int, double *, double *, void *); void fdhess(int n, double *x, double fval, fcn_p fun, void *state, double *h, int nfd, double *step, double *f, int ndigit, double *typx); /* used in nlme */ void optif9(int nr, int n, double *x, fcn_p fcn, fcn_p d1fcn, d2fcn_p d2fcn, void *state, double *typsiz, double fscale, int method, int iexp, int *msg, int ndigit, int itnlim, int iagflg, int iahflg, double dlt, double gradtl, double stepmx, double steptl, double *xpls, double *fpls, double *gpls, int *itrmcd, double *a, double *wrk, int *itncnt); void optif0(int nr, int n, double *x, fcn_p fcn, void *state, double *xpls, double *fpls, double *gpls, int *itrmcd, double *a, double *wrk); /* appl/zeroin.c : non API, but used in package qtl */ double R_zeroin(double ax, double bx, double (*f)(double, void *), void *info, double *Tol, int *Maxit); /* R_zeroin2() is faster for "expensive" f(), in those typical cases where * f(ax) and f(bx) are available anyway : */ double R_zeroin2(double ax, double bx, double fa, double fb, double (*f)(double, void *), void *info, double *Tol, int *Maxit); /* ALL appl/.f [semi-automatically by * f2c -A -P *.f; cat *.P > all.h and editing] */ /* This is not in the applications but in the BLAS, and defined in Lapack.h extern int F77_NAME(lsame)(const char *, const char *); */ /* LINPACK routines also declared in Linpack.h void F77_NAME(dpoco)(double *a, int *lda, int *n, double *rcond, double *z__, int *info); void F77_NAME(dpodi)(double *a, int *lda, int *n, double *det, int *job); void F77_NAME(dpofa)(double *a, int *lda, int *n, int *info); void F77_NAME(dposl)(double *a, int *lda, int *n, double *b); void F77_NAME(dqrdc)(double *x, int *ldx, int *n, int *p, double *qraux, int *jpvt, double *work, int *job); void F77_NAME(dqrsl)(double *x, int *ldx, int *n, int *k, double *qraux, double *y, double *qy, double *qty, double *b, double *rsd, double *xb, int *job, int *info); void F77_NAME(dsvdc)(double *x, int *ldx, int *n, int *p, double *s, double *e, double *u, int *ldu, double *v, int *ldv, double *work, int *job, int *info); void F77_NAME(dtrco)(double *t, int *ldt, int *n, double *rcond, double *z__, int *job); void F77_NAME(dtrsl)(double *t, int *ldt, int *n, double *b, int *job, int *info); */ /* find qr decomposition, dqrdc2() is basis of R's qr(), also used by nlme */ void F77_NAME(dqrdc2)(double *x, int *ldx, int *n, int *p, double *tol, int *rank, double *qraux, int *pivot, double *work); void F77_NAME(dqrls)(double *x, int *n, int *p, double *y, int *ny, double *tol, double *b, double *rsd, double *qty, int *k, int *jpvt, double *qraux, double *work); /* appl/dqrutl.f: interfaces to dqrsl */ void F77_NAME(dqrqty)(double *x, int *n, int *k, double *qraux, double *y, int *ny, double *qty); void F77_NAME(dqrqy)(double *x, int *n, int *k, double *qraux, double *y, int *ny, double *qy); void F77_NAME(dqrcf)(double *x, int *n, int *k, double *qraux, double *y, int *ny, double *b, int *info); void F77_NAME(dqrrsd)(double *x, int *n, int *k, double *qraux, double *y, int *ny, double *rsd); void F77_NAME(dqrxb)(double *x, int *n, int *k, double *qraux, double *y, int *ny, double *xb); #ifdef __cplusplus } #endif #endif /* R_APPLIC_H_ */ ./BNW/src/localscore/postc0.c0000775000076600007660000000474112075041272016121 0ustar abhatta3abhatta3/* -*- Mode: C -*- * postc0.c --- Posterior for continuous node with 0 parents * Author : Claus Dethlefsen * Created On : Tue Mar 12 06:44:35 2002 * Last Modified By: Claus Dethlefsen * Last Modified On: Wed Jun 04 11:57:10 2003 * Update Count : 55 * Status : Unknown, Use with caution! */ /* ## ## Copyright (C) 2002 Susanne Gammelgaard Bøttcher, Claus Dethlefsen ## ## This program is free software; you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation; either version 2 of the License, or ## (at your option) any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with this program; if not, write to the Free Software ## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ###################################################################### */ #include "R.h" #include "Rmath.h" void postc0(double *mu, double *tau, double *rho, double *phi, double *loglik, double *y, int *n) { int i; double logscale,logk,mscore; double oldtau,oldmu; /* Rprintf("her er mu=%f\n",*mu); Rprintf("her er tau=%f\n",*tau); Rprintf("her er rho=%f\n",*rho); Rprintf("her er phi=%f\n",*phi); Rprintf("her er loglik=%f\n",*loglik); */ for(i = 0; i < *n; i++) { logscale = log(*phi)+log1p(1.0/(*tau)); logk = lgammafn( 0.5*(1.0+*rho) ) - lgammafn(*rho*0.5); logk -= 0.5*(logscale + log(M_PI)); mscore = logk - 0.5*(*rho+1.0)*log1p( (y[i]-*mu)*(y[i]-*mu)/exp(logscale)); *loglik += mscore; oldtau = *tau; oldmu = *mu; (*tau)++; (*rho)++; /* Rprintf("her er oldmu=%f\n",oldmu); Rprintf("her er oldtau=%f\n",oldtau); Rprintf("her er mu=%f\n",*mu); Rprintf("her er tau=%f\n",*tau); */ *mu = (oldtau*(*mu)+y[i])/(*tau); *phi+= (y[i]-(*mu))*y[i] + (oldmu-(*mu))*oldtau*oldmu; /* Rprintf("logscale=%f\n",logscale); Rprintf("logk=%f\n",logk); Rprintf("mscore=%f\n",mscore); Rprintf("loglik=%f\n",*loglik); Rprintf("her er mu=%f\n",*mu); Rprintf("her er tau=%f\n",*tau); Rprintf("her er rho=%f\n",*rho); Rprintf("her er phi=%f\n",*phi); Rprintf("her er loglik=%f\n",*loglik); */ } } ./BNW/src/localscore/eventloop.h0000775000076600007660000000561412074111132016721 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2000-2007 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* For use by alternative front-ends and packages which need to share the R event loop (on all platforms). Not part of the API and subject to change without notice. */ #ifndef R_EXT_EVENTLOOP_H #define R_EXT_EVENTLOOP_H #ifndef NO_C_HEADERS #ifdef HAVE_SYS_SELECT_H # include /* for fd_set according to recent POSIX */ #endif /* NOTE: Needed at least on FreeBSD so that fd_set is defined. */ # include #endif #ifdef __cplusplus extern "C" { #endif #define XActivity 1 #define StdinActivity 2 typedef void (*InputHandlerProc)(void *userData); typedef struct _InputHandler { int activity; int fileDescriptor; InputHandlerProc handler; struct _InputHandler *next; /* Whether we should be listening to this file descriptor or not. */ int active; /* Data that can be passed to the routine as its only argument. This might be a user-level function or closure when we implement a callback to R mechanism. */ void *userData; } InputHandler; extern InputHandler *initStdinHandler(void); extern void consoleInputHandler(unsigned char *buf, int len); extern InputHandler *addInputHandler(InputHandler *handlers, int fd, InputHandlerProc handler, int activity); extern InputHandler *getInputHandler(InputHandler *handlers, int fd); extern int removeInputHandler(InputHandler **handlers, InputHandler *it); extern InputHandler *getSelectedHandler(InputHandler *handlers, fd_set *mask); extern fd_set *R_checkActivity(int usec, int ignore_stdin); extern fd_set *R_checkActivityEx(int usec, int ignore_stdin, void (*intr)(void)); extern void R_runHandlers(InputHandler *handlers, fd_set *mask); extern int R_SelectEx(int n, fd_set *readfds, fd_set *writefds, fd_set *exceptfds, struct timeval *timeout, void (*intr)(void)); #ifdef __SYSTEM__ #ifndef __cplusplus /* Would get duplicate conflicting symbols*/ InputHandler *R_InputHandlers; #endif #else extern InputHandler *R_InputHandlers; #endif extern void (* R_PolledEvents)(void); extern int R_wait_usec; #ifdef __cplusplus } #endif #endif /* R_EXT_EVENTLOOP_H */ ./BNW/src/localscore/Error.h0000775000076600007660000000232712074111132015775 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2005 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_ERROR_H_ #define R_ERROR_H_ #ifdef __cplusplus extern "C" { #endif void Rf_error(const char *, ...); void Rf_warning(const char *, ...); void WrongArgCount(const char *); void UNIMPLEMENTED(const char *); void R_ShowMessage(const char *s); #ifdef __cplusplus } #endif #ifndef R_NO_REMAP #define error Rf_error #define warning Rf_warning #endif #endif /* R_ERROR_H_ */ ./BNW/src/localscore/GetX11Image.h0000775000076600007660000000203412074111132016653 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2003 R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ #ifndef GETX11IMAGE_H_ #define GETX11IMAGE_H_ #ifdef __cplusplus extern "C" { #endif /* used by package tkrplot */ Rboolean R_GetX11Image(int d, void *pximage, int *pwidth, int *pheight); /* pximage is really (XImage **) */ #ifdef __cplusplus } #endif #endif ./BNW/src/localscore/stats_stubs.h0000775000076600007660000000453212074111132017262 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2007 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ #include #include #include #ifdef HAVE_VISIBILITY_ATTRIBUTE # define attribute_hidden __attribute__ ((visibility ("hidden"))) #else # define attribute_hidden #endif void attribute_hidden S_Rf_divset(int alg, int iv[], int liv, int lv, double v[]) { static void(*fun)(int,int[],int,int,double[]) = NULL; if (fun == NULL) fun = (void(*)(int,int[],int,int,double[])) R_GetCCallable("stats", "Rf_divset"); fun(alg, iv, liv, lv, v); } void attribute_hidden S_nlminb_iterate(double b[], double d[], double fx, double g[], double h[], int iv[], int liv, int lv, int n, double v[], double x[]) { static void(*fun)(double[],double[],double,double[],double[], int[],int,int,int,double[],double[]) = NULL; if (fun == NULL) fun = (void(*)(double[],double[],double,double[],double[], int[],int,int,int,double[],double[])) R_GetCCallable("stats", "nlminb_iterate"); fun(b, d, fx, g, h, iv, liv, lv, n, v, x); } void attribute_hidden S_nlsb_iterate(double b[], double d[], double dr[], int iv[], int liv, int lv, int n, int nd, int p, double r[], double rd[], double v[], double x[]) { static void(*fun)(double[],double[],double[],int[],int,int, int,int,int,double[],double[],double[], double[]) = NULL; if (fun == NULL) fun = (void(*)(double[],double[],double[],int[],int, int, int,int,int,double[], double[],double[],double[])) R_GetCCallable("stats", "nlsb_iterate"); fun(b, d, dr, iv, liv, lv, n, nd, p, r, rd, v, x); } ./BNW/src/localscore/Callbacks.h0000775000076600007660000000761212074111132016565 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001-2 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Not part of the API, subject to change at any time. */ #ifndef R_CALLBACKS_H #define R_CALLBACKS_H /** These structures are for C (and R function) top-level task handlers. Such routines are called at the end of every (successful) top-level task in the regular REPL. */ #include /** The signature of the C routine that a callback must implement. expr - the expression for the top-level task that was evaluated. value - the result of the top-level task, i.e. evaluating expr. succeeded - a logical value indicating whether the task completed propertly. visible - a logical value indicating whether the result was printed to the R ``console''/stdout. data - user-level data passed to the registration routine. */ typedef Rboolean (*R_ToplevelCallback)(SEXP expr, SEXP value, Rboolean succeeded, Rboolean visible, void *); typedef struct _ToplevelCallback R_ToplevelCallbackEl; /** Linked list element for storing the top-level task callbacks. */ struct _ToplevelCallback { R_ToplevelCallback cb; /* the C routine to call. */ void *data; /* the user-level data to pass to the call to cb() */ void (*finalizer)(void *data); /* Called when the callback is removed. */ char *name; /* a name by which to identify this element. */ R_ToplevelCallbackEl *next; /* the next element in the linked list. */ }; #ifdef __cplusplus extern "C" { #endif Rboolean Rf_removeTaskCallbackByIndex(int id); Rboolean Rf_removeTaskCallbackByName(const char *name); SEXP R_removeTaskCallback(SEXP which); R_ToplevelCallbackEl* Rf_addTaskCallback(R_ToplevelCallback cb, void *data, void (*finalizer)(void *), const char *name, int *pos); /* The following definitions are for callbacks to R functions and methods related to user-level tables. This was implemented in a separate package on Omegahat and these declarations allow the package to interface to the internal R code. See http://developer.r-project.org/RObjectTables.pdf, http://www.omegahat.org/RObjectTables/ */ typedef struct _R_ObjectTable R_ObjectTable; /* Do we actually need the exists() since it is never called but R uses get to see if the symbol is bound to anything? */ typedef Rboolean (*Rdb_exists)(const char * const name, Rboolean *canCache, R_ObjectTable *); typedef SEXP (*Rdb_get)(const char * const name, Rboolean *canCache, R_ObjectTable *); typedef int (*Rdb_remove)(const char * const name, R_ObjectTable *); typedef SEXP (*Rdb_assign)(const char * const name, SEXP value, R_ObjectTable *); typedef SEXP (*Rdb_objects)(R_ObjectTable *); typedef Rboolean (*Rdb_canCache)(const char * const name, R_ObjectTable *); typedef void (*Rdb_onDetach)(R_ObjectTable *); typedef void (*Rdb_onAttach)(R_ObjectTable *); struct _R_ObjectTable{ int type; char **cachedNames; Rboolean active; Rdb_exists exists; Rdb_get get; Rdb_remove remove; Rdb_assign assign; Rdb_objects objects; Rdb_canCache canCache; Rdb_onDetach onDetach; Rdb_onAttach onAttach; void *privateData; }; #ifdef __cplusplus } #endif #endif /* R_CALLBACKS_H */ ./BNW/src/localscore/BLAS.h0000775000076600007660000003672712074111132015440 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2003-12 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* C declarations of BLAS Fortran subroutines always available in R. Part of the API. R packages that use these should have PKG_LIBS in src/Makevars include $(BLAS_LIBS) $(FLIBS) */ /* Part of the API */ #ifndef R_BLAS_H #define R_BLAS_H #include /* for F77_... */ #include /* for Rcomplex */ #ifdef __cplusplus extern "C" { #endif // never defined in R itself. #ifndef BLAS_extern #define BLAS_extern extern #endif /* Double Precision Level 1 BLAS */ BLAS_extern double /* DASUM - sum of absolute values of a one-dimensional array */ F77_NAME(dasum)(const int *n, const double *dx, const int *incx); BLAS_extern void /* DAXPY - replace y by alpha*x + y */ F77_NAME(daxpy)(const int *n, const double *alpha, const double *dx, const int *incx, double *dy, const int *incy); BLAS_extern void /* DCOPY - copy x to y */ F77_NAME(dcopy)(const int *n, const double *dx, const int *incx, double *dy, const int *incy); BLAS_extern double /* DDOT - inner product of x and y */ F77_NAME(ddot)(const int *n, const double *dx, const int *incx, const double *dy, const int *incy); BLAS_extern double /* DNRM2 - 2-norm of a vector */ F77_NAME(dnrm2)(const int *n, const double *dx, const int *incx); BLAS_extern void /* DROT - apply a Given's rotation */ F77_NAME(drot)(const int *n, double *dx, const int *incx, double *dy, const int *incy, const double *c, const double *s); BLAS_extern void /* DROTG - generate a Given's rotation */ F77_NAME(drotg)(const double *a, const double *b, double *c, double *s); BLAS_extern void /* DROTM - apply a modified Given's rotation */ F77_NAME(drotm)(const int *n, double *dx, const int *incx, double *dy, const int *incy, const double *dparam); BLAS_extern void /* DROTMG - generate a modified Given's rotation */ F77_NAME(drotmg)(const double *dd1, const double *dd2, const double *dx1, const double *dy1, double *param); BLAS_extern void /* DSCAL - scale a one-dimensional array */ F77_NAME(dscal)(const int *n, const double *alpha, double *dx, const int *incx); BLAS_extern void /* DSWAP - interchange one-dimensional arrays */ F77_NAME(dswap)(const int *n, double *dx, const int *incx, double *dy, const int *incy); BLAS_extern int /* IDAMAX - return the index of the element with max abs value */ F77_NAME(idamax)(const int *n, const double *dx, const int *incx); /* Double Precision Level 2 BLAS */ /* DGBMV - perform one of the matrix-vector operations */ /* y := alpha*A*x + beta*y, or y := alpha*A'*x + beta*y, */ BLAS_extern void F77_NAME(dgbmv)(const char *trans, const int *m, const int *n, const int *kl,const int *ku, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy); /* DGEMV - perform one of the matrix-vector operations */ /* y := alpha*A*x + beta*y, or y := alpha*A'*x + beta*y, */ BLAS_extern void F77_NAME(dgemv)(const char *trans, const int *m, const int *n, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy); /* DSBMV - perform the matrix-vector operation */ /* y := alpha*A*x + beta*y, */ BLAS_extern void F77_NAME(dsbmv)(const char *uplo, const int *n, const int *k, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy); /* DSPMV - perform the matrix-vector operation */ /* y := alpha*A*x + beta*y, */ BLAS_extern void F77_NAME(dspmv)(const char *uplo, const int *n, const double *alpha, const double *ap, const double *x, const int *incx, const double *beta, double *y, const int *incy); /* DSYMV - perform the matrix-vector operation */ /* y := alpha*A*x + beta*y, */ BLAS_extern void F77_NAME(dsymv)(const char *uplo, const int *n, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy); /* DTBMV - perform one of the matrix-vector operations */ /* x := A*x, or x := A'*x, */ BLAS_extern void F77_NAME(dtbmv)(const char *uplo, const char *trans, const char *diag, const int *n, const int *k, const double *a, const int *lda, double *x, const int *incx); /* DTPMV - perform one of the matrix-vector operations */ /* x := A*x, or x := A'*x, */ BLAS_extern void F77_NAME(dtpmv)(const char *uplo, const char *trans, const char *diag, const int *n, const double *ap, double *x, const int *incx); /* DTRMV - perform one of the matrix-vector operations */ /* x := A*x, or x := A'*x, */ BLAS_extern void F77_NAME(dtrmv)(const char *uplo, const char *trans, const char *diag, const int *n, const double *a, const int *lda, double *x, const int *incx); /* DTBSV - solve one of the systems of equations */ /* A*x = b, or A'*x = b, */ BLAS_extern void F77_NAME(dtbsv)(const char *uplo, const char *trans, const char *diag, const int *n, const int *k, const double *a, const int *lda, double *x, const int *incx); /* DTPSV - solve one of the systems of equations */ /* A*x = b, or A'*x = b, */ BLAS_extern void F77_NAME(dtpsv)(const char *uplo, const char *trans, const char *diag, const int *n, const double *ap, double *x, const int *incx); /* DTRSV - solve one of the systems of equations */ /* A*x = b, or A'*x = b, */ BLAS_extern void F77_NAME(dtrsv)(const char *uplo, const char *trans, const char *diag, const int *n, const double *a, const int *lda, double *x, const int *incx); /* DGER - perform the rank 1 operation A := alpha*x*y' + A */ BLAS_extern void F77_NAME(dger)(const int *m, const int *n, const double *alpha, const double *x, const int *incx, const double *y, const int *incy, double *a, const int *lda); /* DSYR - perform the symmetric rank 1 operation A := alpha*x*x' + A */ BLAS_extern void F77_NAME(dsyr)(const char *uplo, const int *n, const double *alpha, const double *x, const int *incx, double *a, const int *lda); /* DSPR - perform the symmetric rank 1 operation A := alpha*x*x' + A */ BLAS_extern void F77_NAME(dspr)(const char *uplo, const int *n, const double *alpha, const double *x, const int *incx, double *ap); /* DSYR2 - perform the symmetric rank 2 operation */ /* A := alpha*x*y' + alpha*y*x' + A, */ BLAS_extern void F77_NAME(dsyr2)(const char *uplo, const int *n, const double *alpha, const double *x, const int *incx, const double *y, const int *incy, double *a, const int *lda); /* DSPR2 - perform the symmetric rank 2 operation */ /* A := alpha*x*y' + alpha*y*x' + A, */ BLAS_extern void F77_NAME(dspr2)(const char *uplo, const int *n, const double *alpha, const double *x, const int *incx, const double *y, const int *incy, double *ap); /* Double Precision Level 3 BLAS */ /* DGEMM - perform one of the matrix-matrix operations */ /* C := alpha*op( A )*op( B ) + beta*C */ BLAS_extern void F77_NAME(dgemm)(const char *transa, const char *transb, const int *m, const int *n, const int *k, const double *alpha, const double *a, const int *lda, const double *b, const int *ldb, const double *beta, double *c, const int *ldc); /* DTRSM - solve one of the matrix equations */ /* op(A)*X = alpha*B, or X*op(A) = alpha*B */ BLAS_extern void F77_NAME(dtrsm)(const char *side, const char *uplo, const char *transa, const char *diag, const int *m, const int *n, const double *alpha, const double *a, const int *lda, double *b, const int *ldb); /* DTRMM - perform one of the matrix-matrix operations */ /* B := alpha*op( A )*B, or B := alpha*B*op( A ) */ BLAS_extern void F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa, const char *diag, const int *m, const int *n, const double *alpha, const double *a, const int *lda, double *b, const int *ldb); /* DSYMM - perform one of the matrix-matrix operations */ /* C := alpha*A*B + beta*C, */ BLAS_extern void F77_NAME(dsymm)(const char *side, const char *uplo, const int *m, const int *n, const double *alpha, const double *a, const int *lda, const double *b, const int *ldb, const double *beta, double *c, const int *ldc); /* DSYRK - perform one of the symmetric rank k operations */ /* C := alpha*A*A' + beta*C or C := alpha*A'*A + beta*C */ BLAS_extern void F77_NAME(dsyrk)(const char *uplo, const char *trans, const int *n, const int *k, const double *alpha, const double *a, const int *lda, const double *beta, double *c, const int *ldc); /* DSYR2K - perform one of the symmetric rank 2k operations */ /* C := alpha*A*B' + alpha*B*A' + beta*C or */ /* C := alpha*A'*B + alpha*B'*A + beta*C */ BLAS_extern void F77_NAME(dsyr2k)(const char *uplo, const char *trans, const int *n, const int *k, const double *alpha, const double *a, const int *lda, const double *b, const int *ldb, const double *beta, double *c, const int *ldc); /* LSAME is a LAPACK support routine, not part of BLAS */ /* Double complex BLAS routines added for 2.3.0 */ /* #ifdef HAVE_FORTRAN_DOUBLE_COMPLEX */ BLAS_extern double F77_NAME(dcabs1)(double *z); BLAS_extern double F77_NAME(dzasum)(int *n, Rcomplex *zx, int *incx); BLAS_extern double F77_NAME(dznrm2)(int *n, Rcomplex *x, int *incx); BLAS_extern int F77_NAME(izamax)(int *n, Rcomplex *zx, int *incx); BLAS_extern void F77_NAME(zaxpy)(int *n, Rcomplex *za, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy); BLAS_extern void F77_NAME(zcopy)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy); /* WARNING! The next two return a value that may not be compatible between C and Fortran, and even if it is, this might not be the right translation to C. Only use after configure-testing with your compilers. */ BLAS_extern Rcomplex F77_NAME(zdotc)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy); BLAS_extern Rcomplex F77_NAME(zdotu)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy); BLAS_extern void F77_NAME(zdrot)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy, double *c, double *s); BLAS_extern void F77_NAME(zdscal)(int *n, double *da, Rcomplex *zx, int *incx); BLAS_extern void F77_NAME(zgbmv)(char *trans, int *m, int *n, int *kl, int *ku, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *x, int *incx, Rcomplex *beta, Rcomplex *y, int *incy); BLAS_extern void F77_NAME(zgemm)(const char *transa, const char *transb, const int *m, const int *n, const int *k, const Rcomplex *alpha, const Rcomplex *a, const int *lda, const Rcomplex *b, const int *ldb, const Rcomplex *beta, Rcomplex *c, const int *ldc); BLAS_extern void F77_NAME(zgemv)(char *trans, int *m, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *x, int *incx, Rcomplex *beta, Rcomplex *y, int * incy); BLAS_extern void F77_NAME(zgerc)(int *m, int *n, Rcomplex *alpha, Rcomplex *x, int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda); BLAS_extern void F77_NAME(zgeru)(int *m, int *n, Rcomplex *alpha, Rcomplex *x, int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda); BLAS_extern void F77_NAME(zhbmv)(char *uplo, int *n, int *k, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *x, int *incx, Rcomplex *beta, Rcomplex *y, int *incy); BLAS_extern void F77_NAME(zhemm)(char *side, char *uplo, int *m, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(zhemv)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *x, int *incx, Rcomplex *beta, Rcomplex *y, int *incy); BLAS_extern void F77_NAME(zher)(char *uplo, int *n, double *alpha, Rcomplex *x, int *incx, Rcomplex *a, int *lda); BLAS_extern void F77_NAME(zher2)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *x, int *incx, Rcomplex *y, int *incy, Rcomplex *a, int *lda); BLAS_extern void F77_NAME(zher2k)(char *uplo, char *trans, int *n, int *k, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb, double *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(zherk)(char *uplo, char *trans, int *n, int *k, double *alpha, Rcomplex *a, int *lda, double *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(zhpmv)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *ap, Rcomplex *x, int *incx, Rcomplex * beta, Rcomplex *y, int *incy); BLAS_extern void F77_NAME(zhpr)(char *uplo, int *n, double *alpha, Rcomplex *x, int *incx, Rcomplex *ap); BLAS_extern void F77_NAME(zhpr2)(char *uplo, int *n, Rcomplex *alpha, Rcomplex *x, int *incx, Rcomplex *y, int *incy, Rcomplex *ap); BLAS_extern void F77_NAME(zrotg)(Rcomplex *ca, Rcomplex *cb, double *c, Rcomplex *s); BLAS_extern void F77_NAME(zscal)(int *n, Rcomplex *za, Rcomplex *zx, int *incx); BLAS_extern void F77_NAME(zswap)(int *n, Rcomplex *zx, int *incx, Rcomplex *zy, int *incy); BLAS_extern void F77_NAME(zsymm)(char *side, char *uplo, int *m, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(zsyr2k)(char *uplo, char *trans, int *n, int *k, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb, Rcomplex *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(zsyrk)(char *uplo, char *trans, int *n, int *k, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *beta, Rcomplex *c, int *ldc); BLAS_extern void F77_NAME(ztbmv)(char *uplo, char *trans, char *diag, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *x, int *incx); BLAS_extern void F77_NAME(ztbsv)(char *uplo, char *trans, char *diag, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *x, int *incx); BLAS_extern void F77_NAME(ztpmv)(char *uplo, char *trans, char *diag, int *n, Rcomplex *ap, Rcomplex *x, int *incx); BLAS_extern void F77_NAME(ztpsv)(char *uplo, char *trans, char *diag, int *n, Rcomplex *ap, Rcomplex *x, int *incx); BLAS_extern void F77_NAME(ztrmm)(char *side, char *uplo, char *transa, char *diag, int *m, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb); BLAS_extern void F77_NAME(ztrmv)(char *uplo, char *trans, char *diag, int *n, Rcomplex *a, int *lda, Rcomplex *x, int *incx); BLAS_extern void F77_NAME(ztrsm)(char *side, char *uplo, char *transa, char *diag, int *m, int *n, Rcomplex *alpha, Rcomplex *a, int *lda, Rcomplex *b, int *ldb); BLAS_extern void F77_NAME(ztrsv)(char *uplo, char *trans, char *diag, int *n, Rcomplex *a, int *lda, Rcomplex *x, int *incx); /* #endif */ #ifdef __cplusplus } #endif #endif /* R_BLAS_H */ ./BNW/src/localscore/Print.h0000775000076600007660000000264512074111132016003 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2010 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_EXT_PRINT_H_ #define R_EXT_PRINT_H_ #ifdef __cplusplus /* If the vprintf interface is defined at all in C++ it may only be defined in namespace std. */ # ifdef R_USE_C99_IN_CXX # include # ifdef __SUNPRO_CC using _STLP_VENDOR_CSTD::va_list; # endif # endif extern "C" { #else # include #endif void Rprintf(const char *, ...); void REprintf(const char *, ...); #if !defined(__cplusplus) || defined R_USE_C99_IN_CXX void Rvprintf(const char *, va_list); void REvprintf(const char *, va_list); #endif #ifdef __cplusplus } #endif #endif /* R_EXT_PRINT_H_ */ ./BNW/src/localscore/RS.h0000775000076600007660000000573112074112322015234 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1999-2007 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_RS_H #define R_RS_H #ifndef NO_C_HEADERS # include /* for memcpy */ #endif #include "Rconfig.h" /* for F77_APPEND_UNDERSCORE */ #ifdef __cplusplus extern "C" { #endif /* S Like Error Handling */ #include "Error.h" /* for error and warning */ #ifndef STRICT_R_HEADERS #define R_PROBLEM_BUFSIZE 4096 /* Parentheses added for FC4 with gcc4 and -D_FORTIFY_SOURCE=2 */ #define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf, #define ERROR ),error(R_problem_buf);} #define RECOVER(x) ),error(R_problem_buf);} #define WARNING(x) ),warning(R_problem_buf);} #define LOCAL_EVALUATOR /**/ #define NULL_ENTRY /**/ #define WARN WARNING(NULL) #endif /* S Like Memory Management */ extern void *R_chk_calloc(size_t, size_t); extern void *R_chk_realloc(void *, size_t); extern void R_chk_free(void *); #ifndef STRICT_R_HEADERS /* S-PLUS 3.x but not 5.x NULLs the pointer in the following */ #define Calloc(n, t) (t *) R_chk_calloc( (size_t) (n), sizeof(t) ) #define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) #endif #define R_Calloc(n, t) (t *) R_chk_calloc( (size_t) (n), sizeof(t) ) #define R_Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) ) #define R_Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) #define Memcpy(p,q,n) memcpy( p, q, (size_t)( (n) * sizeof(*p) ) ) #define CallocCharBuf(n) (char *) R_chk_calloc((size_t) ((n)+1), sizeof(char)) /* S Like Fortran Interface */ /* These may not be adequate everywhere. Convex had _ prepending common blocks, and some compilers may need to specify Fortran linkage */ #ifdef HAVE_F77_UNDERSCORE # define F77_CALL(x) x ## _ #else # define F77_CALL(x) x #endif #define F77_NAME(x) F77_CALL(x) #define F77_SUB(x) F77_CALL(x) #define F77_COM(x) F77_CALL(x) #define F77_COMDECL(x) F77_CALL(x) #ifndef NO_CALL_R void call_R(char*, long, void**, char**, long*, char**, long, char**); #endif #ifdef __cplusplus } #endif #endif /* R_RS_H */ ./BNW/src/localscore/stats_package.h0000775000076600007660000000461512074111132017517 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2007 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ #ifndef R_STATS_PACKAGE_H #define R_STATS_PACKAGE_H #include #ifdef HAVE_VISIBILITY_ATTRIBUTE # define attribute_hidden __attribute__ ((visibility ("hidden"))) #else # define attribute_hidden #endif enum AlgType {NREG = 1, OPT = 2}; /* 0-based indices into v */ enum VPos {F = 9, F0 = 12, FDIF = 10, G = 27, HC = 70}; /* 0-based indices into iv */ enum IVPos {AI = 90, AM = 94, ALGSAV = 50, COVMAT = 25, COVPRT = 13, COVREQ = 14, DRADPR = 100, DTYPE = 15, IERR = 74, INITH = 24, INITS = 24, IPIVOT = 75, IVNEED = 2, LASTIV = 42, LASTV = 44, LMAT = 41, MXFCAL = 16, MXITER = 17, NEXTV = 46, NFCALL = 5, NFCOV = 51, NFGCAL = 6, NGCOV = 52, NITER = 30, NVDFLT = 49, NVSAVE = 8, OUTLEV = 18, PARPRT = 19, PARSAV = 48, PERM = 57, PRUNIT = 20, QRTYP = 79, RDREQ = 56, RMAT = 77, SOLPRT = 21, STATPR = 22, TOOBIG = 1, VNEED = 3, VSAVE = 59, X0PRT = 23}; void attribute_hidden S_Rf_divset(int alg, int iv[], int liv, int lv, double v[]); void attribute_hidden S_nlsb_iterate(double b[], double d[], double dr[], int iv[], int liv, int lv, int n, int nd, int p, double r[], double rd[], double v[], double x[]); void attribute_hidden S_nlminb_iterate(double b[], double d[], double fx, double g[], double h[], int iv[], int liv, int lv, int n, double v[], double x[]); static R_INLINE int S_v_length(int alg, int n) { return (alg - 1) ? (105 + (n * (2 * n + 20))) : (130 + (n * (n + 27))/2); } static R_INLINE int S_iv_length(int alg, int n) { return (alg - 1) ? (82 + 4 * n) : (78 + 3 * n); } #endif /* R_STATS_PACKAGE_H */ ./BNW/src/localscore/GraphicsDevice.h0000775000076600007660000007235112074111132017570 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2001-11 The R Core Team. * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Used by third-party graphics devices. * * This defines DevDesc, whereas GraphicsEngine.h defines GEDevDesc. * Also contains entry points from gevents.c */ #ifndef R_GRAPHICSDEVICE_H_ #define R_GRAPHICSDEVICE_H_ /* ideally we would use prototypes in DevDesc. Some devices have taken to passing pointers to their own structure instead of DevDesc* , defining R_USE_PROTOTYPES 0 allows them to opt out. */ #ifndef R_USE_PROTOTYPES # define R_USE_PROTOTYPES 1 # ifndef R_GRAPHICSENGINE_H_ # error R_ext/GraphicsEngine.h must be included first, and includes this header # endif #endif #include #ifdef __cplusplus extern "C" { #endif /* --------- New (in 1.4.0) device driver structure --------- * NOTES: * 1. All locations and dimensions are in device coordinates. * 2. I found this comment in the doc for dev_Open -- looks nasty * Any known instances of such a thing happening? Should be * replaced by a function to query the device for preferred gpars * settings? (to be called when the device is initialised) * * NOTE that it is perfectly acceptable for this * function to set generic graphics parameters too * (i.e., override the generic parameter settings * which GInit sets up) all at the author's own risk * of course :) * * 3. Do we really need dev_StrWidth as well as dev_MetricInfo? * I can see the difference between the two -- its just a * question of whether dev_MetricInfo should just return * what dev_StrWidth would give if font metric information is * not available. I guess having both allows the developer * to decide when to ask for which sort of value, and to decide * what to do when font metric information is not available. * And why not a dev_StrHeight? * 4. Should "ipr", "asp", and "cra" be in the device description? * If not, then where? * I guess they don't need to be if no device makes use of them. * On the other hand, they would need to be replaced by a device * call that R base graphics could use to get enough information * to figure them out. (e.g., some sort of dpi() function to * complement the size() function.) */ typedef struct _DevDesc DevDesc; typedef DevDesc* pDevDesc; struct _DevDesc { /******************************************************** * Device physical characteristics ********************************************************/ double left; /* left raster coordinate */ double right; /* right raster coordinate */ double bottom; /* bottom raster coordinate */ double top; /* top raster coordinate */ /* R only has the notion of a rectangular clipping region */ double clipLeft; double clipRight; double clipBottom; double clipTop; /* I hate these next three -- they seem like a real fudge * BUT I'm not sure what to replace them with so they stay for now. */ double xCharOffset; /* x character addressing offset - unused */ double yCharOffset; /* y character addressing offset */ double yLineBias; /* 1/2 interline space as frac of line height */ double ipr[2]; /* Inches per raster; [0]=x, [1]=y */ /* I hate this guy too -- seems to assume that a device can only * have one font size during its lifetime * BUT removing/replacing it would take quite a lot of work * to design and insert a good replacement so it stays for now. */ double cra[2]; /* Character size in rasters; [0]=x, [1]=y */ double gamma; /* (initial) Device Gamma Correction */ /******************************************************** * Device capabilities ********************************************************/ Rboolean canClip; /* Device-level clipping */ Rboolean canChangeGamma; /* can the gamma factor be modified? */ int canHAdj; /* Can do at least some horiz adjust of text 0 = none, 1 = {0,0.5,1}, 2 = [0,1] */ /******************************************************** * Device initial settings ********************************************************/ /* These are things that the device must set up when it is created. * The graphics system can modify them and track current values, */ double startps; int startcol; /* sets par("fg"), par("col") and gpar("col") */ int startfill; /* sets par("bg") and gpar("fill") */ int startlty; int startfont; double startgamma; /******************************************************** * Device specific information ********************************************************/ void *deviceSpecific; /* pointer to device specific parameters */ /******************************************************** * Device display list ********************************************************/ Rboolean displayListOn; /* toggle for initial display list status */ /******************************************************** * Event handling entries ********************************************************/ /* Used in do_setGraphicsEventEnv */ Rboolean canGenMouseDown; /* can the device generate mousedown events */ Rboolean canGenMouseMove; /* can the device generate mousemove events */ Rboolean canGenMouseUp; /* can the device generate mouseup events */ Rboolean canGenKeybd; /* can the device generate keyboard events */ Rboolean gettingEvent; /* This is set while getGraphicsEvent is actively looking for events */ /******************************************************** * Device procedures. ********************************************************/ /* * --------------------------------------- * GENERAL COMMENT ON GRAPHICS PARAMETERS: * --------------------------------------- * Graphical parameters are now passed in a pointer to a * graphics context structure (pGEcontext) rather than individually. * Each device action should extract the parameters it needs * and ignore the others. Thought should be given to which * parameters are relevant in each case -- the graphics engine * does not REQUIRE that each parameter is honoured, but if * a parameter is NOT honoured, it might be a good idea to * issue a warning when a parameter is not honoured (or at * the very least document which parameters are not honoured * in the user-level documentation for the device). [An example * of a parameter that may not be honoured by many devices is * transparency.] */ /* * device_Activate is called when a device becomes the * active device. For example, it can be used to change the * title of a window to indicate the active status of * the device to the user. Not all device types will * do anything. * The only parameter is a device driver structure. * An example is ... * * static void X11_Activate(pDevDesc dd); * * As from R 2.14.0 this can be omitted or set to NULL. */ #if R_USE_PROTOTYPES void (*activate)(const pDevDesc ); #else void (*activate)(); #endif /* * device_Circle should have the side-effect that a * circle is drawn, centred at the given location, with * the given radius. * (If the device has non-square pixels, 'radius' should * be interpreted in the units of the x direction.) * The border of the circle should be * drawn in the given "col", and the circle should be * filled with the given "fill" colour. * If "col" is NA_INTEGER then no border should be drawn * If "fill" is NA_INTEGER then the circle should not * be filled. * An example is ... * * static void X11_Circle(double x, double y, double r, * pGEcontext gc, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * col, fill, gamma, lty, lwd */ #if R_USE_PROTOTYPES void (*circle)(double x, double y, double r, const pGEcontext gc, pDevDesc dd); #else void (*circle)(); #endif /* * device_Clip is given the left, right, bottom, and * top of a rectangle (in DEVICE coordinates). * It should have the side-effect that subsequent output * is clipped to the given rectangle. * NOTE that R's graphics engine already clips to the * extent of the device. * NOTE also that this will probably only be called if * the flag canClip is true. * An example is ... * * static void X11_Clip(double x0, double x1, double y0, double y1, * pDevDesc dd) */ #if R_USE_PROTOTYPES void (*clip)(double x0, double x1, double y0, double y1, pDevDesc dd); #else void (*clip)(); #endif /* * device_Close is called when the device is killed. * This function is responsible for destroying any * device-specific resources that were created in * device_Open and for FREEing the device-specific * parameters structure. * An example is ... * * static void X11_Close(pDevDesc dd) * */ #if R_USE_PROTOTYPES void (*close)(pDevDesc dd); #else void (*close)(); #endif /* * device_Deactivate is called when a device becomes * inactive. * This allows the device to undo anything it did in * dev_Activate. * Not all device types will do anything. * An example is ... * * static void X11_Deactivate(pDevDesc dd) * * As from R 2.14.0 this can be omitted or set to NULL. */ #if R_USE_PROTOTYPES void (*deactivate)(pDevDesc ); #else void (*deactivate)(); #endif /* * device_Locator should return the location of the next * mouse click (in DEVICE coordinates) * Not all devices will do anything (e.g., postscript) * An example is ... * * static Rboolean X11_Locator(double *x, double *y, pDevDesc dd) * * As from R 2.14.0 this can be omitted or set to NULL. */ #if R_USE_PROTOTYPES Rboolean (*locator)(double *x, double *y, pDevDesc dd); #else Rboolean (*locator)(); #endif /* * device_Line should have the side-effect that a single * line is drawn (from x1,y1 to x2,y2) * An example is ... * * static void X11_Line(double x1, double y1, double x2, double y2, * const pGEcontext gc, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * col, gamma, lty, lwd */ #if R_USE_PROTOTYPES void (*line)(double x1, double y1, double x2, double y2, const pGEcontext gc, pDevDesc dd); #else void (*line)(); #endif /* * device_MetricInfo should return height, depth, and * width information for the given character in DEVICE * units. * Note: in an 8-bit locale, c is 'char'. * In an mbcslocale, it is wchar_t, and at least some * of code assumes that is UCS-2 (Windows, true) or UCS-4. * This is used for formatting mathematical expressions * and for exact centering of text (see GText) * If the device cannot provide metric information then * it MUST return 0.0 for ascent, descent, and width. * An example is ... * * static void X11_MetricInfo(int c, * const pGEcontext gc, * double* ascent, double* descent, * double* width, pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * font, cex, ps */ #if R_USE_PROTOTYPES void (*metricInfo)(int c, const pGEcontext gc, double* ascent, double* descent, double* width, pDevDesc dd); #else void (*metricInfo)(); #endif /* * device_Mode is called whenever the graphics engine * starts drawing (mode=1) or stops drawing (mode=0) * GMode (in graphics.c) also says that * mode = 2 (graphical input on) exists. * The device is not required to do anything * An example is ... * * static void X11_Mode(int mode, pDevDesc dd); * * As from R 2.14.0 this can be omitted or set to NULL. */ #if R_USE_PROTOTYPES void (*mode)(int mode, pDevDesc dd); #else void (*mode)(); #endif /* * device_NewPage is called whenever a new plot requires * a new page. * A new page might mean just clearing the * device (e.g., X11) or moving to a new page * (e.g., postscript) * An example is ... * * * static void X11_NewPage(const pGEcontext gc, * pDevDesc dd); * */ #if R_USE_PROTOTYPES void (*newPage)(const pGEcontext gc, pDevDesc dd); #else void (*newPage)(); #endif /* * device_Polygon should have the side-effect that a * polygon is drawn using the given x and y values * the polygon border should be drawn in the "col" * colour and filled with the "fill" colour. * If "col" is NA_INTEGER don't draw the border * If "fill" is NA_INTEGER don't fill the polygon * An example is ... * * static void X11_Polygon(int n, double *x, double *y, * const pGEcontext gc, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * col, fill, gamma, lty, lwd */ #if R_USE_PROTOTYPES void (*polygon)(int n, double *x, double *y, const pGEcontext gc, pDevDesc dd); #else void (*polygon)(); #endif /* * device_Polyline should have the side-effect that a * series of line segments are drawn using the given x * and y values. * An example is ... * * static void X11_Polyline(int n, double *x, double *y, * const pGEcontext gc, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * col, gamma, lty, lwd */ #if R_USE_PROTOTYPES void (*polyline)(int n, double *x, double *y, const pGEcontext gc, pDevDesc dd); #else void (*polyline)(); #endif /* * device_Rect should have the side-effect that a * rectangle is drawn with the given locations for its * opposite corners. The border of the rectangle * should be in the given "col" colour and the rectangle * should be filled with the given "fill" colour. * If "col" is NA_INTEGER then no border should be drawn * If "fill" is NA_INTEGER then the rectangle should not * be filled. * An example is ... * * static void X11_Rect(double x0, double y0, double x1, double y1, * const pGEcontext gc, * pDevDesc dd); * */ #if R_USE_PROTOTYPES void (*rect)(double x0, double y0, double x1, double y1, const pGEcontext gc, pDevDesc dd); #else void (*rect)(); #endif /* * device_Path should draw one or more sets of points * as a single path * * 'x' and 'y' give the points * * 'npoly' gives the number of polygons in the path * MUST be at least 1 * * 'nper' gives the number of points in each polygon * each value MUST be at least 2 * * 'winding' says whether to fill using the nonzero * winding rule or the even-odd rule * * Added 2010-06-27 * * As from R 2.13.2 this can be left unimplemented as NULL. */ #if R_USE_PROTOTYPES void (*path)(double *x, double *y, int npoly, int *nper, Rboolean winding, const pGEcontext gc, pDevDesc dd); #else void (*path)(); #endif /* * device_Raster should draw a raster image justified * at the given location, * size, and rotation (not all devices may be able to rotate?) * * 'raster' gives the image data BY ROW, with every four bytes * giving one R colour (ABGR). * * 'x and 'y' give the bottom-left corner. * * 'rot' is in degrees (as per device_Text), with positive * rotation anticlockwise from the positive x-axis. * * As from R 2.13.2 this can be left unimplemented as NULL. */ #if R_USE_PROTOTYPES void (*raster)(unsigned int *raster, int w, int h, double x, double y, double width, double height, double rot, Rboolean interpolate, const pGEcontext gc, pDevDesc dd); #else void (*raster)(); #endif /* * device_Cap should return an integer matrix (R colors) * representing the current contents of the device display. * * The result is expected to be ROW FIRST. * * This will only make sense for raster devices and can * probably only be implemented for screen devices. * * added 2010-06-27 * * As from R 2.13.2 this can be left unimplemented as NULL. * For earlier versions of R it should return R_NilValue. */ #if R_USE_PROTOTYPES SEXP (*cap)(pDevDesc dd); #else SEXP (*cap)(); #endif /* * device_Size is called whenever the device is * resized. * The function returns (left, right, bottom, and top) for the * new device size. * This is not usually called directly by the graphics * engine because the detection of device resizes * (e.g., a window resize) are usually detected by * device-specific code. * An example is ... * * static void X11_Size(double *left, double *right, * double *bottom, double *top, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * col, fill, gamma, lty, lwd * * As from R 2.13.2 this can be left unimplemented as NULL. */ #if R_USE_PROTOTYPES void (*size)(double *left, double *right, double *bottom, double *top, pDevDesc dd); #else void (*size)(); #endif /* * device_StrWidth should return the width of the given * string in DEVICE units. * An example is ... * * static double X11_StrWidth(const char *str, * const pGEcontext gc, * pDevDesc dd) * * R_GE_gcontext parameters that should be honoured (if possible): * font, cex, ps */ #if R_USE_PROTOTYPES double (*strWidth)(const char *str, const pGEcontext gc, pDevDesc dd); #else double (*strWidth)(); #endif /* * device_Text should have the side-effect that the * given text is drawn at the given location. * The text should be rotated according to rot (degrees) * An example is ... * * static void X11_Text(double x, double y, const char *str, * double rot, double hadj, * const pGEcontext gc, * pDevDesc dd); * * R_GE_gcontext parameters that should be honoured (if possible): * font, cex, ps, col, gamma */ #if R_USE_PROTOTYPES void (*text)(double x, double y, const char *str, double rot, double hadj, const pGEcontext gc, pDevDesc dd); #else void (*text)(); #endif /* * device_onExit is called by GEonExit when the user has aborted * some operation, and so an R_ProcessEvents call may not return normally. * It need not be set to any value; if null, it will not be called. * * An example is ... * * static void GA_onExit(pDevDesc dd); */ #if R_USE_PROTOTYPES void (*onExit)(pDevDesc dd); #else void (*onExit)(); #endif /* * device_getEvent is no longer used, but the slot is kept for back * compatibility of the structure. */ SEXP (*getEvent)(SEXP, const char *); /* --------- Optional features introduced in 2.7.0 --------- */ /* Does the device have a device-specific way to confirm a new frame (for e.g. par(ask=TRUE))? This should be NULL if it does not. If it does, it returns TRUE if the device handled this, and FALSE if it wants the engine to do so. There is an example in the windows() device. Can be left unimplemented as NULL. */ #if R_USE_PROTOTYPES Rboolean (*newFrameConfirm)(pDevDesc dd); #else Rboolean (*newFrameConfirm)(); #endif /* Some devices can plot UTF-8 text directly without converting to the native encoding, e.g. windows(), quartz() .... If this flag is true, all text *not in the symbol font* is sent in UTF8 to the textUTF8/strWidthUTF8 entry points. If the flag is TRUE, the metricInfo entry point should accept negative values for 'c' and treat them as indicating Unicode points (as well as positive values in a MBCS locale). */ Rboolean hasTextUTF8; /* and strWidthUTF8 */ #if R_USE_PROTOTYPES void (*textUTF8)(double x, double y, const char *str, double rot, double hadj, const pGEcontext gc, pDevDesc dd); double (*strWidthUTF8)(const char *str, const pGEcontext gc, pDevDesc dd); #else void (*textUTF8)(); double (*strWidthUTF8)(); #endif Rboolean wantSymbolUTF8; /* Is rotated text good enough to be preferable to Hershey in contour labels? Old default was FALSE. */ Rboolean useRotatedTextInContour; /* --------- Post-2.7.0 features --------- */ /* Added in 2.12.0: Changed graphics event handling. */ SEXP eventEnv; /* This is an environment holding event handlers. */ /* * eventHelper(dd, 1) is called by do_getGraphicsEvent before looking for a * graphics event. It will then call R_ProcessEvents() and eventHelper(dd, 2) * until this or another device returns sets a non-null result value in eventEnv, * at which time eventHelper(dd, 0) will be called. * * An example is ... * * static SEXP GA_eventHelper(pDevDesc dd, int code); * Can be left unimplemented as NULL */ #if R_USE_PROTOTYPES void (*eventHelper)(pDevDesc dd, int code); #else void (*eventHelper)(); #endif /* added in 2.14.0, only used by screen devices. Allows graphics devices to have multiple levels of suspension: when this reaches zero output is flushed. Can be left unimplemented as NULL. */ #if R_USE_PROTOTYPES int (*holdflush)(pDevDesc dd, int level); #else int (*holdflush)(); #endif /* added in 2.14.0, for dev.capabilities. In all cases 0 means NA (unset). */ int haveTransparency; /* 1 = no, 2 = yes */ int haveTransparentBg; /* 1 = no, 2 = fully, 3 = semi */ int haveRaster; /* 1 = no, 2 = yes, 3 = except for missing values */ int haveCapture, haveLocator; /* 1 = no, 2 = yes */ /* Area for future expansion. By zeroing this, devices are more likely to work if loaded into a later version of R than that they were compiled under. */ char reserved[64]; }; /********************************************************/ /* the device-driver entry point is given a device */ /* description structure that it must set up. this */ /* involves several important jobs ... */ /* (1) it must ALLOCATE a new device-specific parameters*/ /* structure and FREE that structure if anything goes */ /* wrong (i.e., it won't report a successful setup to */ /* the graphics engine (the graphics engine is NOT */ /* responsible for allocating or freeing device-specific*/ /* resources or parameters) */ /* (2) it must initialise the device-specific resources */ /* and parameters (mostly done by calling device_Open) */ /* (3) it must initialise the generic graphical */ /* parameters that are not initialised by GInit (because*/ /* only the device knows what values they should have) */ /* see Graphics.h for the official list of these */ /* (4) it may reset generic graphics parameters that */ /* have already been initialised by GInit (although you */ /* should know what you are doing if you do this) */ /* (5) it must attach the device-specific parameters */ /* structure to the device description structure */ /* e.g., dd->deviceSpecfic = (void *) xd; */ /* (6) it must FREE the overall device description if */ /* it wants to bail out to the top-level */ /* the graphics engine is responsible for allocating */ /* the device description and freeing it in most cases */ /* but if the device driver freaks out it needs to do */ /* the clean-up itself */ /********************************************************/ /* moved from Rgraphics.h */ /* * Some Notes on Color * * R uses a 24-bit color model. Colors are specified in 32-bit * integers which are partitioned into 4 bytes as follows. * * <-- most sig least sig --> * +-------------------------------+ * | 0 | blue | green | red | * +-------------------------------+ * * The red, green and blue bytes can be extracted as follows. * * red = ((color ) & 255) * green = ((color >> 8) & 255) * blue = ((color >> 16) & 255) */ /* * Changes as from 1.4.0: use top 8 bits as an alpha channel. * 0 = opaque, 255 = transparent. */ /* * Changes as from 2.0.0: use top 8 bits as full alpha channel * 255 = opaque, 0 = transparent * [to conform with SVG, PDF and others] * and everything in between is used * [which means that NA is not stored as an internal colour; * it is converted to R_RGBA(255, 255, 255, 0)] */ #define R_RGB(r,g,b) ((r)|((g)<<8)|((b)<<16)|0xFF000000) #define R_RGBA(r,g,b,a) ((r)|((g)<<8)|((b)<<16)|((a)<<24)) #define R_RED(col) (((col) )&255) #define R_GREEN(col) (((col)>> 8)&255) #define R_BLUE(col) (((col)>>16)&255) #define R_ALPHA(col) (((col)>>24)&255) #define R_OPAQUE(col) (R_ALPHA(col) == 255) #define R_TRANSPARENT(col) (R_ALPHA(col) == 0) /* * A transparent white */ #define R_TRANWHITE (R_RGBA(255, 255, 255, 0)) /* used in various devices */ #define curDevice Rf_curDevice #define killDevice Rf_killDevice #define ndevNumber Rf_ndevNumber #define NewFrameConfirm Rf_NewFrameConfirm #define nextDevice Rf_nextDevice #define NoDevices Rf_NoDevices #define NumDevices Rf_NumDevices #define prevDevice Rf_prevDevice #define selectDevice Rf_selectDevice #define AdobeSymbol2utf8 Rf_AdobeSymbol2utf8 /* Properly declared version of devNumber */ int ndevNumber(pDevDesc ); /* Formerly in Rdevices.h */ /* How many devices exist ? (>= 1) */ int NumDevices(void); /* Check for an available device slot */ void R_CheckDeviceAvailable(void); Rboolean R_CheckDeviceAvailableBool(void); /* Return the number of the current device. */ int curDevice(void); /* Return the number of the next device. */ int nextDevice(int); /* Return the number of the previous device. */ int prevDevice(int); /* Make the specified device (specified by number) the current device */ int selectDevice(int); /* Kill device which is identified by number. */ void killDevice(int); int NoDevices(void); /* used in engine, graphics, plot, grid */ void NewFrameConfirm(pDevDesc); /* used in graphics.c, grid */ /* Graphics events: defined in gevents.c */ /* These give the indices of some known keys */ typedef enum {knUNKNOWN = -1, knLEFT = 0, knUP, knRIGHT, knDOWN, knF1, knF2, knF3, knF4, knF5, knF6, knF7, knF8, knF9, knF10, knF11, knF12, knPGUP, knPGDN, knEND, knHOME, knINS, knDEL} R_KeyName; /* These are the three possible mouse events */ typedef enum {meMouseDown = 0, meMouseUp, meMouseMove} R_MouseEvent; #define leftButton 1 #define middleButton 2 #define rightButton 4 #define doKeybd Rf_doKeybd #define doMouseEvent Rf_doMouseEvent void doMouseEvent(pDevDesc dd, R_MouseEvent event, int buttons, double x, double y); void doKeybd(pDevDesc dd, R_KeyName rkey, const char *keyname); /* For use in third-party devices when setting up a device: * duplicates Defn.h which is used internally. * (Tested in devNull.c) */ #ifndef BEGIN_SUSPEND_INTERRUPTS /* Macros for suspending interrupts */ #define BEGIN_SUSPEND_INTERRUPTS do { \ Rboolean __oldsusp__ = R_interrupts_suspended; \ R_interrupts_suspended = TRUE; #define END_SUSPEND_INTERRUPTS R_interrupts_suspended = __oldsusp__; \ if (R_interrupts_pending && ! R_interrupts_suspended) \ Rf_onintr(); \ } while(0) #include LibExtern Rboolean R_interrupts_suspended; LibExtern int R_interrupts_pending; extern void Rf_onintr(void); LibExtern Rboolean mbcslocale; #endif /* Useful for devices: translates Adobe symbol encoding to UTF-8 */ extern void *AdobeSymbol2utf8(char*out, const char *in, int nwork); /* Translates Unicode point to UTF-8 */ extern size_t Rf_ucstoutf8(char *s, const unsigned int c); #ifdef __cplusplus } #endif #endif /* R_GRAPHICSDEVICE_ */ ./BNW/src/localscore/RConverters.h0000775000076600007660000001174412074111132017163 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2006 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * * */ /* Not part of the API, concerns .C() converters which are deprecated. */ #ifndef R_CCONVERTERS_H #define R_CCONVERTERS_H #include #ifdef __cplusplus extern "C" { #endif #define freeCConverter RC_freeCConverter #define R_addToCConverter RC_addToCConverter #define R_converterMatchClass RC_converterMatchClass #define R_converterMatchClass RC_converterMatchClass #define R_getToCConverterByDescription RC_getToCConverterByDescription #define R_getToCConverterByIndex RC_getToCConverterByIndex #define R_getToCConverterByIndex RC_getToCConverterByIndex #define R_removeToCConverter RC_removeToCConverter /* Context information controlling how the conversion is performed, passed to RObjToCPtr in dotcode.c and the different user level converters. */ typedef struct { int naok; int narg; int dup; int Fort; char const * name ; SEXP classes; } R_CConvertInfo; /* Typedefs for structs defined below with future/cross-referencing. */ typedef struct RtoCConverter R_toCConverter; typedef struct RFromCConvertInfo R_FromCConvertInfo; /* The matching routine which determines whether the converter can process the given SEXP. */ typedef Rboolean (*R_ToCPredicate)(SEXP obj, R_CConvertInfo *info, R_toCConverter *el); /* The converter routine that returns the value to be passed to the C routine. (We may have to make the return type a union to handle the different types.) */ typedef void* (*R_ToCConverter)(SEXP obj, R_CConvertInfo *info, R_toCConverter *el); /* The reverse converter from the C argument to the R object that is returned via the .C() call. */ typedef SEXP (*R_FromCConverter)(void *value, SEXP arg, R_FromCConvertInfo *info, R_toCConverter *el); /* The definition of the converter element which are stored as a linked list. */ struct RtoCConverter { R_ToCPredicate matcher; /* check if converter applies to R object */ R_ToCConverter converter; /* convert the R object to C value */ R_FromCConverter reverse; /* convert the C value back to an R object. */ char *description; /* user-readable string describing the converter. */ void *userData; /* additional information used in (any of) the matcher, converter, and reverse routines to parameterize them. */ Rboolean active; /* allows the converter to be in the list but ignored temporarily. */ R_toCConverter *next; /* next element in the linked list. */ }; /* Information used to convert C values to R objects at the end of do_dotCode() */ struct RFromCConvertInfo { const char *functionName; /* the name of the routine being called (S's name for it). */ int argIndex; /* the pariticular argument being processed. */ /* We provide all of the arguments and the corresponding C values. This gives the full context of the call to the reverse converter */ SEXP allArgs; void **cargs; int nargs; }; /* Internal mechanism for employing the converter mechanism, used in do_dotCode() in dotcode.c */ void *Rf_convertToC(SEXP s, R_CConvertInfo *info, int *success, R_toCConverter **converter); /* Converter management facilities. */ R_toCConverter *R_addToCConverter(R_ToCPredicate match, R_ToCConverter converter, R_FromCConverter reverse, void *userData, char *desc); R_toCConverter *R_getToCConverterByIndex(int which); R_toCConverter *R_getToCConverterByDescription(const char *desc); void R_removeToCConverter(R_toCConverter *el); Rboolean R_converterMatchClass(SEXP obj, R_CConvertInfo *inf, R_toCConverter *el); void freeCConverter(R_toCConverter *el); /* The routines corresponding to the .Internal() providing access to the management facilities of the converter list. */ SEXP do_getNumRtoCConverters(SEXP call, SEXP op, SEXP args, SEXP env); SEXP do_getRtoCConverterDescriptions(SEXP call, SEXP op, SEXP args, SEXP env); SEXP do_getRtoCConverterStatus(SEXP call, SEXP op, SEXP args, SEXP env); SEXP do_setToCConverterActiveStatus(SEXP call, SEXP op, SEXP args, SEXP env); #ifdef __cplusplus } #endif #endif /* R_CCONVERTERS_H */ ./BNW/src/localscore/Random.h0000775000076600007660000000333612074112246016134 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2011 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Included by R.h: API */ #ifndef R_RANDOM_H #define R_RANDOM_H #ifdef __cplusplus extern "C" { #endif #include "Boolean.h" typedef enum { WICHMANN_HILL, MARSAGLIA_MULTICARRY, SUPER_DUPER, MERSENNE_TWISTER, KNUTH_TAOCP, USER_UNIF, KNUTH_TAOCP2, LECUYER_CMRG } RNGtype; /* Different kinds of "N(0,1)" generators :*/ typedef enum { BUGGY_KINDERMAN_RAMAGE, AHRENS_DIETER, BOX_MULLER, USER_NORM, INVERSION, KINDERMAN_RAMAGE } N01type; void GetRNGstate(void); void PutRNGstate(void); double unif_rand(void); /* These are also defined in Rmath.h */ double norm_rand(void); double exp_rand(void); typedef unsigned int Int32; double * user_unif_rand(void); void user_unif_init(Int32); int * user_unif_nseed(void); int * user_unif_seedloc(void); double * user_norm_rand(void); void FixupProb(double *, int, int, Rboolean); #ifdef __cplusplus } #endif #endif /* R_RANDOM_H */ ./BNW/src/localscore/Visibility.h0000775000076600007660000000233412074111132017031 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2008 the R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* Definitions controlling visibility on some platforms. Part of the API. */ #ifndef R_EXT_VISIBILITY_H_ #define R_EXT_VISIBILITY_H_ #include #ifdef HAVE_VISIBILITY_ATTRIBUTE # define attribute_visible __attribute__ ((visibility ("default"))) # define attribute_hidden __attribute__ ((visibility ("hidden"))) #else # define attribute_visible # define attribute_hidden #endif #endif /* R_EXT_VISIBILITY_H_ */ ./BNW/src/localscore/Lapack.h0000775000076600007660000035654712074111132016117 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2003-12 The R Core Team. * Copyright (C) 2008 The R Foundation * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* C declarations of LAPACK Fortran subroutines included in R. Just those used (currently or previously) by C routines in R itself. Part of the API. R packages that use these should have PKG_LIBS in src/Makevars include $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) */ #ifndef R_LAPACK_H #define R_LAPACK_H #include /* for F77_... */ #include /* for Rcomplex */ #include /* LAPACK function names are [dz](), where d denotes the real version of the function, z the complex version. (Only double-precision versions are used in R.) */ #ifdef __cplusplus extern "C" { #endif // Never defined by R itself. #ifndef La_extern #define La_extern extern #endif /* Utilities for Lapack-using packages : */ /* matrix norms: converting typstr[] to one of {'M', 'O', 'I', 'F'} * or signal error(): */ La_extern char La_norm_type(const char *typstr); /* matrix (reciprocal) condition numbers: convert typstr[] to 'O'(ne) or 'I'(nf) * or signal error(): */ La_extern char La_rcond_type(const char *typstr); /* Selected Double Precision Lapack Routines ======== */ /* Double precision BiDiagonal matrices */ /* DBDSQR - compute the singular value decomposition (SVD) of a real */ /* N-by-N (upper or lower) bidiagonal matrix B */ La_extern void F77_NAME(dbdsqr)(const char* uplo, const int* n, const int* ncvt, const int* nru, const int* ncc, double* d, double* e, double* vt, const int* ldvt, double* u, const int* ldu, double* c, const int* ldc, double* work, int* info); /* DDISNA - compute the reciprocal condition numbers for the */ /* eigenvectors of a real symmetric or complex Hermitian matrix or */ /* for the left or right singular vectors of a general m-by-n */ /* matrix */ La_extern void F77_NAME(ddisna)(const char* job, const int* m, const int* n, double* d, double* sep, int* info); /* Double precision General Banded matrices */ /* DGBBRD - reduce a real general m-by-n band matrix A to upper */ /* bidiagonal form B by an orthogonal transformation */ La_extern void F77_NAME(dgbbrd)(const char* vect, const int* m, const int* n, const int* ncc, const int* kl, const int* ku, double* ab, const int* ldab, double* d, double* e, double* q, const int* ldq, double* pt, const int* ldpt, double* c, const int* ldc, double* work, int* info); /* DGBCON - estimate the reciprocal of the condition number of a */ /* real general band matrix A, in either the 1-norm or the */ /* infinity-norm */ La_extern void F77_NAME(dgbcon)(const char* norm, const int* n, const int* kl, const int* ku, double* ab, const int* ldab, int* ipiv, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DGBEQU - compute row and column scalings intended to equilibrate */ /* an M-by-N band matrix A and reduce its condition number */ La_extern void F77_NAME(dgbequ)(const int* m, const int* n, const int* kl, const int* ku, double* ab, const int* ldab, double* r, double* c, double* rowcnd, double* colcnd, double* amax, int* info); /* DGBRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is banded, and provides */ /* error bounds and backward error estimates for the solution */ La_extern void F77_NAME(dgbrfs)(const char* trans, const int* n, const int* kl, const int* ku, const int* nrhs, double* ab, const int* ldab, double* afb, const int* ldafb, int* ipiv, double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGBSV - compute the solution to a real system of linear */ /* equations A * X = B, where A is a band matrix of order N with */ /* KL subdiagonals and KU superdiagonals, and X and B are */ /* N-by-NRHS matrices */ La_extern void F77_NAME(dgbsv)(const int* n, const int* kl,const int* ku, const int* nrhs, double* ab, const int* ldab, int* ipiv, double* b, const int* ldb, int* info); /* DGBSVX - use the LU factorization to compute the solution to a */ /* real system of linear equations A * X = B or A**T * X = B */ La_extern void F77_NAME(dgbsvx)(const int* fact, const char* trans, const int* n, const int* kl,const int* ku, const int* nrhs, double* ab, const int* ldab, double* afb, const int* ldafb, int* ipiv, const char* equed, double* r, double* c, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGBTF2 - compute an LU factorization of a real m-by-n band */ /* matrix A using partial pivoting with row interchanges */ La_extern void F77_NAME(dgbtf2)(const int* m, const int* n, const int* kl,const int* ku, double* ab, const int* ldab, int* ipiv, int* info); /* DGBTRF - compute an LU factorization of a real m-by-n band */ /* matrix A using partial pivoting with row interchanges */ La_extern void F77_NAME(dgbtrf)(const int* m, const int* n, const int* kl,const int* ku, double* ab, const int* ldab, int* ipiv, int* info); /* DGBTRS - solve a system of linear equations A * X = B or */ /* A' * X = B with a general band matrix A using the LU */ /* factorization computed by DGBTRF */ La_extern void F77_NAME(dgbtrs)(const char* trans, const int* n, const int* kl, const int* ku, const int* nrhs, const double* ab, const int* ldab, const int* ipiv, double* b, const int* ldb, int* info); /* Double precision GEneral matrices */ /* DGEBAK - form the right or left eigenvectors of a real general */ /* matrix by backward transformation on the computed eigenvectors */ /* of the balanced matrix output by DGEBAL */ La_extern void F77_NAME(dgebak)(const char* job, const char* side, const int* n, const int* ilo, const int* ihi, double* scale, const int* m, double* v, const int* ldv, int* info); /* DGEBAL - balance a general real matrix A */ La_extern void F77_NAME(dgebal)(const char* job, const int* n, double* a, const int* lda, int* ilo, int* ihi, double* scale, int* info); /* DGEBD2 - reduce a real general m by n matrix A to upper or */ /* lower bidiagonal form B by an orthogonal transformation */ La_extern void F77_NAME(dgebd2)(const int* m, const int* n, double* a, const int* lda, double* d, double* e, double* tauq, double* taup, double* work, int* info); /* DGEBRD - reduce a general real M-by-N matrix A to upper or */ /* lower bidiagonal form B by an orthogonal transformation */ La_extern void F77_NAME(dgebrd)(const int* m, const int* n, double* a, const int* lda, double* d, double* e, double* tauq, double* taup, double* work, const int* lwork, int* info); /* DGECON - estimate the reciprocal of the condition number of a */ /* general real matrix A, in either the 1-norm or the */ /* infinity-norm, using the LU factorization computed by DGETRF */ La_extern void F77_NAME(dgecon)(const char* norm, const int* n, const double* a, const int* lda, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DGEEQU - compute row and column scalings intended to equilibrate */ /* an M-by-N matrix A and reduce its condition number */ La_extern void F77_NAME(dgeequ)(const int* m, const int* n, double* a, const int* lda, double* r, double* c, double* rowcnd, double* colcnd, double* amax, int* info); /* DGEES - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues, the real Schur form T, and, optionally, the matrix */ /* of Schur vectors Z */ La_extern void F77_NAME(dgees)(const char* jobvs, const char* sort, int (*select)(const double*, const double*), const int* n, double* a, const int* lda, int* sdim, double* wr, double* wi, double* vs, const int* ldvs, double* work, const int* lwork, int* bwork, int* info); /* DGEESX - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues, the real Schur form T, and, optionally, the matrix */ /* of Schur vectors Z */ La_extern void F77_NAME(dgeesx)(const char* jobvs, const char* sort, int (*select)(const double*, const double*), const char* sense, const int* n, double* a, const int* lda, int* sdim, double* wr, double* wi, double* vs, const int* ldvs, double* rconde, double* rcondv, double* work, const int* lwork, int* iwork, const int* liwork, int* bwork, int* info); /* DGEEV - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues and, optionally, the left and/or right eigenvectors */ La_extern void F77_NAME(dgeev)(const char* jobvl, const char* jobvr, const int* n, double* a, const int* lda, double* wr, double* wi, double* vl, const int* ldvl, double* vr, const int* ldvr, double* work, const int* lwork, int* info); /* DGEEVX - compute for an N-by-N real nonsymmetric matrix A, the */ /* eigenvalues and, optionally, the left and/or right eigenvectors */ La_extern void F77_NAME(dgeevx)(const char* balanc, const char* jobvl, const char* jobvr, const char* sense, const int* n, double* a, const int* lda, double* wr, double* wi, double* vl, const int* ldvl, double* vr, const int* ldvr, int* ilo, int* ihi, double* scale, double* abnrm, double* rconde, double* rcondv, double* work, const int* lwork, int* iwork, int* info); /* DGEGV - compute for a pair of n-by-n real nonsymmetric */ /* matrices A and B, the generalized eigenvalues (alphar +/- */ /* alphai*i, beta);, and optionally, the left and/or right */ /* generalized eigenvectors (VL and VR); */ La_extern void F77_NAME(dgegv)(const char* jobvl, const char* jobvr, const int* n, double* a, const int* lda, double* b, const int* ldb, double* alphar, double* alphai, const double* beta, double* vl, const int* ldvl, double* vr, const int* ldvr, double* work, const int* lwork, int* info); /* DGEHD2 - reduce a real general matrix A to upper Hessenberg */ /* form H by an orthogonal similarity transformation */ La_extern void F77_NAME(dgehd2)(const int* n, const int* ilo, const int* ihi, double* a, const int* lda, double* tau, double* work, int* info); /* DGEHRD - reduce a real general matrix A to upper Hessenberg */ /* form H by an orthogonal similarity transformation */ La_extern void F77_NAME(dgehrd)(const int* n, const int* ilo, const int* ihi, double* a, const int* lda, double* tau, double* work, const int* lwork, int* info); /* DGELQ2 - compute an LQ factorization of a real m by n matrix A */ La_extern void F77_NAME(dgelq2)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, int* info); /* DGELQF - compute an LQ factorization of a real M-by-N matrix A */ La_extern void F77_NAME(dgelqf)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, const int* lwork, int* info); /* DGELS - solve overdetermined or underdetermined real linear */ /* systems involving an M-by-N matrix A, or its transpose, using a */ /* QR or LQ factorization of A */ La_extern void F77_NAME(dgels)(const char* trans, const int* m, const int* n, const int* nrhs, double* a, const int* lda, double* b, const int* ldb, double* work, const int* lwork, int* info); /* DGELSS - compute the minimum norm solution to a real linear */ /* least squares problem */ La_extern void F77_NAME(dgelss)(const int* m, const int* n, const int* nrhs, double* a, const int* lda, double* b, const int* ldb, double* s, double* rcond, int* rank, double* work, const int* lwork, int* info); /* DGELSY - compute the minimum-norm solution to a real linear */ /* least squares problem */ La_extern void F77_NAME(dgelsy)(const int* m, const int* n, const int* nrhs, double* a, const int* lda, double* b, const int* ldb, int* jpvt, const double* rcond, int* rank, double* work, const int* lwork, int* info); /* DGEQL2 - compute a QL factorization of a real m by n matrix A */ La_extern void F77_NAME(dgeql2)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, int* info); /* DGEQLF - compute a QL factorization of a real M-by-N matrix A */ La_extern void F77_NAME(dgeqlf)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, const int* lwork, int* info); /* DGEQP3 - compute a QR factorization with column pivoting of a */ /* real M-by-N matrix A using level 3 BLAS */ La_extern void F77_NAME(dgeqp3)(const int* m, const int* n, double* a, const int* lda, int* jpvt, double* tau, double* work, const int* lwork, int* info); /* DGEQPF - compute a QR factorization with column pivoting of a */ /* real M-by-N matrix A */ La_extern void F77_NAME(dgeqpf)(const int* m, const int* n, double* a, const int* lda, int* jpvt, double* tau, double* work, int* info); /* DGEQR2 - compute a QR factorization of a real m by n matrix A */ La_extern void F77_NAME(dgeqr2)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, int* info); /* DGEQRF - compute a QR factorization of a real M-by-N matrix A */ La_extern void F77_NAME(dgeqrf)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, const int* lwork, int* info); /* DGERFS - improve the computed solution to a system of linear */ /* equations and provides error bounds and backward error */ /* estimates for the solution */ La_extern void F77_NAME(dgerfs)(const char* trans, const int* n, const int* nrhs, double* a, const int* lda, double* af, const int* ldaf, int* ipiv, double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGERQ2 - compute an RQ factorization of a real m by n matrix A */ La_extern void F77_NAME(dgerq2)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, int* info); /* DGERQF - compute an RQ factorization of a real M-by-N matrix A */ La_extern void F77_NAME(dgerqf)(const int* m, const int* n, double* a, const int* lda, double* tau, double* work, const int* lwork, int* info); /* DGESV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dgesv)(const int* n, const int* nrhs, double* a, const int* lda, int* ipiv, double* b, const int* ldb, int* info); /* DGESVD - compute the singular value decomposition (SVD); of a */ /* real M-by-N matrix A, optionally computing the left and/or */ /* right singular vectors */ La_extern void F77_NAME(dgesvd)(const char* jobu, const char* jobvt, const int* m, const int* n, double* a, const int* lda, double* s, double* u, const int* ldu, double* vt, const int* ldvt, double* work, const int* lwork, int* info); /* DGESVX - use the LU factorization to compute the solution to a */ /* real system of linear equations A * X = B, */ La_extern void F77_NAME(dgesvx)(const int* fact, const char* trans, const int* n, const int* nrhs, double* a, const int* lda, double* af, const int* ldaf, int* ipiv, char *equed, double* r, double* c, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGETF2 - compute an LU factorization of a general m-by-n */ /* matrix A using partial pivoting with row interchanges */ La_extern void F77_NAME(dgetf2)(const int* m, const int* n, double* a, const int* lda, int* ipiv, int* info); /* DGETRF - compute an LU factorization of a general M-by-N */ /* matrix A using partial pivoting with row interchanges */ La_extern void F77_NAME(dgetrf)(const int* m, const int* n, double* a, const int* lda, int* ipiv, int* info); /* DGETRI - compute the inverse of a matrix using the LU */ /* factorization computed by DGETRF */ La_extern void F77_NAME(dgetri)(const int* n, double* a, const int* lda, int* ipiv, double* work, const int* lwork, int* info); /* DGETRS - solve a system of linear equations A * X = B or A' * */ /* X = B with a general N-by-N matrix A using the LU factorization */ /* computed by DGETRF */ La_extern void F77_NAME(dgetrs)(const char* trans, const int* n, const int* nrhs, const double* a, const int* lda, const int* ipiv, double* b, const int* ldb, int* info); /* Double precision General matrices Generalized problems */ /* DGGBAK - form the right or left eigenvectors of a real */ /* generalized eigenvalue problem A*x = lambda*B*x, by backward */ /* transformation on the computed eigenvectors of the balanced */ /* pair of matrices output by DGGBAL */ La_extern void F77_NAME(dggbak)(const char* job, const char* side, const int* n, const int* ilo, const int* ihi, double* lscale, double* rscale, const int* m, double* v, const int* ldv, int* info); /* DGGBAL - balance a pair of general real matrices (A,B); */ La_extern void F77_NAME(dggbal)(const char* job, const int* n, double* a, const int* lda, double* b, const int* ldb, int* ilo, int* ihi, double* lscale, double* rscale, double* work, int* info); /* DGGES - compute for a pair of N-by-N real nonsymmetric */ /* matrices A, B the generalized eigenvalues, the generalized */ /* real Schur form (S,T), optionally, the left and/or right matrices */ /* of Schur vectors (VSL and VSR)*/ La_extern void F77_NAME(dgges)(const char* jobvsl, const char* jobvsr, const char* sort, int (*delztg)(double*, double*, double*), const int* n, double* a, const int* lda, double* b, const int* ldb, double* alphar, double* alphai, const double* beta, double* vsl, const int* ldvsl, double* vsr, const int* ldvsr, double* work, const int* lwork, int* bwork, int* info); /* DGGGLM - solve a general Gauss-Markov linear model (GLM) problem */ La_extern void F77_NAME(dggglm)(const int* n, const int* m, const int* p, double* a, const int* lda, double* b, const int* ldb, double* d, double* x, double* y, double* work, const int* lwork, int* info); /* DGGHRD - reduce a pair of real matrices (A,B); to generalized */ /* upper Hessenberg form using orthogonal transformations, where A */ /* is a general matrix and B is upper triangular */ La_extern void F77_NAME(dgghrd)(const char* compq, const char* compz, const int* n, const int* ilo, const int* ihi, double* a, const int* lda, double* b, const int* ldb, double* q, const int* ldq, double* z, const int* ldz, int* info); /* DGGLSE - solve the linear equality-constrained least squares */ /* (LSE) problem */ La_extern void F77_NAME(dgglse)(const int* m, const int* n, const int* p, double* a, const int* lda, double* b, const int* ldb, double* c, double* d, double* x, double* work, const int* lwork, int* info); /* DGGQRF - compute a generalized QR factorization of an N-by-M */ /* matrix A and an N-by-P matrix B */ La_extern void F77_NAME(dggqrf)(const int* n, const int* m, const int* p, double* a, const int* lda, double* taua, double* b, const int* ldb, double* taub, double* work, const int* lwork, int* info); /* DGGRQF - compute a generalized RQ factorization of an M-by-N */ /* matrix A and a P-by-N matrix B */ La_extern void F77_NAME(dggrqf)(const int* m, const int* p, const int* n, double* a, const int* lda, double* taua, double* b, const int* ldb, double* taub, double* work, const int* lwork, int* info); /* DGGSVD - compute the generalized singular value decomposition */ /* (GSVD) of an M-by-N real matrix A and P-by-N real matrix B */ La_extern void F77_NAME(dggsvd)(const char* jobu, const char* jobv, const char* jobq, const int* m, const int* n, const int* p, const int* k, const int* l, double* a, const int* lda, double* b, const int* ldb, const double* alpha, const double* beta, double* u, const int* ldu, double* v, const int* ldv, double* q, const int* ldq, double* work, int* iwork, int* info); /* Double precision General Tridiagonal matrices */ /* DGTCON - estimate the reciprocal of the condition number of a real */ /* tridiagonal matrix A using the LU factorization as computed by DGTTRF */ La_extern void F77_NAME(dgtcon)(const char* norm, const int* n, double* dl, double* d, double* du, double* du2, int* ipiv, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DGTRFS - improve the computed solution to a system of linear equations */ /* when the coefficient matrix is tridiagonal, and provides error bounds */ /* and backward error estimates for the solution */ La_extern void F77_NAME(dgtrfs)(const char* trans, const int* n, const int* nrhs, double* dl, double* d, double* du, double* dlf, double* df, double* duf, double* du2, int* ipiv, double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGTSV - solve the equation A*X = B, */ La_extern void F77_NAME(dgtsv)(const int* n, const int* nrhs, double* dl, double* d, double* du, double* b, const int* ldb, int* info); /* DGTSVX - use the LU factorization to compute the solution to a */ /* real system of linear equations A * X = B or A**T * X = B, */ La_extern void F77_NAME(dgtsvx)(const int* fact, const char* trans, const int* n, const int* nrhs, double* dl, double* d, double* du, double* dlf, double* df, double* duf, double* du2, int* ipiv, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DGTTRF - compute an LU factorization of a real tridiagonal matrix */ /* A using elimination with partial pivoting and row interchanges */ La_extern void F77_NAME(dgttrf)(const int* n, double* dl, double* d, double* du, double* du2, int* ipiv, int* info); /* DGTTRS - solve one of the systems of equations A*X = B or */ /* A'*X = B, */ La_extern void F77_NAME(dgttrs)(const char* trans, const int* n, const int* nrhs, double* dl, double* d, double* du, double* du2, int* ipiv, double* b, const int* ldb, int* info); /* Double precision Orthogonal matrices */ /* DOPGTR - generate a real orthogonal matrix Q which is defined */ /* as the product of n-1 elementary reflectors H(i); of order n, */ /* as returned by DSPTRD using packed storage */ La_extern void F77_NAME(dopgtr)(const char* uplo, const int* n, const double* ap, const double* tau, double* q, const int* ldq, double* work, int* info); /* DOPMTR - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dopmtr)(const char* side, const char* uplo, const char* trans, const int* m, const int* n, const double* ap, const double* tau, double* c, const int* ldc, double* work, int* info); /* DORG2L - generate an m by n real matrix Q with orthonormal */ /* columns, */ La_extern void F77_NAME(dorg2l)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, int* info); /* DORG2R - generate an m by n real matrix Q with orthonormal */ /* columns, */ La_extern void F77_NAME(dorg2r)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, int* info); /* DORGBR - generate one of the real orthogonal matrices Q or */ /* P**T determined by DGEBRD when reducing a real matrix A to */ /* bidiagonal form */ La_extern void F77_NAME(dorgbr)(const char* vect, const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGHR - generate a real orthogonal matrix Q which is defined */ /* as the product of IHI-ILO elementary reflectors of order N, as */ /* returned by DGEHRD */ La_extern void F77_NAME(dorghr)(const int* n, const int* ilo, const int* ihi, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGL2 - generate an m by n real matrix Q with orthonormal */ /* rows, */ La_extern void F77_NAME(dorgl2)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, int* info); /* DORGLQ - generate an M-by-N real matrix Q with orthonormal */ /* rows, */ La_extern void F77_NAME(dorglq)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGQL - generate an M-by-N real matrix Q with orthonormal */ /* columns, */ La_extern void F77_NAME(dorgql)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGQR - generate an M-by-N real matrix Q with orthonormal */ /* columns, */ La_extern void F77_NAME(dorgqr)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGR2 - generate an m by n real matrix Q with orthonormal */ /* rows, */ La_extern void F77_NAME(dorgr2)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, int* info); /* DORGRQ - generate an M-by-N real matrix Q with orthonormal rows */ La_extern void F77_NAME(dorgrq)(const int* m, const int* n, const int* k, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORGTR - generate a real orthogonal matrix Q which is defined */ /* as the product of n-1 elementary reflectors of order const int* n, as */ /* returned by DSYTRD */ La_extern void F77_NAME(dorgtr)(const char* uplo, const int* n, double* a, const int* lda, const double* tau, double* work, const int* lwork, int* info); /* DORM2L - overwrite the general real m by n matrix C with Q * */ /* C if SIDE = 'L' and TRANS = 'N', or Q'* C if SIDE = 'L' and */ /* TRANS = 'T', or C * Q if SIDE = 'R' and TRANS = 'N', or C * */ /* Q' if SIDE = 'R' and TRANS = 'T', */ La_extern void F77_NAME(dorm2l)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, int* info); /* DORM2R - overwrite the general real m by n matrix C with Q * C */ /* if SIDE = 'L' and TRANS = 'N', or Q'* C if SIDE = 'L' and */ /* TRANS = 'T', or C * Q if SIDE = 'R' and TRANS = 'N', or C * */ /* Q' if SIDE = 'R' and TRANS = 'T', */ La_extern void F77_NAME(dorm2r)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, int* info); /* DORMBR - VECT = 'Q', DORMBR overwrites the general real M-by-N */ /* matrix C with SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormbr)(const char* vect, const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORMHR - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormhr)(const char* side, const char* trans, const int* m, const int* n, const int* ilo, const int* ihi, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORML2 - overwrite the general real m by n matrix C with Q * */ /* C if SIDE = 'L' and TRANS = 'N', or Q'* C if SIDE = 'L' and */ /* TRANS = 'T', or C * Q if SIDE = 'R' and TRANS = 'N', or C * */ /* Q' if SIDE = 'R' and TRANS = 'T', */ La_extern void F77_NAME(dorml2)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, int* info); /* DORMLQ - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormlq)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORMQL - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormql)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORMQR - overwrite the general real M-by-N matrix C with SIDE = */ /* 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormqr)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORMR2 - overwrite the general real m by n matrix C with Q * */ /* C if SIDE = 'L' and TRANS = 'N', or Q'* C if SIDE = 'L' and */ /* TRANS = 'T', or C * Q if SIDE = 'R' and TRANS = 'N', or C * */ /* Q' if SIDE = 'R' and TRANS = 'T', */ La_extern void F77_NAME(dormr2)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, int* info); /* DORMRQ - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormrq)(const char* side, const char* trans, const int* m, const int* n, const int* k, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* DORMTR - overwrite the general real M-by-N matrix C with */ /* SIDE = 'L' SIDE = 'R' TRANS = 'N' */ La_extern void F77_NAME(dormtr)(const char* side, const char* uplo, const char* trans, const int* m, const int* n, const double* a, const int* lda, const double* tau, double* c, const int* ldc, double* work, const int* lwork, int* info); /* Double precision Positive definite Band matrices */ /* DPBCON - estimate the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric positive definite band matrix */ /* using the Cholesky factorization A = U**T*U or A = L*L**T */ /* computed by DPBTRF */ La_extern void F77_NAME(dpbcon)(const char* uplo, const int* n, const int* kd, const double* ab, const int* ldab, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DPBEQU - compute row and column scalings intended to */ /* equilibrate a symmetric positive definite band matrix A and */ /* reduce its condition number (with respect to the two-norm); */ La_extern void F77_NAME(dpbequ)(const char* uplo, const int* n, const int* kd, const double* ab, const int* ldab, double* s, double* scond, double* amax, int* info); /* DPBRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric positive */ /* definite and banded, and provides error bounds and backward */ /* error estimates for the solution */ La_extern void F77_NAME(dpbrfs)(const char* uplo, const int* n, const int* kd, const int* nrhs, const double* ab, const int* ldab, const double* afb, const int* ldafb, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPBSTF - compute a split Cholesky factorization of a real */ /* symmetric positive definite band matrix A */ La_extern void F77_NAME(dpbstf)(const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, int* info); /* DPBSV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dpbsv)(const char* uplo, const int* n, const int* kd, const int* nrhs, double* ab, const int* ldab, double* b, const int* ldb, int* info); /* DPBSVX - use the Cholesky factorization A = U**T*U or A = */ /* L*L**T to compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dpbsvx)(const int* fact, const char* uplo, const int* n, const int* kd, const int* nrhs, double* ab, const int* ldab, double* afb, const int* ldafb, char* equed, double* s, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPBTF2 - compute the Cholesky factorization of a real */ /* symmetric positive definite band matrix A */ La_extern void F77_NAME(dpbtf2)(const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, int* info); /* DPBTRF - compute the Cholesky factorization of a real */ /* symmetric positive definite band matrix A */ La_extern void F77_NAME(dpbtrf)(const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, int* info); /* DPBTRS - solve a system of linear equations A*X = B with a */ /* symmetric positive definite band matrix A using the Cholesky */ /* factorization A = U**T*U or A = L*L**T computed by DPBTRF */ La_extern void F77_NAME(dpbtrs)(const char* uplo, const int* n, const int* kd, const int* nrhs, const double* ab, const int* ldab, double* b, const int* ldb, int* info); /* Double precision Positive definite matrices */ /* DPOCON - estimate the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric positive definite matrix using */ /* the Cholesky factorization A = U**T*U or A = L*L**T computed by */ /* DPOTRF */ La_extern void F77_NAME(dpocon)(const char* uplo, const int* n, const double* a, const int* lda, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DPOEQU - compute row and column scalings intended to */ /* equilibrate a symmetric positive definite matrix A and reduce */ /* its condition number (with respect to the two-norm); */ La_extern void F77_NAME(dpoequ)(const int* n, const double* a, const int* lda, double* s, double* scond, double* amax, int* info); /* DPORFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric positive */ /* definite, */ La_extern void F77_NAME(dporfs)(const char* uplo, const int* n, const int* nrhs, const double* a, const int* lda, const double* af, const int* ldaf, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPOSV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dposv)(const char* uplo, const int* n, const int* nrhs, double* a, const int* lda, double* b, const int* ldb, int* info); /* DPOSVX - use the Cholesky factorization A = U**T*U or A = */ /* L*L**T to compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dposvx)(const int* fact, const char* uplo, const int* n, const int* nrhs, double* a, const int* lda, double* af, const int* ldaf, char* equed, double* s, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPOTF2 - compute the Cholesky factorization of a real */ /* symmetric positive definite matrix A */ La_extern void F77_NAME(dpotf2)(const char* uplo, const int* n, double* a, const int* lda, int* info); /* DPOTRF - compute the Cholesky factorization of a real */ /* symmetric positive definite matrix A */ La_extern void F77_NAME(dpotrf)(const char* uplo, const int* n, double* a, const int* lda, int* info); /* DPOTRI - compute the inverse of a real symmetric positive */ /* definite matrix A using the Cholesky factorization A = U**T*U */ /* or A = L*L**T computed by DPOTRF */ La_extern void F77_NAME(dpotri)(const char* uplo, const int* n, double* a, const int* lda, int* info); /* DPOTRS - solve a system of linear equations A*X = B with a */ /* symmetric positive definite matrix A using the Cholesky */ /* factorization A = U**T*U or A = L*L**T computed by DPOTRF */ La_extern void F77_NAME(dpotrs)(const char* uplo, const int* n, const int* nrhs, const double* a, const int* lda, double* b, const int* ldb, int* info); /* DPPCON - estimate the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric positive definite packed */ /* matrix using the Cholesky factorization A = U**T*U or A = */ /* L*L**T computed by DPPTRF */ La_extern void F77_NAME(dppcon)(const char* uplo, const int* n, const double* ap, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DPPEQU - compute row and column scalings intended to */ /* equilibrate a symmetric positive definite matrix A in packed */ /* storage and reduce its condition number (with respect to the */ /* two-norm); */ La_extern void F77_NAME(dppequ)(const char* uplo, const int* n, const double* ap, double* s, double* scond, double* amax, int* info); /* Double precision Positive definite matrices in Packed storage */ /* DPPRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric positive */ /* definite and packed, and provides error bounds and backward */ /* error estimates for the solution */ La_extern void F77_NAME(dpprfs)(const char* uplo, const int* n, const int* nrhs, const double* ap, const double* afp, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPPSV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dppsv)(const char* uplo, const int* n, const int* nrhs, const double* ap, double* b, const int* ldb, int* info); /* DPPSVX - use the Cholesky factorization A = U**T*U or A = */ /* L*L**T to compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dppsvx)(const int* fact, const char* uplo, const int* n, const int* nrhs, double* ap, double* afp, char* equed, double* s, double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DPPTRF - compute the Cholesky factorization of a real */ /* symmetric positive definite matrix A stored in packed format */ La_extern void F77_NAME(dpptrf)(const char* uplo, const int* n, double* ap, int* info); /* DPPTRI - compute the inverse of a real symmetric positive */ /* definite matrix A using the Cholesky factorization A = U**T*U */ /* or A = L*L**T computed by DPPTRF */ La_extern void F77_NAME(dpptri)(const char* uplo, const int* n, double* ap, int* info); /* DPPTRS - solve a system of linear equations A*X = B with a */ /* symmetric positive definite matrix A in packed storage using */ /* the Cholesky factorization A = U**T*U or A = L*L**T computed by */ /* DPPTRF */ La_extern void F77_NAME(dpptrs)(const char* uplo, const int* n, const int* nrhs, const double* ap, double* b, const int* ldb, int* info); /* Double precision symmetric Positive definite Tridiagonal matrices */ /* DPTCON - compute the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric positive definite tridiagonal */ /* matrix using the factorization A = L*D*L**T or A = U**T*D*U */ /* computed by DPTTRF */ La_extern void F77_NAME(dptcon)(const int* n, const double* d, const double* e, const double* anorm, double* rcond, double* work, int* info); /* DPTEQR - compute all eigenvalues and, optionally, eigenvectors */ /* of a symmetric positive definite tridiagonal matrix by first */ /* factoring the matrix using DPTTRF, and then calling DBDSQR to */ /* compute the singular values of the bidiagonal factor */ La_extern void F77_NAME(dpteqr)(const char* compz, const int* n, double* d, double* e, double* z, const int* ldz, double* work, int* info); /* DPTRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric positive */ /* definite and tridiagonal, and provides error bounds and */ /* backward error estimates for the solution */ La_extern void F77_NAME(dptrfs)(const int* n, const int* nrhs, const double* d, const double* e, const double* df, const double* ef, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* info); /* DPTSV - compute the solution to a real system of linear */ /* equations A*X = B, where A is an N-by-N symmetric positive */ /* definite tridiagonal matrix, and X and B are N-by-NRHS matrices */ La_extern void F77_NAME(dptsv)(const int* n, const int* nrhs, double* d, double* e, double* b, const int* ldb, int* info); /* DPTSVX - use the factorization A = L*D*L**T to compute the */ /* solution to a real system of linear equations A*X = B, where A */ /* is an N-by-N symmetric positive definite tridiagonal matrix and */ /* X and B are N-by-NRHS matrices */ La_extern void F77_NAME(dptsvx)(const int* fact, const int* n, const int* nrhs, const double* d, const double* e, double* df, double* ef, const double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* info); /* DPTTRF - compute the factorization of a real symmetric */ /* positive definite tridiagonal matrix A */ La_extern void F77_NAME(dpttrf)(const int* n, double* d, double* e, int* info); /* DPTTRS - solve a system of linear equations A * X = B with a */ /* symmetric positive definite tridiagonal matrix A using the */ /* factorization A = L*D*L**T or A = U**T*D*U computed by DPTTRF */ La_extern void F77_NAME(dpttrs)(const int* n, const int* nrhs, const double* d, const double* e, double* b, const int* ldb, int* info); /* DRSCL - multiply an n-element real vector x by the real scalar */ /* 1/a */ La_extern void F77_NAME(drscl)(const int* n, const double* da, double* x, const int* incx); /* Double precision Symmetric Band matrices */ /* DSBEV - compute all the eigenvalues and, optionally, */ /* eigenvectors of a real symmetric band matrix A */ La_extern void F77_NAME(dsbev)(const char* jobz, const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, double* w, double* z, const int* ldz, double* work, int* info); /* DSBEVD - compute all the eigenvalues and, optionally, */ /* eigenvectors of a real symmetric band matrix A */ La_extern void F77_NAME(dsbevd)(const char* jobz, const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, double* w, double* z, const int* ldz, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DSBEVX - compute selected eigenvalues and, optionally, */ /* eigenvectors of a real symmetric band matrix A */ La_extern void F77_NAME(dsbevx)(const char* jobz, const char* range, const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, double* q, const int* ldq, const double* vl, const double* vu, const int* il, const int* iu, const double* abstol, int* m, double* w, double* z, const int* ldz, double* work, int* iwork, int* ifail, int* info); /* DSBGST - reduce a real symmetric-definite banded generalized */ /* eigenproblem A*x = lambda*B*x to standard form C*y = lambda*y, */ La_extern void F77_NAME(dsbgst)(const char* vect, const char* uplo, const int* n, const int* ka, const int* kb, double* ab, const int* ldab, double* bb, const int* ldbb, double* x, const int* ldx, double* work, int* info); /* DSBGV - compute all the eigenvalues, and optionally, the */ /* eigenvectors of a real generalized symmetric-definite banded */ /* eigenproblem, of the form A*x=(lambda);*B*x */ La_extern void F77_NAME(dsbgv)(const char* jobz, const char* uplo, const int* n, const int* ka, const int* kb, double* ab, const int* ldab, double* bb, const int* ldbb, double* w, double* z, const int* ldz, double* work, int* info); /* DSBTRD - reduce a real symmetric band matrix A to symmetric */ /* tridiagonal form T by an orthogonal similarity transformation */ La_extern void F77_NAME(dsbtrd)(const char* vect, const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, double* d, double* e, double* q, const int* ldq, double* work, int* info); /* Double precision Symmetric Packed matrices */ /* DSPCON - estimate the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric packed matrix A using the */ /* factorization A = U*D*U**T or A = L*D*L**T computed by DSPTRF */ La_extern void F77_NAME(dspcon)(const char* uplo, const int* n, const double* ap, const int* ipiv, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DSPEV - compute all the eigenvalues and, optionally, */ /* eigenvectors of a real symmetric matrix A in packed storage */ La_extern void F77_NAME(dspev)(const char* jobz, const char* uplo, const int* n, double* ap, double* w, double* z, const int* ldz, double* work, int* info); /* DSPEVD - compute all the eigenvalues and, optionally, */ /* eigenvectors of a real symmetric matrix A in packed storage */ La_extern void F77_NAME(dspevd)(const char* jobz, const char* uplo, const int* n, double* ap, double* w, double* z, const int* ldz, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DSPEVX - compute selected eigenvalues and, optionally, */ /* eigenvectors of a real symmetric matrix A in packed storage */ La_extern void F77_NAME(dspevx)(const char* jobz, const char* range, const char* uplo, const int* n, double* ap, const double* vl, const double* vu, const int* il, const int* iu, const double* abstol, int* m, double* w, double* z, const int* ldz, double* work, int* iwork, int* ifail, int* info); /* DSPGST - reduce a real symmetric-definite generalized */ /* eigenproblem to standard form, using packed storage */ La_extern void F77_NAME(dspgst)(const int* itype, const char* uplo, const int* n, double* ap, double* bp, int* info); /* DSPGV - compute all the eigenvalues and, optionally, the */ /* eigenvectors of a real generalized symmetric-definite */ /* eigenproblem, of the form A*x=(lambda)*B*x, A*Bx=(lambda)*x, */ /* or B*A*x=(lambda)*x */ La_extern void F77_NAME(dspgv)(const int* itype, const char* jobz, const char* uplo, const int* n, double* ap, double* bp, double* w, double* z, const int* ldz, double* work, int* info); /* DSPRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric indefinite */ /* and packed, and provides error bounds and backward error */ /* estimates for the solution */ La_extern void F77_NAME(dsprfs)(const char* uplo, const int* n, const int* nrhs, const double* ap, const double* afp, const int* ipiv, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DSPSV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dspsv)(const char* uplo, const int* n, const int* nrhs, double* ap, int* ipiv, double* b, const int* ldb, int* info); /* DSPSVX - use the diagonal pivoting factorization A = U*D*U**T */ /* or A = L*D*L**T to compute the solution to a real system of */ /* linear equations A * X = B, where A is an N-by-N symmetric */ /* matrix stored in packed format and X and B are N-by-NRHS */ /* matrices */ La_extern void F77_NAME(dspsvx)(const int* fact, const char* uplo, const int* n, const int* nrhs, const double* ap, double* afp, int* ipiv, const double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, int* iwork, int* info); /* DSPTRD - reduce a real symmetric matrix A stored in packed */ /* form to symmetric tridiagonal form T by an orthogonal */ /* similarity transformation */ La_extern void F77_NAME(dsptrd)(const char* uplo, const int* n, double* ap, double* d, double* e, double* tau, int* info); /* DSPTRF - compute the factorization of a real symmetric matrix */ /* A stored in packed format using the Bunch-Kaufman diagonal */ /* pivoting method */ La_extern void F77_NAME(dsptrf)(const char* uplo, const int* n, double* ap, int* ipiv, int* info); /* DSPTRI - compute the inverse of a real symmetric indefinite */ /* matrix A in packed storage using the factorization A = U*D*U**T */ /* or A = L*D*L**T computed by DSPTRF */ La_extern void F77_NAME(dsptri)(const char* uplo, const int* n, double* ap, const int* ipiv, double* work, int* info); /* DSPTRS - solve a system of linear equations A*X = B with a */ /* real symmetric matrix A stored in packed format using the */ /* factorization A = U*D*U**T or A = L*D*L**T computed by DSPTRF */ La_extern void F77_NAME(dsptrs)(const char* uplo, const int* n, const int* nrhs, const double* ap, const int* ipiv, double* b, const int* ldb, int* info); /* Double precision Symmetric Tridiagonal matrices */ /* DSTEBZ - compute the eigenvalues of a symmetric tridiagonal */ /* matrix T */ La_extern void F77_NAME(dstebz)(const char* range, const char* order, const int* n, const double* vl, const double* vu, const int* il, const int* iu, const double *abstol, const double* d, const double* e, int* m, int* nsplit, double* w, int* iblock, int* isplit, double* work, int* iwork, int* info); /* DSTEDC - compute all eigenvalues and, optionally, eigenvectors */ /* of a symmetric tridiagonal matrix using the divide and conquer */ /* method */ La_extern void F77_NAME(dstedc)(const char* compz, const int* n, double* d, double* e, double* z, const int* ldz, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DSTEIN - compute the eigenvectors of a real symmetric */ /* tridiagonal matrix T corresponding to specified eigenvalues, */ /* using inverse iteration */ La_extern void F77_NAME(dstein)(const int* n, const double* d, const double* e, const int* m, const double* w, const int* iblock, const int* isplit, double* z, const int* ldz, double* work, int* iwork, int* ifail, int* info); /* DSTEQR - compute all eigenvalues and, optionally, eigenvectors */ /* of a symmetric tridiagonal matrix using the implicit QL or QR */ /* method */ La_extern void F77_NAME(dsteqr)(const char* compz, const int* n, double* d, double* e, double* z, const int* ldz, double* work, int* info); /* DSTERF - compute all eigenvalues of a symmetric tridiagonal */ /* matrix using the Pal-Walker-Kahan variant of the QL or QR */ /* algorithm */ La_extern void F77_NAME(dsterf)(const int* n, double* d, double* e, int* info); /* DSTEV - compute all eigenvalues and, optionally, eigenvectors */ /* of a real symmetric tridiagonal matrix A */ La_extern void F77_NAME(dstev)(const char* jobz, const int* n, double* d, double* e, double* z, const int* ldz, double* work, int* info); /* DSTEVD - compute all eigenvalues and, optionally, eigenvectors */ /* of a real symmetric tridiagonal matrix */ La_extern void F77_NAME(dstevd)(const char* jobz, const int* n, double* d, double* e, double* z, const int* ldz, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DSTEVX - compute selected eigenvalues and, optionally, */ /* eigenvectors of a real symmetric tridiagonal matrix A */ La_extern void F77_NAME(dstevx)(const char* jobz, const char* range, const int* n, double* d, double* e, const double* vl, const double* vu, const int* il, const int* iu, const double* abstol, int* m, double* w, double* z, const int* ldz, double* work, int* iwork, int* ifail, int* info); /* Double precision SYmmetric matrices */ /* DSYCON - estimate the reciprocal of the condition number (in */ /* the 1-norm); of a real symmetric matrix A using the */ /* factorization A = U*D*U**T or A = L*D*L**T computed by DSYTRF */ La_extern void F77_NAME(dsycon)(const char* uplo, const int* n, const double* a, const int* lda, const int* ipiv, const double* anorm, double* rcond, double* work, int* iwork, int* info); /* DSYEV - compute all eigenvalues and, optionally, eigenvectors */ /* of a real symmetric matrix A */ La_extern void F77_NAME(dsyev)(const char* jobz, const char* uplo, const int* n, double* a, const int* lda, double* w, double* work, const int* lwork, int* info); /* DSYEVD - compute all eigenvalues and, optionally, eigenvectors */ /* of a real symmetric matrix A */ La_extern void F77_NAME(dsyevd)(const char* jobz, const char* uplo, const int* n, double* a, const int* lda, double* w, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DSYEVX - compute selected eigenvalues and, optionally, */ /* eigenvectors of a real symmetric matrix A */ La_extern void F77_NAME(dsyevx)(const char* jobz, const char* range, const char* uplo, const int* n, double* a, const int* lda, const double* vl, const double* vu, const int* il, const int* iu, const double* abstol, int* m, double* w, double* z, const int* ldz, double* work, const int* lwork, int* iwork, int* ifail, int* info); /* DSYEVR - compute all eigenvalues and, optionally, eigenvectors */ /* of a real symmetric matrix A */ La_extern void F77_NAME(dsyevr)(const char *jobz, const char *range, const char *uplo, const int *n, double *a, const int *lda, const double *vl, const double *vu, const int *il, const int *iu, const double *abstol, int *m, double *w, double *z, const int *ldz, int *isuppz, double *work, const int *lwork, int *iwork, const int *liwork, int *info); /* DSYGS2 - reduce a real symmetric-definite generalized */ /* eigenproblem to standard form */ La_extern void F77_NAME(dsygs2)(const int* itype, const char* uplo, const int* n, double* a, const int* lda, const double* b, const int* ldb, int* info); /* DSYGST - reduce a real symmetric-definite generalized */ /* eigenproblem to standard form */ La_extern void F77_NAME(dsygst)(const int* itype, const char* uplo, const int* n, double* a, const int* lda, const double* b, const int* ldb, int* info); /* DSYGV - compute all the eigenvalues, and optionally, the */ /* eigenvectors of a real generalized symmetric-definite */ /* eigenproblem, of the form A*x=(lambda);*B*x, A*Bx=(lambda);*x, */ /* or B*A*x=(lambda);*x */ La_extern void F77_NAME(dsygv)(const int* itype, const char* jobz, const char* uplo, const int* n, double* a, const int* lda, double* b, const int* ldb, double* w, double* work, const int* lwork, int* info); /* DSYRFS - improve the computed solution to a system of linear */ /* equations when the coefficient matrix is symmetric indefinite, */ /* and provides error bounds and backward error estimates for the */ /* solution */ La_extern void F77_NAME(dsyrfs)(const char* uplo, const int* n, const int* nrhs, const double* a, const int* lda, const double* af, const int* ldaf, const int* ipiv, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DSYSV - compute the solution to a real system of linear */ /* equations A * X = B, */ La_extern void F77_NAME(dsysv)(const char* uplo, const int* n, const int* nrhs, double* a, const int* lda, int* ipiv, double* b, const int* ldb, double* work, const int* lwork, int* info); /* DSYSVX - use the diagonal pivoting factorization to compute */ /* the solution to a real system of linear equations A * X = B, */ La_extern void F77_NAME(dsysvx)(const int* fact, const char* uplo, const int* n, const int* nrhs, const double* a, const int* lda, double* af, const int* ldaf, int* ipiv, const double* b, const int* ldb, double* x, const int* ldx, double* rcond, double* ferr, double* berr, double* work, const int* lwork, int* iwork, int* info); /* DSYTD2 - reduce a real symmetric matrix A to symmetric */ /* tridiagonal form T by an orthogonal similarity transformation */ La_extern void F77_NAME(dsytd2)(const char* uplo, const int* n, double* a, const int* lda, double* d, double* e, double* tau, int* info); /* DSYTF2 - compute the factorization of a real symmetric matrix */ /* A using the Bunch-Kaufman diagonal pivoting method */ La_extern void F77_NAME(dsytf2)(const char* uplo, const int* n, double* a, const int* lda, int* ipiv, int* info); /* DSYTRD - reduce a real symmetric matrix A to real symmetric */ /* tridiagonal form T by an orthogonal similarity transformation */ La_extern void F77_NAME(dsytrd)(const char* uplo, const int* n, double* a, const int* lda, double* d, double* e, double* tau, double* work, const int* lwork, int* info); /* DSYTRF - compute the factorization of a real symmetric matrix */ /* A using the Bunch-Kaufman diagonal pivoting method */ La_extern void F77_NAME(dsytrf)(const char* uplo, const int* n, double* a, const int* lda, int* ipiv, double* work, const int* lwork, int* info); /* DSYTRI - compute the inverse of a real symmetric indefinite */ /* matrix A using the factorization A = U*D*U**T or A = L*D*L**T */ /* computed by DSYTRF */ La_extern void F77_NAME(dsytri)(const char* uplo, const int* n, double* a, const int* lda, const int* ipiv, double* work, int* info); /* DSYTRS - solve a system of linear equations A*X = B with a */ /* real symmetric matrix A using the factorization A = U*D*U**T or */ /* A = L*D*L**T computed by DSYTRF */ La_extern void F77_NAME(dsytrs)(const char* uplo, const int* n, const int* nrhs, const double* a, const int* lda, const int* ipiv, double* b, const int* ldb, int* info); /* Double precision Triangular Band matrices */ /* DTBCON - estimate the reciprocal of the condition number of a */ /* triangular band matrix A, in either the 1-norm or the */ /* infinity-norm */ La_extern void F77_NAME(dtbcon)(const char* norm, const char* uplo, const char* diag, const int* n, const int* kd, const double* ab, const int* ldab, double* rcond, double* work, int* iwork, int* info); /* DTBRFS - provide error bounds and backward error estimates for */ /* the solution to a system of linear equations with a triangular */ /* band coefficient matrix */ La_extern void F77_NAME(dtbrfs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* kd, const int* nrhs, const double* ab, const int* ldab, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DTBTRS - solve a triangular system of the form A * X = B or */ /* A**T * X = B, */ La_extern void F77_NAME(dtbtrs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* kd, const int* nrhs, const double* ab, const int* ldab, double* b, const int* ldb, int* info); /* Double precision Triangular matrices Generalized problems */ /* DTGEVC - compute some or all of the right and/or left */ /* generalized eigenvectors of a pair of real upper triangular */ /* matrices (A,B); */ La_extern void F77_NAME(dtgevc)(const char* side, const char* howmny, const int* select, const int* n, const double* a, const int* lda, const double* b, const int* ldb, double* vl, const int* ldvl, double* vr, const int* ldvr, const int* mm, int* m, double* work, int* info); /* DTGSJA - compute the generalized singular value decomposition */ /* (GSVD); of two real upper triangular (or trapezoidal); matrices */ /* A and B */ La_extern void F77_NAME(dtgsja)(const char* jobu, const char* jobv, const char* jobq, const int* m, const int* p, const int* n, const int* k, const int* l, double* a, const int* lda, double* b, const int* ldb, const double* tola, const double* tolb, double* alpha, double* beta, double* u, const int* ldu, double* v, const int* ldv, double* q, const int* ldq, double* work, int* ncycle, int* info); /* Double precision Triangular matrices Packed storage */ /* DTPCON - estimate the reciprocal of the condition number of a */ /* packed triangular matrix A, in either the 1-norm or the */ /* infinity-norm */ La_extern void F77_NAME(dtpcon)(const char* norm, const char* uplo, const char* diag, const int* n, const double* ap, double* rcond, double* work, int* iwork, int* info); /* DTPRFS - provide error bounds and backward error estimates for */ /* the solution to a system of linear equations with a triangular */ /* packed coefficient matrix */ La_extern void F77_NAME(dtprfs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* nrhs, const double* ap, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* Double precision TRiangular matrices */ /* DTPTRI - compute the inverse of a real upper or lower */ /* triangular matrix A stored in packed format */ La_extern void F77_NAME(dtptri)(const char* uplo, const char* diag, const int* n, double* ap, int* info); /* DTPTRS - solve a triangular system of the form A * X = B or */ /* A**T * X = B, */ La_extern void F77_NAME(dtptrs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* nrhs, const double* ap, double* b, const int* ldb, int* info); /* DTRCON - estimate the reciprocal of the condition number of a */ /* triangular matrix A, in either the 1-norm or the infinity-norm */ La_extern void F77_NAME(dtrcon)(const char* norm, const char* uplo, const char* diag, const int* n, const double* a, const int* lda, double* rcond, double* work, int* iwork, int* info); /* DTREVC - compute some or all of the right and/or left */ /* eigenvectors of a real upper quasi-triangular matrix T */ La_extern void F77_NAME(dtrevc)(const char* side, const char* howmny, const int* select, const int* n, const double* t, const int* ldt, double* vl, const int* ldvl, double* vr, const int* ldvr, const int* mm, int* m, double* work, int* info); /* DTREXC - reorder the real Schur factorization of a real matrix */ /* A = Q*T*Q**T, so that the diagonal block of T with row index */ /* IFST is moved to row ILST */ La_extern void F77_NAME(dtrexc)(const char* compq, const int* n, double* t, const int* ldt, double* q, const int* ldq, int* ifst, int* ILST, double* work, int* info); /* DTRRFS - provide error bounds and backward error estimates for */ /* the solution to a system of linear equations with a triangular */ /* coefficient matrix */ La_extern void F77_NAME(dtrrfs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* nrhs, const double* a, const int* lda, const double* b, const int* ldb, double* x, const int* ldx, double* ferr, double* berr, double* work, int* iwork, int* info); /* DTRSEN - reorder the real Schur factorization of a real matrix */ /* A = Q*T*Q**T, so that a selected cluster of eigenvalues appears */ /* in the leading diagonal blocks of the upper quasi-triangular */ /* matrix T, */ La_extern void F77_NAME(dtrsen)(const char* job, const char* compq, const int* select, const int* n, double* t, const int* ldt, double* q, const int* ldq, double* wr, double* wi, int* m, double* s, double* sep, double* work, const int* lwork, int* iwork, const int* liwork, int* info); /* DTRSNA - estimate reciprocal condition numbers for specified */ /* eigenvalues and/or right eigenvectors of a real upper */ /* quasi-triangular matrix T (or of any matrix Q*T*Q**T with Q */ /* orthogonal); */ La_extern void F77_NAME(dtrsna)(const char* job, const char* howmny, const int* select, const int* n, const double* t, const int* ldt, const double* vl, const int* ldvl, const double* vr, const int* ldvr, double* s, double* sep, const int* mm, int* m, double* work, const int* lwork, int* iwork, int* info); /* DTRSYL - solve the real Sylvester matrix equation */ La_extern void F77_NAME(dtrsyl)(const char* trana, const char* tranb, const int* isgn, const int* m, const int* n, const double* a, const int* lda, const double* b, const int* ldb, double* c, const int* ldc, double* scale, int* info); /* DTRTI2 - compute the inverse of a real upper or lower */ /* triangular matrix */ La_extern void F77_NAME(dtrti2)(const char* uplo, const char* diag, const int* n, double* a, const int* lda, int* info); /* DTRTRI - compute the inverse of a real upper or lower */ /* triangular matrix A */ La_extern void F77_NAME(dtrtri)(const char* uplo, const char* diag, const int* n, double* a, const int* lda, int* info); /* DTRTRS - solve a triangular system of the form A * X = B or */ /* A**T * X = B */ La_extern void F77_NAME(dtrtrs)(const char* uplo, const char* trans, const char* diag, const int* n, const int* nrhs, const double* a, const int* lda, double* b, const int* ldb, int* info); /* DTZRQF - reduce the M-by-N ( M<=N ); real upper trapezoidal */ /* matrix A to upper triangular form by means of orthogonal */ /* transformations */ La_extern void F77_NAME(dtzrqf)(const int* m, const int* n, double* a, const int* lda, double* tau, int* info); /* Double precision utilties in Lapack */ /* DHGEQZ - implement a single-/double-shift version of the QZ */ /* method for finding the generalized eigenvalues */ /* w(j);=(ALPHAR(j); + i*ALPHAI(j););/BETAR(j); of the equation */ /* det( A - w(i); B ); = 0 In addition, the pair A,B may be */ /* reduced to generalized Schur form */ La_extern void F77_NAME(dhgeqz)(const char* job, const char* compq, const char* compz, const int* n, const int *ILO, const int* IHI, double* a, const int* lda, double* b, const int* ldb, double* alphar, double* alphai, const double* beta, double* q, const int* ldq, double* z, const int* ldz, double* work, const int* lwork, int* info); /* DHSEIN - use inverse iteration to find specified right and/or */ /* left eigenvectors of a real upper Hessenberg matrix H */ La_extern void F77_NAME(dhsein)(const char* side, const char* eigsrc, const char* initv, int* select, const int* n, double* h, const int* ldh, double* wr, double* wi, double* vl, const int* ldvl, double* vr, const int* ldvr, const int* mm, int* m, double* work, int* ifaill, int* ifailr, int* info); /* DHSEQR - compute the eigenvalues of a real upper Hessenberg */ /* matrix H and, optionally, the matrices T and Z from the Schur */ /* decomposition H = Z T Z**T, where T is an upper */ /* quasi-triangular matrix (the Schur form);, and Z is the */ /* orthogonal matrix of Schur vectors */ La_extern void F77_NAME(dhseqr)(const char* job, const char* compz, const int* n, const int* ilo, const int* ihi, double* h, const int* ldh, double* wr, double* wi, double* z, const int* ldz, double* work, const int* lwork, int* info); /* DLABAD - take as input the values computed by SLAMCH for */ /* underflow and overflow, and returns the square root of each of */ /* these values if the log of LARGE is sufficiently large */ La_extern void F77_NAME(dlabad)(double* small, double* large); /* DLABRD - reduce the first NB rows and columns of a real */ /* general m by n matrix A to upper or lower bidiagonal form by an */ /* orthogonal transformation Q' * A * P, and returns the matrices */ /* X and Y which are needed to apply the transformation to the */ /* unreduced part of A */ La_extern void F77_NAME(dlabrd)(const int* m, const int* n, const int* nb, double* a, const int* lda, double* d, double* e, double* tauq, double* taup, double* x, const int* ldx, double* y, const int* ldy); /* DLACON - estimate the 1-norm of a square, real matrix A */ La_extern void F77_NAME(dlacon)(const int* n, double* v, double* x, int* isgn, double* est, int* kase); /* DLACPY - copy all or part of a two-dimensional matrix A to */ /* another matrix B */ La_extern void F77_NAME(dlacpy)(const char* uplo, const int* m, const int* n, const double* a, const int* lda, double* b, const int* ldb); /* DLADIV - perform complex division in real arithmetic */ La_extern void F77_NAME(dladiv)(const double* a, const double* b, const double* c, const double* d, double* p, double* q); /* DLAE2 - compute the eigenvalues of a 2-by-2 symmetric matrix [ A B ] */ /* [ B C ] */ La_extern void F77_NAME(dlae2)(const double* a, const double* b, const double* c, double* rt1, double* rt2); /* DLAEBZ - contain the iteration loops which compute and use the */ /* function N(w);, which is the count of eigenvalues of a */ /* symmetric tridiagonal matrix T less than or equal to its */ /* argument w */ La_extern void F77_NAME(dlaebz)(const int* ijob, const int* nitmax, const int* n, const int* mmax, const int* minp, const int* nbmin, const double* abstol, const double* reltol, const double* pivmin, double* d, double* e, double* e2, int* nval, double* ab, double* c, int* mout, int* nab, double* work, int* iwork, int* info); /* DLAED0 - compute all eigenvalues and corresponding */ /* eigenvectors of a symmetric tridiagonal matrix using the divide */ /* and conquer method */ La_extern void F77_NAME(dlaed0)(const int* icompq, const int* qsiz, const int* n, double* d, double* e, double* q, const int* ldq, double* qstore, const int* ldqs, double* work, int* iwork, int* info); /* DLAED1 - compute the updated eigensystem of a diagonal matrix */ /* after modification by a rank-one symmetric matrix */ La_extern void F77_NAME(dlaed1)(const int* n, double* d, double* q, const int* ldq, int* indxq, const double* rho, const int* cutpnt, double* work, int* iwork, int* info); /* DLAED2 - merge the two sets of eigenvalues together into a */ /* single sorted set */ La_extern void F77_NAME(dlaed2)(const int* k, const int* n, double* d, double* q, const int* ldq, int* indxq, double* rho, const int* cutpnt, double* z, double* dlamda, double* q2, const int *ldq2, int* indxc, int* w, int* indxp, int* indx, int* coltyp, int* info); /* DLAED3 - find the roots of the secular equation, as defined by */ /* the values in double* d, W, and RHO, between KSTART and KSTOP */ La_extern void F77_NAME(dlaed3)(const int* k, const int* kstart, const int *kstop, const int* n, double* d, double* q, const int* ldq, const double* rho, const int* cutpnt, double* dlamda, int* q2, const int* ldq2, int* indxc, int* ctot, double* w, double* s, const int* lds, int* info); /* DLAED4 - subroutine computes the I-th updated eigenvalue of a */ /* symmetric rank-one modification to a diagonal matrix whose */ /* elements are given in the array d, and that D(i); < D(j); for */ /* i < j and that RHO > 0 */ La_extern void F77_NAME(dlaed4)(const int* n, const int* i, const double* d, const double* z, const double* delta, const double* rho, double* dlam, int* info); /* DLAED5 - subroutine computes the I-th eigenvalue of a */ /* symmetric rank-one modification of a 2-by-2 diagonal matrix */ /* diag( D ); + RHO The diagonal elements in the array D are */ /* assumed to satisfy D(i); < D(j); for i < j */ La_extern void F77_NAME(dlaed5)(const int* i, const double* d, const double* z, double* delta, const double* rho, double* dlam); /* DLAED6 - compute the positive or negative root (closest to the */ /* origin); of z(1); z(2); z(3); f(x); = rho + --------- + */ /* ---------- + --------- d(1);-x d(2);-x d(3);-x It is assumed */ /* that if ORGATI = .true */ La_extern void F77_NAME(dlaed6)(const int* kniter, const int* orgati, const double* rho, const double* d, const double* z, const double* finit, double* tau, int* info); /* DLAED7 - compute the updated eigensystem of a diagonal matrix */ /* after modification by a rank-one symmetric matrix */ La_extern void F77_NAME(dlaed7)(const int* icompq, const int* n, const int* qsiz, const int* tlvls, const int* curlvl, const int* curpbm, double* d, double* q, const int* ldq, int* indxq, const double* rho, const int* cutpnt, double* qstore, double* qptr, const int* prmptr, const int* perm, const int* givptr, const int* givcol, const double* givnum, double* work, int* iwork, int* info); /* DLAED8 - merge the two sets of eigenvalues together into a */ /* single sorted set */ La_extern void F77_NAME(dlaed8)(const int* icompq, const int* k, const int* n, const int* qsiz, double* d, double* q, const int* ldq, const int* indxq, double* rho, const int* cutpnt, const double* z, double* dlamda, double* q2, const int* ldq2, double* w, int* perm, int* givptr, int* givcol, double* givnum, int* indxp, int* indx, int* info); /* DLAED9 - find the roots of the secular equation, as defined by */ /* the values in double* d, Z, and RHO, between KSTART and KSTOP */ La_extern void F77_NAME(dlaed9)(const int* k, const int* kstart, const int* kstop, const int* n, double* d, double* q, const int* ldq, const double* rho, const double* dlamda, const double* w, double* s, const int* lds, int* info); /* DLAEDA - compute the Z vector corresponding to the merge step */ /* in the CURLVLth step of the merge process with TLVLS steps for */ /* the CURPBMth problem */ La_extern void F77_NAME(dlaeda)(const int* n, const int* tlvls, const int* curlvl, const int* curpbm, const int* prmptr, const int* perm, const int* givptr, const int* givcol, const double* givnum, const double* q, const int* qptr, double* z, double* ztemp, int* info); /* DLAEIN - use inverse iteration to find a right or left */ /* eigenvector corresponding to the eigenvalue (WR,WI); of a real */ /* upper Hessenberg matrix H */ La_extern void F77_NAME(dlaein)(const int* rightv, const int* noinit, const int* n, const double* h, const int* ldh, const double* wr, const double* wi, double* vr, double* vi, double* b, const int* ldb, double* work, const double* eps3, const double* smlnum, const double* bignum, int* info); /* DLAEV2 - compute the eigendecomposition of a 2-by-2 symmetric */ /* matrix [ A B ] [ B C ] */ La_extern void F77_NAME(dlaev2)(const double* a, const double* b, const double* c, double* rt1, double* rt2, double* cs1, double *sn1); /* DLAEXC - swap adjacent diagonal blocks T11 and T22 of order 1 */ /* or 2 in an upper quasi-triangular matrix T by an orthogonal */ /* similarity transformation */ La_extern void F77_NAME(dlaexc)(const int* wantq, const int* n, double* t, const int* ldt, double* q, const int* ldq, const int* j1, const int* n1, const int* n2, double* work, int* info); /* DLAG2 - compute the eigenvalues of a 2 x 2 generalized */ /* eigenvalue problem A - w B, with scaling as necessary to aextern void */ /* over-/underflow */ La_extern void F77_NAME(dlag2)(const double* a, const int* lda, const double* b, const int* ldb, const double* safmin, double* scale1, double* scale2, double* wr1, double* wr2, double* wi); /* DLAGS2 - compute 2-by-2 orthogonal matrices U, V and Q, such */ /* that if ( UPPER ); then U'*A*Q = U'*( A1 A2 );*Q = ( x 0 ); */ /* ( 0 A3 ); ( x x ); and V'*B*Q = V'*( B1 B2 );*Q = ( x 0 ); ( */ /* 0 B3 ); ( x x ); or if ( .NOT.UPPER ); then U'*A*Q = U'*( A1 */ /* 0 );*Q = ( x x ); ( A2 A3 ); ( 0 x ); and V'*B*Q = V'*( B1 0 */ /* );*Q = ( x x ); ( B2 B3 ); ( 0 x ); The rows of the */ /* transformed A and B are parallel, where U = ( CSU SNU );, V = */ /* ( CSV SNV );, Q = ( CSQ SNQ ); ( -SNU CSU ); ( -SNV CSV ); ( */ /* -SNQ CSQ ); Z' denotes the transpose of Z */ La_extern void F77_NAME(dlags2)(const int* upper, const double* a1, const double* a2, const double* a3, const double* b1, const double* b2, const double* b3, double* csu, double* snu, double* csv, double* snv, double *csq, double *snq); /* DLAGTF - factorize the matrix (T - lambda*I);, where T is an n */ /* by n tridiagonal matrix and lambda is a scalar, as T - */ /* lambda*I = PLU, */ La_extern void F77_NAME(dlagtf)(const int* n, double* a, const double* lambda, double* b, double* c, const double *tol, double* d, int* in, int* info); /* DLAGTM - perform a matrix-vector product of the form B := */ /* alpha * A * X + beta * B where A is a tridiagonal matrix of */ /* order N, B and X are N by NRHS matrices, and alpha and beta are */ /* real scalars, each of which may be 0., 1., or -1 */ La_extern void F77_NAME(dlagtm)(const char* trans, const int* n, const int* nrhs, const double* alpha, const double* dl, const double* d, const double* du, const double* x, const int* ldx, const double* beta, double* b, const int* ldb); /* DLAGTS - may be used to solve one of the systems of equations */ /* (T - lambda*I);*x = y or (T - lambda*I);'*x = y, */ La_extern void F77_NAME(dlagts)(const int* job, const int* n, const double* a, const double* b, const double* c, const double* d, const int* in, double* y, double* tol, int* info); /* DLAHQR - an auxiliary routine called by DHSEQR to update the */ /* eigenvalues and Schur decomposition already computed by DHSEQR, */ /* by dealing with the Hessenberg submatrix in rows and columns */ /* ILO to IHI */ La_extern void F77_NAME(dlahqr)(const int* wantt, const int* wantz, const int* n, const int* ilo, const int* ihi, double* H, const int* ldh, double* wr, double* wi, const int* iloz, const int* ihiz, double* z, const int* ldz, int* info); /* DLAHRD - reduce the first NB columns of a real general */ /* n-by-(n-k+1); matrix A so that elements below the k-th */ /* subdiagonal are zero */ La_extern void F77_NAME(dlahrd)(const int* n, const int* k, const int* nb, double* a, const int* lda, double* tau, double* t, const int* ldt, double* y, const int* ldy); /* DLAIC1 - apply one step of incremental condition estimation in */ /* its simplest version */ La_extern void F77_NAME(dlaic1)(const int* job, const int* j, const double* x, const double* sest, const double* w, const double* gamma, double* sestpr, double* s, double* c); /* DLALN2 - solve a system of the form (ca A - w D ); X = s B or */ /* (ca A' - w D); X = s B with possible scaling ("s"); and */ /* perturbation of A */ La_extern void F77_NAME(dlaln2)(const int* ltrans, const int* na, const int* nw, const double* smin, const double* ca, const double* a, const int* lda, const double* d1, const double* d2, const double* b, const int* ldb, const double* wr, const double* wi, double* x, const int* ldx, double* scale, double* xnorm, int* info); /* DLAMCH - determine double precision machine parameters */ La_extern double F77_NAME(dlamch)(const char* cmach); /* DLAMRG - will create a permutation list which will merge the */ /* elements of A (which is composed of two independently sorted */ /* sets); into a single set which is sorted in ascending order */ La_extern void F77_NAME(dlamrg)(const int* n1, const int* n2, const double* a, const int* dtrd1, const int* dtrd2, int* index); /* DLANGB - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of an n by n band matrix A, with kl sub-diagonals and ku */ /* super-diagonals */ La_extern double F77_NAME(dlangb)(const char* norm, const int* n, const int* kl, const int* ku, const double* ab, const int* ldab, double* work); /* DLANGE - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a real matrix A */ La_extern double F77_NAME(dlange)(const char* norm, const int* m, const int* n, const double* a, const int* lda, double* work); /* DLANGT - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a real tridiagonal matrix A */ La_extern double F77_NAME(dlangt)(const char* norm, const int* n, const double* dl, const double* d, const double* du); /* DLANHS - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a Hessenberg matrix A */ La_extern double F77_NAME(dlanhs)(const char* norm, const int* n, const double* a, const int* lda, double* work); /* DLANSB - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of an n by n symmetric band matrix A, with k */ /* super-diagonals */ La_extern double F77_NAME(dlansb)(const char* norm, const char* uplo, const int* n, const int* k, const double* ab, const int* ldab, double* work); /* DLANSP - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a real symmetric matrix A, supplied in packed form */ La_extern double F77_NAME(dlansp)(const char* norm, const char* uplo, const int* n, const double* ap, double* work); /* DLANST - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a real symmetric tridiagonal matrix A */ La_extern double F77_NAME(dlanst)(const char* norm, const int* n, const double* d, const double* e); /* DLANSY - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a real symmetric matrix A */ La_extern double F77_NAME(dlansy)(const char* norm, const char* uplo, const int* n, const double* a, const int* lda, double* work); /* DLANTB - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of an n by n triangular band matrix A, with ( k + 1 ) diagonals */ La_extern double F77_NAME(dlantb)(const char* norm, const char* uplo, const char* diag, const int* n, const int* k, const double* ab, const int* ldab, double* work); /* DLANTP - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a triangular matrix A, supplied in packed form */ La_extern double F77_NAME(dlantp)(const char* norm, const char* uplo, const char* diag, const int* n, const double* ap, double* work); /* DLANTR - return the value of the one norm, or the Frobenius */ /* norm, or the infinity norm, or the element of largest absolute */ /* value of a trapezoidal or triangular matrix A */ La_extern double F77_NAME(dlantr)(const char* norm, const char* uplo, const char* diag, const int* m, const int* n, const double* a, const int* lda, double* work); /* DLANV2 - compute the Schur factorization of a real 2-by-2 */ /* nonsymmetric matrix in standard form */ La_extern void F77_NAME(dlanv2)(double* a, double* b, double* c, double* d, double* rt1r, double* rt1i, double* rt2r, double* rt2i, double* cs, double *sn); /* DLAPLL - two column vectors X and Y, let A = ( X Y ); */ La_extern void F77_NAME(dlapll)(const int* n, double* x, const int* incx, double* y, const int* incy, double* ssmin); /* DLAPMT - rearrange the columns of the M by N matrix X as */ /* specified by the permutation K(1);,K(2);,...,K(N); of the */ /* integers 1,...,N */ La_extern void F77_NAME(dlapmt)(const int* forwrd, const int* m, const int* n, double* x, const int* ldx, const int* k); /* DLAPY2 - return sqrt(x**2+y**2);, taking care not to cause */ /* unnecessary overflow */ La_extern double F77_NAME(dlapy2)(const double* x, const double* y); /* DLAPY3 - return sqrt(x**2+y**2+z**2);, taking care not to */ /* cause unnecessary overflow */ La_extern double F77_NAME(dlapy3)(const double* x, const double* y, const double* z); /* DLAQGB - equilibrate a general M by N band matrix A with KL */ /* subdiagonals and KU superdiagonals using the row and scaling */ /* factors in the vectors R and C */ La_extern void F77_NAME(dlaqgb)(const int* m, const int* n, const int* kl, const int* ku, double* ab, const int* ldab, double* r, double* c, double* rowcnd, double* colcnd, const double* amax, char* equed); /* DLAQGE - equilibrate a general M by N matrix A using the row */ /* and scaling factors in the vectors R and C */ La_extern void F77_NAME(dlaqge)(const int* m, const int* n, double* a, const int* lda, double* r, double* c, double* rowcnd, double* colcnd, const double* amax, char* equed); /* DLAQSB - equilibrate a symmetric band matrix A using the */ /* scaling factors in the vector S */ La_extern void F77_NAME(dlaqsb)(const char* uplo, const int* n, const int* kd, double* ab, const int* ldab, const double* s, const double* scond, const double* amax, char* equed); /* DLAQSP - equilibrate a symmetric matrix A using the scaling */ /* factors in the vector S */ La_extern void F77_NAME(dlaqsp)(const char* uplo, const int* n, double* ap, const double* s, const double* scond, const double* amax, int* equed); /* DLAQSY - equilibrate a symmetric matrix A using the scaling */ /* factors in the vector S */ La_extern void F77_NAME(dlaqsy)(const char* uplo, const int* n, double* a, const int* lda, const double* s, const double* scond, const double* amax, int* equed); /* DLAQTR - solve the real quasi-triangular system */ /* op(T) * p = scale*c */ La_extern void F77_NAME(dlaqtr)(const int* ltran, const int* lreal, const int* n, const double* t, const int* ldt, const double* b, const double* w, double* scale, double* x, double* work, int* info); /* DLAR2V - apply a vector of real plane rotations from both */ /* sides to a sequence of 2-by-2 real symmetric matrices, defined */ /* by the elements of the vectors x, y and z */ La_extern void F77_NAME(dlar2v)(const int* n, double* x, double* y, double* z, const int* incx, const double* c, const double* s, const int* incc); /* DLARF - apply a real elementary reflector H to a real m by n */ /* matrix C, from either the left or the right */ La_extern void F77_NAME(dlarf)(const char* side, const int* m, const int* n, const double* v, const int* incv, const double* tau, double* c, const int* ldc, double* work); /* DLARFB - apply a real block reflector H or its transpose H' */ /* to a real m by n matrix C, from either the left or the right */ La_extern void F77_NAME(dlarfb)(const char* side, const char* trans, const char* direct, const char* storev, const int* m, const int* n, const int* k, const double* v, const int* ldv, const double* t, const int* ldt, double* c, const int* ldc, double* work, const int* lwork); /* DLARFG - generate a real elementary reflector H of order n, */ /* such that H * ( alpha ) = ( beta ), H' * H = I */ La_extern void F77_NAME(dlarfg)(const int* n, const double* alpha, double* x, const int* incx, double* tau); /* DLARFT - form the triangular factor T of a real block */ /* reflector H of order n, which is defined as a product of k */ /* elementary reflectors */ La_extern void F77_NAME(dlarft)(const char* direct, const char* storev, const int* n, const int* k, double* v, const int* ldv, const double* tau, double* t, const int* ldt); /* DLARFX - apply a real elementary reflector H to a real m by n */ /* matrix C, from either the left or the right */ La_extern void F77_NAME(dlarfx)(const char* side, const int* m, const int* n, const double* v, const double* tau, double* c, const int* ldc, double* work); /* DLARGV - generate a vector of real plane rotations, determined */ /* by elements of the real vectors x and y */ La_extern void F77_NAME(dlargv)(const int* n, double* x, const int* incx, double* y, const int* incy, double* c, const int* incc); /* DLARNV - return a vector of n random real numbers from a */ /* uniform or normal distribution */ La_extern void F77_NAME(dlarnv)(const int* idist, int* iseed, const int* n, double* x); /* DLARTG - generate a plane rotation so that [ CS SN ] */ La_extern void F77_NAME(dlartg)(const double* f, const double* g, double* cs, double* sn, double *r); /* DLARTV - apply a vector of real plane rotations to elements of */ /* the real vectors x and y */ La_extern void F77_NAME(dlartv)(const int* n, double* x, const int* incx, double* y, const int* incy, const double* c, const double* s, const int* incc); /* DLARUV - return a vector of n random real numbers from a */ /* uniform (0,1); */ La_extern void F77_NAME(dlaruv)(int* iseed, const int* n, double* x); /* DLAS2 - compute the singular values of the 2-by-2 matrix */ /* [ F G ] [ 0 H ] */ La_extern void F77_NAME(dlas2)(const double* f, const double* g, const double* h, double* ssmin, double* ssmax); /* DLASCL - multiply the M by N real matrix A by the real scalar */ /* CTO/CFROM */ La_extern void F77_NAME(dlascl)(const char* type, const int* kl,const int* ku, double* cfrom, double* cto, const int* m, const int* n, double* a, const int* lda, int* info); /* DLASET - initialize an m-by-n matrix A to BETA on the diagonal */ /* and ALPHA on the offdiagonals */ La_extern void F77_NAME(dlaset)(const char* uplo, const int* m, const int* n, const double* alpha, const double* beta, double* a, const int* lda); /* DLASQ1 - DLASQ1 computes the singular values of a real N-by-N */ /* bidiagonal matrix with diagonal D and off-diagonal E */ La_extern void F77_NAME(dlasq1)(const int* n, double* d, double* e, double* work, int* info); /* DLASQ2 - DLASQ2 computes the singular values of a real N-by-N */ /* unreduced bidiagonal matrix with squared diagonal elements in */ /* Q and squared off-diagonal elements in E */ La_extern void F77_NAME(dlasq2)(const int* m, double* q, double* e, double* qq, double* ee, const double* eps, const double* tol2, const double* small2, double* sup, int* kend, int* info); /* DLASQ3 - DLASQ3 is the workhorse of the whole bidiagonal SVD */ /* algorithm */ La_extern void F77_NAME(dlasq3)(int* n, double* q, double* e, double* qq, double* ee, double* sup, double *sigma, int* kend, int* off, int* iphase, const int* iconv, const double* eps, const double* tol2, const double* small2); /* DLASQ4 - DLASQ4 estimates TAU, the smallest eigenvalue of a */ /* matrix */ La_extern void F77_NAME(dlasq4)(const int* n, const double* q, const double* e, double* tau, double* sup); /* DLASR - perform the transformation A := P*A, when SIDE = 'L' */ /* or 'l' ( Left-hand side ); A := A*P', when SIDE = 'R' or 'r' */ /* ( Right-hand side ); where A is an m by n real matrix and P is */ /* an orthogonal matrix, */ La_extern void F77_NAME(dlasr)(const char* side, const char* pivot, const char* direct, const int* m, const int* n, const double* c, const double* s, double* a, const int* lda); /* DLASRT - the numbers in D in increasing order (if ID = 'I'); */ /* or in decreasing order (if ID = 'D' ); */ La_extern void F77_NAME(dlasrt)(const char* id, const int* n, double* d, int* info); /* DLASSQ - return the values scl and smsq such that ( scl**2 */ /* );*smsq = x( 1 );**2 +...+ x( n );**2 + ( scale**2 );*sumsq, */ La_extern void F77_NAME(dlassq)(const int* n, const double* x, const int* incx, double* scale, double* sumsq); /* DLASV2 - compute the singular value decomposition of a 2-by-2 */ /* triangular matrix [ F G ] [ 0 H ] */ La_extern void F77_NAME(dlasv2)(const double* f, const double* g, const double* h, double* ssmin, double* ssmax, double* snr, double* csr, double* snl, double* csl); /* DLASWP - perform a series of row interchanges on the matrix A */ La_extern void F77_NAME(dlaswp)(const int* n, double* a, const int* lda, const int* k1, const int* k2, const int* ipiv, const int* incx); /* DLASY2 - solve for the N1 by N2 matrix double* x, 1 <= N1,N2 <= 2, in */ /* op(TL);*X + ISGN*X*op(TR); = SCALE*B, */ La_extern void F77_NAME(dlasy2)(const int* ltranl, const int* ltranr, const int* isgn, const int* n1, const int* n2, const double* tl, const int* ldtl, const double* tr, const int* ldtr, const double* b, const int* ldb, double* scale, double* x, const int* ldx, double* xnorm, int* info); /* DLASYF - compute a partial factorization of a real symmetric */ /* matrix A using the Bunch-Kaufman diagonal pivoting method */ La_extern void F77_NAME(dlasyf)(const char* uplo, const int* n, const int* nb, const int* kb, double* a, const int* lda, int* ipiv, double* w, const int* ldw, int* info); /* DLATBS - solve one of the triangular systems A *x = s*b or */ /* A'*x = s*b with scaling to prevent overflow, where A is an */ /* upper or lower triangular band matrix */ La_extern void F77_NAME(dlatbs)(const char* uplo, const char* trans, const char* diag, const char* normin, const int* n, const int* kd, const double* ab, const int* ldab, double* x, double* scale, double* cnorm, int* info); /* DLATPS - solve one of the triangular systems A *x = s*b or */ /* A'*x = s*b with scaling to prevent overflow, where A is an */ /* upper or lower triangular matrix stored in packed form */ La_extern void F77_NAME(dlatps)(const char* uplo, const char* trans, const char* diag, const char* normin, const int* n, const double* ap, double* x, double* scale, double* cnorm, int* info); /* DLATRD - reduce NB rows and columns of a real symmetric matrix */ /* A to symmetric tridiagonal form by an orthogonal similarity */ /* transformation Q' * A * Q, and returns the matrices V and W */ /* which are needed to apply the transformation to the unreduced */ /* part of A */ La_extern void F77_NAME(dlatrd)(const char* uplo, const int* n, const int* nb, double* a, const int* lda, double* e, double* tau, double* w, const int* ldw); /* DLATRS - solve one of the triangular systems A *x = s*b or */ /* A'*x = s*b with scaling to prevent overflow */ La_extern void F77_NAME(dlatrs)(const char* uplo, const char* trans, const char* diag, const char* normin, const int* n, const double* a, const int* lda, double* x, double* scale, double* cnorm, int* info); /* DLATZM - apply a Householder matrix generated by DTZRQF to a */ /* matrix */ La_extern void F77_NAME(dlatzm)(const char* side, const int* m, const int* n, const double* v, const int* incv, const double* tau, double* c1, double* c2, const int* ldc, double* work); /* DLAUU2 - compute the product U * U' or L' * const int* l, where the */ /* triangular factor U or L is stored in the upper or lower */ /* triangular part of the array A */ La_extern void F77_NAME(dlauu2)(const char* uplo, const int* n, double* a, const int* lda, int* info); /* DLAUUM - compute the product U * U' or L' * L, where the */ /* triangular factor U or L is stored in the upper or lower */ /* triangular part of the array A */ La_extern void F77_NAME(dlauum)(const char* uplo, const int* n, double* a, const int* lda, int* info); /* ======================================================================== */ /* Selected Double Complex Lapack Routines ======== */ /* IZMAX1 finds the index of the element whose real part has maximum * absolute value. */ La_extern int F77_NAME(izmax1)(const int *n, Rcomplex *cx, const int *incx); /* ZGECON estimates the reciprocal of the condition number of a general * complex matrix A, in either the 1-norm or the infinity-norm, using * the LU factorization computed by ZGETRF. */ La_extern void F77_NAME(zgecon)(const char *norm, const int *n, const Rcomplex *a, const int *lda, const double *anorm, double *rcond, Rcomplex *work, double *rwork, int *info); /* ZGESV computes the solution to a complex system of linear equations */ La_extern void F77_NAME(zgesv)(const int *n, const int *nrhs, Rcomplex *a, const int *lda, int *ipiv, Rcomplex *b, const int *ldb, int *info); /* ZGEQP3 computes a QR factorization with column pivoting */ La_extern void F77_NAME(zgeqp3)(const int *m, const int *n, Rcomplex *a, const int *lda, int *jpvt, Rcomplex *tau, Rcomplex *work, const int *lwork, double *rwork, int *info); /* ZUNMQR applies Q or Q**H from the Left or Right */ La_extern void F77_NAME(zunmqr)(const char *side, const char *trans, const int *m, const int *n, const int *k, Rcomplex *a, const int *lda, Rcomplex *tau, Rcomplex *c, const int *ldc, Rcomplex *work, const int *lwork, int *info); /* ZTRTRS solves triangular systems */ La_extern void F77_NAME(ztrtrs)(const char *uplo, const char *trans, const char *diag, const int *n, const int *nrhs, Rcomplex *a, const int *lda, Rcomplex *b, const int *ldb, int *info); /* ZGESVD - compute the singular value decomposition (SVD); of a */ /* real M-by-N matrix A, optionally computing the left and/or */ /* right singular vectors */ La_extern void F77_NAME(zgesvd)(const char *jobu, const char *jobvt, const int *m, const int *n, Rcomplex *a, const int *lda, double *s, Rcomplex *u, const int *ldu, Rcomplex *vt, const int *ldvt, Rcomplex *work, const int *lwork, double *rwork, int *info); /* ZGHEEV - compute all eigenvalues and, optionally, eigenvectors */ /* of a Hermitian matrix A */ La_extern void F77_NAME(zheev)(const char *jobz, const char *uplo, const int *n, Rcomplex *a, const int *lda, double *w, Rcomplex *work, const int *lwork, double *rwork, int *info); /* ZGGEEV - compute all eigenvalues and, optionally, eigenvectors */ /* of a complex non-symmetric matrix A */ La_extern void F77_NAME(zgeev)(const char *jobvl, const char *jobvr, const int *n, Rcomplex *a, const int *lda, Rcomplex *wr, Rcomplex *vl, const int *ldvl, Rcomplex *vr, const int *ldvr, Rcomplex *work, const int *lwork, double *rwork, int *info); /* NOTE: The following entry points were traditionally in this file, but are not provided by R's libRlapack */ /* DZSUM1 - take the sum of the absolute values of a complex */ /* vector and returns a double precision result */ La_extern double F77_NAME(dzsum1)(const int *n, Rcomplex *CX, const int *incx); /* ZLACN2 estimates the 1-norm of a square, complex matrix A. * Reverse communication is used for evaluating matrix-vector products. */ La_extern void F77_NAME(zlacn2)(const int *n, Rcomplex *v, Rcomplex *x, double *est, int *kase, int *isave); /* ZLANTR - return the value of the one norm, or the Frobenius norm, */ /* or the infinity norm, or the element of largest absolute value of */ /* a trapezoidal or triangular matrix A */ La_extern double F77_NAME(zlantr)(const char *norm, const char *uplo, const char *diag, const int *m, const int *n, Rcomplex *a, const int *lda, double *work); /* ======================================================================== */ /* Other double precision and double complex Lapack routines provided by libRlapack. These are extracted from the CLAPACK headers. */ La_extern void F77_NAME(dbdsdc)(char *uplo, char *compq, int *n, double * d, double *e, double *u, int *ldu, double *vt, int *ldvt, double *q, int *iq, double *work, int * iwork, int *info); La_extern void F77_NAME(dgegs)(char *jobvsl, char *jobvsr, int *n, double *a, int *lda, double *b, int *ldb, double * alphar, double *alphai, double *beta, double *vsl, int *ldvsl, double *vsr, int *ldvsr, double *work, int *lwork, int *info); La_extern void F77_NAME(dgelsd)(int *m, int *n, int *nrhs, double *a, int *lda, double *b, int *ldb, double * s, double *rcond, int *rank, double *work, int *lwork, int *iwork, int *info); La_extern void F77_NAME(dgelsx)(int *m, int *n, int *nrhs, double *a, int *lda, double *b, int *ldb, int * jpvt, double *rcond, int *rank, double *work, int * info); La_extern void F77_NAME(dgesc2)(int *n, double *a, int *lda, double *rhs, int *ipiv, int *jpiv, double *scale); /* DGESDD - compute the singular value decomposition (SVD); of a */ /* real M-by-N matrix A, optionally computing the left and/or */ /* right singular vectors. If singular vectors are desired, it uses a */ /* divide-and-conquer algorithm. */ La_extern void F77_NAME(dgesdd)(const char *jobz, const int *m, const int *n, double *a, const int *lda, double *s, double *u, const int *ldu, double *vt, const int *ldvt, double *work, const int *lwork, int *iwork, int *info); La_extern void F77_NAME(dgetc2)(int *n, double *a, int *lda, int *ipiv, int *jpiv, int *info); typedef int (*L_fp)(); La_extern void F77_NAME(dggesx)(char *jobvsl, char *jobvsr, char *sort, L_fp delctg, char *sense, int *n, double *a, int *lda, double *b, int *ldb, int *sdim, double *alphar, double *alphai, double *beta, double *vsl, int *ldvsl, double *vsr, int *ldvsr, double *rconde, double * rcondv, double *work, int *lwork, int *iwork, int * liwork, int *bwork, int *info); La_extern void F77_NAME(dggev)(char *jobvl, char *jobvr, int *n, double * a, int *lda, double *b, int *ldb, double *alphar, double *alphai, double *beta, double *vl, int *ldvl, double *vr, int *ldvr, double *work, int *lwork, int *info); La_extern void F77_NAME(dggevx)(char *balanc, char *jobvl, char *jobvr, char * sense, int *n, double *a, int *lda, double *b, int *ldb, double *alphar, double *alphai, double * beta, double *vl, int *ldvl, double *vr, int *ldvr, int *ilo, int *ihi, double *lscale, double *rscale, double *abnrm, double *bbnrm, double *rconde, double * rcondv, double *work, int *lwork, int *iwork, int * bwork, int *info); La_extern void F77_NAME(dggsvp)(char *jobu, char *jobv, char *jobq, int *m, int *p, int *n, double *a, int *lda, double *b, int *ldb, double *tola, double *tolb, int *k, int *l, double *u, int *ldu, double *v, int *ldv, double *q, int *ldq, int *iwork, double *tau, double *work, int *info); La_extern void F77_NAME(dgtts2)(int *itrans, int *n, int *nrhs, double *dl, double *d, double *du, double *du2, int *ipiv, double *b, int *ldb); La_extern void F77_NAME(dlagv2)(double *a, int *lda, double *b, int *ldb, double *alphar, double *alphai, double * beta, double *csl, double *snl, double *csr, double * snr); La_extern void F77_NAME(dlals0)(int *icompq, int *nl, int *nr, int *sqre, int *nrhs, double *b, int *ldb, double *bx, int *ldbx, int *perm, int *givptr, int *givcol, int *ldgcol, double *givnum, int *ldgnum, double * poles, double *difl, double *difr, double *z, int * k, double *c, double *s, double *work, int *info); La_extern void F77_NAME(dlalsa)(int *icompq, int *smlsiz, int *n, int *nrhs, double *b, int *ldb, double *bx, int * ldbx, double *u, int *ldu, double *vt, int *k, double *difl, double *difr, double *z, double * poles, int *givptr, int *givcol, int *ldgcol, int * perm, double *givnum, double *c, double *s, double * work, int *iwork, int *info); La_extern void F77_NAME(dlalsd)(char *uplo, int *smlsiz, int *n, int *nrhs, double *d, double *e, double *b, int *ldb, double *rcond, int *rank, double *work, int *iwork, int *info); La_extern void F77_NAME(dlamc1)(int *beta, int *t, int *rnd, int *ieee1); La_extern void F77_NAME(dlamc2)(int *beta, int *t, int *rnd, double *eps, int *emin, double *rmin, int *emax, double *rmax); La_extern double F77_NAME(dlamc3)(double *a, double *b); La_extern void F77_NAME(dlamc4)(int *emin, double *start, int *base); La_extern void F77_NAME(dlamc5)(int *beta, int *p, int *emin, int *ieee, int *emax, double *rmax); La_extern void F77_NAME(dlaqp2)(int *m, int *n, int *offset, double *a, int *lda, int *jpvt, double *tau, double *vn1, double *vn2, double *work); La_extern void F77_NAME(dlaqps)(int *m, int *n, int *offset, int *nb, int *kb, double *a, int *lda, int *jpvt, double *tau, double *vn1, double *vn2, double *auxv, double *f, int *ldf); La_extern void F77_NAME(dlar1v)(int *n, int *b1, int *bn, double *sigma, double *d, double *l, double *ld, double * lld, double *gersch, double *z, double *ztz, double *mingma, int *r, int *isuppz, double *work); La_extern void F77_NAME(dlarrb)(int *n, double *d, double *l, double *ld, double *lld, int *ifirst, int *ilast, double *sigma, double *reltol, double *w, double * wgap, double *werr, double *work, int *iwork, int * info); La_extern void F77_NAME(dlarre)(int *n, double *d, double *e, double *tol, int *nsplit, int *isplit, int *m, double *w, double *woff, double *gersch, double *work, int *info); La_extern void F77_NAME(dlarrf)(int *n, double *d, double *l, double *ld, double *lld, int *ifirst, int *ilast, double *w, double *dplus, double *lplus, double *work, int *iwork, int *info); La_extern void F77_NAME(dlarrv)(int *n, double *d, double *l, int *isplit, int *m, double *w, int *iblock, double *gersch, double *tol, double *z, int *ldz, int *isuppz, double *work, int *iwork, int *info); La_extern void F77_NAME(dlarz)(char *side, int *m, int *n, int *l, double *v, int *incv, double *tau, double *c, int *ldc, double *work); La_extern void F77_NAME(dlarzb)(char *side, char *trans, char *direct, char * storev, int *m, int *n, int *k, int *l, double *v, int *ldv, double *t, int *ldt, double *c, int * ldc, double *work, int *ldwork); La_extern void F77_NAME(dlarzt)(char *direct, char *storev, int *n, int * k, double *v, int *ldv, double *tau, double *t, int *ldt); La_extern void F77_NAME(dlasd0)(int *n, int *sqre, double *d, double *e, double *u, int *ldu, double *vt, int * ldvt, int *smlsiz, int *iwork, double *work, int * info); La_extern void F77_NAME(dlasd1)(int *nl, int *nr, int *sqre, double *d, double *alpha, double *beta, double *u, int *ldu, double *vt, int *ldvt, int *idxq, int * iwork, double *work, int *info); La_extern void F77_NAME(dlasd2)(int *nl, int *nr, int *sqre, int *k, double *d, double *z, double *alpha, double * beta, double *u, int *ldu, double *vt, int *ldvt, double *dsigma, double *u2, int *ldu2, double *vt2, int *ldvt2, int *idxp, int *idx, int *idxc, int * idxq, int *coltyp, int *info); La_extern void F77_NAME(dlasd3)(int *nl, int *nr, int *sqre, int *k, double *d, double *q, int *ldq, double *dsigma, double *u, int *ldu, double *u2, int *ldu2, double *vt, int *ldvt, double *vt2, int *ldvt2, int *idxc, int *ctot, double *z, int *info); La_extern void F77_NAME(dlasd4)(int *n, int *i, double *d, double *z, double *delta, double *rho, double * sigma, double *work, int *info); La_extern void F77_NAME(dlasd5)(int *i, double *d, double *z, double *delta, double *rho, double *dsigma, double * work); La_extern void F77_NAME(dlasd6)(int *icompq, int *nl, int *nr, int *sqre, double *d, double *vf, double *vl, double *alpha, double *beta, int *idxq, int *perm, int *givptr, int *givcol, int *ldgcol, double *givnum, int *ldgnum, double *poles, double *difl, double * difr, double *z, int *k, double *c, double *s, double *work, int *iwork, int *info); La_extern void F77_NAME(dlasd7)(int *icompq, int *nl, int *nr, int *sqre, int *k, double *d, double *z, double *zw, double *vf, double *vfw, double *vl, double *vlw, double *alpha, double *beta, double * dsigma, int *idx, int *idxp, int *idxq, int *perm, int *givptr, int *givcol, int *ldgcol, double *givnum, int *ldgnum, double *c, double *s, int *info); La_extern void F77_NAME(dlasd8)(int *icompq, int *k, double *d, double *z, double *vf, double *vl, double *difl, double *difr, int *lddifr, double *dsigma, double * work, int *info); La_extern void F77_NAME(dlasd9)(int *icompq, int *ldu, int *k, double *d, double *z, double *vf, double *vl, double *difl, double *difr, double *dsigma, double * work, int *info); La_extern void F77_NAME(dlasda)(int *icompq, int *smlsiz, int *n, int *sqre, double *d, double *e, double *u, int *ldu, double *vt, int *k, double *difl, double *difr, double *z, double *poles, int *givptr, int *givcol, int *ldgcol, int *perm, double *givnum, double *c, double *s, double *work, int *iwork, int *info); La_extern void F77_NAME(dlasdq)(char *uplo, int *sqre, int *n, int * ncvt, int *nru, int *ncc, double *d, double *e, double *vt, int *ldvt, double *u, int *ldu, double *c, int *ldc, double *work, int *info); La_extern void F77_NAME(dlasdt)(int *n, int *lvl, int *nd, int * inode, int *ndiml, int *ndimr, int *msub); La_extern void F77_NAME(dlasq5)(int *i0, int *n0, double *z, int *pp, double *tau, double *dmin, double *dmin1, double *dmin2, double *dn, double *dnm1, double *dnm2, int *ieee); La_extern void F77_NAME(dlasq6)(int *i0, int *n0, double *z, int *pp, double *dmin, double *dmin1, double *dmin2, double *dn, double *dnm1, double *dnm2); La_extern void F77_NAME(dlatdf)(int *ijob, int *n, double *z, int *ldz, double *rhs, double *rdsum, double *rdscal, int *ipiv, int *jpiv); La_extern void F77_NAME(dlatrz)(int *m, int *n, int *l, double * a, int *lda, double *tau, double *work); La_extern void F77_NAME(dormr3)(char *side, char *trans, int *m, int *n, int *k, int *l, double *a, int *lda, double *tau, double *c, int *ldc, double *work, int *info); La_extern void F77_NAME(dormrz)(char *side, char *trans, int *m, int *n, int *k, int *l, double *a, int *lda, double *tau, double *c, int *ldc, double *work, int *lwork, int *info); La_extern void F77_NAME(dptts2)(int *n, int *nrhs, double *d, double *e, double *b, int *ldb); La_extern void F77_NAME(dsbgvd)(char *jobz, char *uplo, int *n, int *ka, int *kb, double *ab, int *ldab, double *bb, int * ldbb, double *w, double *z, int *ldz, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dsbgvx)(char *jobz, char *range, char *uplo, int *n, int *ka, int *kb, double *ab, int *ldab, double * bb, int *ldbb, double *q, int *ldq, double *vl, double *vu, int *il, int *iu, double *abstol, int *m, double *w, double *z, int *ldz, double *work, int *iwork, int *ifail, int *info); La_extern void F77_NAME(dspgvd)(int *itype, char *jobz, char *uplo, int * n, double *ap, double *bp, double *w, double *z, int *ldz, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dspgvx)(int *itype, char *jobz, char *range, char * uplo, int *n, double *ap, double *bp, double *vl, double *vu, int *il, int *iu, double *abstol, int *m, double *w, double *z, int *ldz, double *work, int *iwork, int *ifail, int *info); La_extern void F77_NAME(dstegr)(char *jobz, char *range, int *n, double * d, double *e, double *vl, double *vu, int *il, int *iu, double *abstol, int *m, double *w, double *z, int *ldz, int *isuppz, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dstevr)(char *jobz, char *range, int *n, double * d, double *e, double *vl, double *vu, int *il, int *iu, double *abstol, int *m, double *w, double *z, int *ldz, int *isuppz, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dsygvd)(int *itype, char *jobz, char *uplo, int * n, double *a, int *lda, double *b, int *ldb, double *w, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dsygvx)(int *itype, char *jobz, char *range, char * uplo, int *n, double *a, int *lda, double *b, int *ldb, double *vl, double *vu, int *il, int *iu, double *abstol, int *m, double *w, double *z, int *ldz, double *work, int *lwork, int *iwork, int *ifail, int *info); La_extern void F77_NAME(dtgex2)(int *wantq, int *wantz, int *n, double *a, int *lda, double *b, int *ldb, double * q, int *ldq, double *z, int *ldz, int *j1, int * n1, int *n2, double *work, int *lwork, int *info); La_extern void F77_NAME(dtgexc)(int *wantq, int *wantz, int *n, double *a, int *lda, double *b, int *ldb, double * q, int *ldq, double *z, int *ldz, int *ifst, int *ilst, double *work, int *lwork, int *info); La_extern void F77_NAME(dtgsen)(int *ijob, int *wantq, int *wantz, int *select, int *n, double *a, int *lda, double * b, int *ldb, double *alphar, double *alphai, double * beta, double *q, int *ldq, double *z, int *ldz, int *m, double *pl, double *pr, double *dif, double *work, int *lwork, int *iwork, int *liwork, int *info); La_extern void F77_NAME(dtgsna)(char *job, char *howmny, int *select, int *n, double *a, int *lda, double *b, int *ldb, double *vl, int *ldvl, double *vr, int *ldvr, double *s, double *dif, int *mm, int *m, double * work, int *lwork, int *iwork, int *info); La_extern void F77_NAME(dtgsy2)(char *trans, int *ijob, int *m, int * n, double *a, int *lda, double *b, int *ldb, double *c, int *ldc, double *d, int *ldd, double *e, int *lde, double *f, int *ldf, double * scale, double *rdsum, double *rdscal, int *iwork, int *pq, int *info); La_extern void F77_NAME(dtgsyl)(char *trans, int *ijob, int *m, int * n, double *a, int *lda, double *b, int *ldb, double *c, int *ldc, double *d, int *ldd, double *e, int *lde, double *f, int *ldf, double * scale, double *dif, double *work, int *lwork, int * iwork, int *info); La_extern void F77_NAME(dtzrzf)(int *m, int *n, double *a, int * lda, double *tau, double *work, int *lwork, int *info); La_extern void F77_NAME(dpstrf)(const char* uplo, const int* n, double* a, const int* lda, int* piv, int* rank, double* tol, double *work, int* info); La_extern int F77_NAME(lsame)(char *ca, char *cb); La_extern void F77_NAME(zbdsqr)(char *uplo, int *n, int *ncvt, int * nru, int *ncc, double *d, double *e, Rcomplex *vt, int *ldvt, Rcomplex *u, int *ldu, Rcomplex *c, int *ldc, double *rwork, int *info); La_extern void F77_NAME(zdrot)(int *n, Rcomplex *cx, int *incx, Rcomplex *cy, int *incy, double *c, double *s); La_extern void F77_NAME(zgebak)(char *job, char *side, int *n, int *ilo, int *ihi, double *scale, int *m, Rcomplex *v, int *ldv, int *info); La_extern void F77_NAME(zgebal)(char *job, int *n, Rcomplex *a, int *lda, int *ilo, int *ihi, double *scale, int *info); La_extern void F77_NAME(zgebd2)(int *m, int *n, Rcomplex *a, int *lda, double *d, double *e, Rcomplex *tauq, Rcomplex *taup, Rcomplex *work, int *info); La_extern void F77_NAME(zgebrd)(int *m, int *n, Rcomplex *a, int *lda, double *d, double *e, Rcomplex *tauq, Rcomplex *taup, Rcomplex *work, int *lwork, int * info); La_extern void F77_NAME(zgehd2)(int *n, int *ilo, int *ihi, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *info); La_extern void F77_NAME(zgehrd)(int *n, int *ilo, int *ihi, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zgelq2)(int *m, int *n, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *work, int *info); La_extern void F77_NAME(zgelqf)(int *m, int *n, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *work, int *lwork, int *info); La_extern void F77_NAME(zgeqr2)(int *m, int *n, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *work, int *info); La_extern void F77_NAME(zgeqrf)(int *m, int *n, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *work, int *lwork, int *info); La_extern void F77_NAME(zgetf2)(int *m, int *n, Rcomplex *a, int *lda, int *ipiv, int *info); La_extern void F77_NAME(zgetrf)(int *m, int *n, Rcomplex *a, int *lda, int *ipiv, int *info); La_extern void F77_NAME(zgetrs)(char *trans, int *n, int *nrhs, Rcomplex *a, int *lda, int *ipiv, Rcomplex *b, int *ldb, int *info); La_extern void F77_NAME(zhetd2)(char *uplo, int *n, Rcomplex *a, int *lda, double *d, double *e, Rcomplex *tau, int *info); La_extern void F77_NAME(zhetrd)(char *uplo, int *n, Rcomplex *a, int *lda, double *d, double *e, Rcomplex *tau, Rcomplex *work, int *lwork, int *info); La_extern void F77_NAME(zhseqr)(char *job, char *compz, int *n, int *ilo, int *ihi, Rcomplex *h, int *ldh, Rcomplex *w, Rcomplex *z, int *ldz, Rcomplex *work, int *lwork, int *info); La_extern void F77_NAME(zlabrd)(int *m, int *n, int *nb, Rcomplex *a, int *lda, double *d, double *e, Rcomplex *tauq, Rcomplex *taup, Rcomplex *x, int * ldx, Rcomplex *y, int *ldy); La_extern void F77_NAME(zlacgv)(int *n, Rcomplex *x, int *incx); La_extern void F77_NAME(zlacpy)(char *uplo, int *m, int *n, Rcomplex *a, int *lda, Rcomplex *b, int *ldb); La_extern void F77_NAME(zlahqr)(int *wantt, int *wantz, int *n, int *ilo, int *ihi, Rcomplex *h, int *ldh, Rcomplex *w, int *iloz, int *ihiz, Rcomplex *z, int *ldz, int *info); La_extern void F77_NAME(zlahrd)(int *n, int *k, int *nb, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *t, int *ldt, Rcomplex *y, int *ldy); La_extern double F77_NAME(zlange)(char *norm, int *m, int *n, Rcomplex *a, int *lda, double *work); La_extern double F77_NAME(zlanhe)(char *norm, char *uplo, int *n, Rcomplex *a, int *lda, double *work); La_extern double F77_NAME(zlanhs)(char *norm, int *n, Rcomplex *a, int *lda, double *work); La_extern void F77_NAME(zlaqp2)(int *m, int *n, int *offset, Rcomplex *a, int *lda, int *jpvt, Rcomplex *tau, double *vn1, double *vn2, Rcomplex *work); La_extern void F77_NAME(zlaqps)(int *m, int *n, int *offset, int *nb, int *kb, Rcomplex *a, int *lda, int *jpvt, Rcomplex *tau, double *vn1, double *vn2, Rcomplex * auxv, Rcomplex *f, int *ldf); La_extern void F77_NAME(zlarf)(char *side, int *m, int *n, Rcomplex *v, int *incv, Rcomplex *tau, Rcomplex *c, int * ldc, Rcomplex *work); La_extern void F77_NAME(zlarfb)(char *side, char *trans, char *direct, char * storev, int *m, int *n, int *k, Rcomplex *v, int *ldv, Rcomplex *t, int *ldt, Rcomplex *c, int * ldc, Rcomplex *work, int *ldwork); La_extern void F77_NAME(zlarfg)(int *n, Rcomplex *alpha, Rcomplex * x, int *incx, Rcomplex *tau); La_extern void F77_NAME(zlarft)(char *direct, char *storev, int *n, int * k, Rcomplex *v, int *ldv, Rcomplex *tau, Rcomplex * t, int *ldt); La_extern void F77_NAME(zlarfx)(char *side, int *m, int *n, Rcomplex *v, Rcomplex *tau, Rcomplex *c, int * ldc, Rcomplex *work); La_extern void F77_NAME(zlascl)(char *type, int *kl, int *ku, double *cfrom, double *cto, int *m, int *n, Rcomplex *a, int *lda, int *info); La_extern void F77_NAME(zlaset)(char *uplo, int *m, int *n, Rcomplex *alpha, Rcomplex *beta, Rcomplex *a, int * lda); La_extern void F77_NAME(zlasr)(char *side, char *pivot, char *direct, int *m, int *n, double *c, double *s, Rcomplex *a, int *lda); La_extern void F77_NAME(zlassq)(int *n, Rcomplex *x, int *incx, double *scale, double *sumsq); La_extern void F77_NAME(zlaswp)(int *n, Rcomplex *a, int *lda, int *k1, int *k2, int *ipiv, int *incx); La_extern void F77_NAME(zlatrd)(char *uplo, int *n, int *nb, Rcomplex *a, int *lda, double *e, Rcomplex *tau, Rcomplex *w, int *ldw); La_extern void F77_NAME(zlatrs)(char *uplo, char *trans, char *diag, char * normin, int *n, Rcomplex *a, int *lda, Rcomplex *x, double *scale, double *cnorm, int *info); La_extern void F77_NAME(zsteqr)(char *compz, int *n, double *d, double *e, Rcomplex *z, int *ldz, double *work, int *info); /* ZTRCON estimates the reciprocal of the condition number of a * triangular matrix A, in either the 1-norm or the infinity-norm. */ La_extern void F77_NAME(ztrcon)(const char *norm, const char *uplo, const char *diag, const int *n, const Rcomplex *a, const int *lda, double *rcond, Rcomplex *work, double *rwork, int *info); La_extern void F77_NAME(ztrevc)(char *side, char *howmny, int *select, int *n, Rcomplex *t, int *ldt, Rcomplex *vl, int *ldvl, Rcomplex *vr, int *ldvr, int *mm, int *m, Rcomplex *work, double *rwork, int *info); La_extern void F77_NAME(zung2l)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *info); La_extern void F77_NAME(zung2r)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *info); La_extern void F77_NAME(zungbr)(char *vect, int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zunghr)(int *n, int *ilo, int *ihi, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zungl2)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *info); La_extern void F77_NAME(zunglq)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zungql)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zungqr)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zungr2)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *info); La_extern void F77_NAME(zungrq)(int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex * work, int *lwork, int *info); La_extern void F77_NAME(zungtr)(char *uplo, int *n, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *work, int *lwork, int *info); La_extern void F77_NAME(zunm2r)(char *side, char *trans, int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *c, int *ldc, Rcomplex *work, int *info); La_extern void F77_NAME(zunmbr)(char *vect, char *side, char *trans, int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *c, int *ldc, Rcomplex *work, int * lwork, int *info); La_extern void F77_NAME(zunml2)(char *side, char *trans, int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *c, int *ldc, Rcomplex *work, int *info); La_extern void F77_NAME(zunmlq)(char *side, char *trans, int *m, int *n, int *k, Rcomplex *a, int *lda, Rcomplex *tau, Rcomplex *c, int *ldc, Rcomplex *work, int *lwork, int *info); #ifdef __cplusplus } #endif #endif /* R_LAPACK_H */ ./BNW/src/localscore/QuartzDevice.h0000775000076600007660000002522712074111132017316 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 2007 The R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ * *--------------------------------------------------------------------- * This header file constitutes the (unofficial) API to the Quartz * device. Being unofficial, the API may change at any point without * warning. * * Quartz is a general device-independent way of drawing in Mac OS X, * therefore the Quartz device modularizes the actual drawing target * implementation into separate modules (e.g. Carbon and Cocoa for * on-screen display and PDF, Bitmap for off-screen drawing). The API * below is used by the modules to talk to the Quartz device without * having to know anything about R graphics device API. * * Key functions are listed here: * QuartzDevice_Create - creates a Quartz device * QuartzDevice_ResetContext - should be called after the target * context has been created to initialize it. * QuartzDevice_Kill - closes the Quartz device (e.g. on window close) * QuartzDevice_SetScaledSize - resize device (does not include * re-painting, it should be followed by a call to * QuartzDevice_ReplayDisplayList) * QuartzDevice_ReplayDisplayList - replays all plot commands * * Key concepts * - all Quartz modules are expected to provide a device context * (CGContextRef) for drawing. A device can temporarily return NULL * (e.g. if the context is not available immediately) and replay * the display list later to catch up. * * - interactive devices can use QuartzDevice_SetScaledSize to resize * the device (no context is necessary), then prepare the context * (call QuartzDevice_ResetContext if a new context was created) * and finally re-draw using QuartzDevice_ReplayDisplayList. * * - snapshots can be created either off the current display list * (last=0) or off the last known one (last=1). NewPage callback * can only use last=1 as there is no display list during that * call. Restored snapshots become the current display list and * thus can be extended by further painting (yet the original saved * copy is not influenced). Also note that all snapshots are SEXPs * (the declaration doesn't use SEXP as to not depend on * Rinternals.h) therefore must be protected or preserved immediately * (i.e. the Quartz device does NOT protect them - except in the * call to RestoreSnapshot). * * - dirty flag: the dirty flag is not used internally by the Quartz * device, but can be useful for the modules to determine whether * the current graphics is a restored copy or in-progress * drawing. The Quartz device manages the flag as follows: a) * display list replay does NOT change the flag, b) snapshot * restoration resets the flag, c) all other paint operations * (i.e. outside of restore/replay) set the flag. Most common use * is to determine whether restored snapshots have been * subsequently modified. * * - history: currently the history management is not used by any * modules and as such is untested and strictly experimental. It * may be removed in the future as it is not clear whether it makes * sense to be part of the device. See Cocoa module for a * module-internal implementation of the display history. * * Quartz device creation path: * quartz() function -> SEXP Quartz(args) -> * setup QuartzParameters_t, call backend constructor * [e.g. QuartzCocoa_DeviceCreate(dd, fn, QuartzParameters_t *pars)] -> * create backend definition (QuartzBackend_t backend) -> * fn->Create(dd, &backend), return the result */ #ifndef R_EXT_QUARTZDEVICE_H_ #define R_EXT_QUARTZDEVICE_H_ /* FIXME: this is installed, but can it really work without config.h */ #ifdef HAVE_CONFIG_H #include #endif #ifdef __cplusplus extern "C" { #endif #if HAVE_AQUA #include #else typedef void* CGContextRef; #endif /* flags passed to the newPage callback */ #define QNPF_REDRAW 0x0001 /* is set when NewPage really means re-draw of an existing page */ /* flags passed to QuartzDevice_Create (as fs parameter) */ #define QDFLAG_DISPLAY_LIST 0x0001 #define QDFLAG_INTERACTIVE 0x0002 #define QDFLAG_RASTERIZED 0x0004 /* rasterized media - may imply disabling AA paritally for rects etc. */ /* parameter flags (they should not conflict with QDFLAGS to allow chaining) */ #define QPFLAG_ANTIALIAS 0x0100 typedef void* QuartzDesc_t; typedef struct QuartzBackend_s { int size; /* structure size */ double width, height; double scalex, scaley, pointsize; int bg, canvas; int flags; void* userInfo; CGContextRef (*getCGContext)(QuartzDesc_t dev, void*userInfo); /* Get the context for this device */ int (*locatePoint)(QuartzDesc_t dev, void*userInfo, double*x, double*y); void (*close)(QuartzDesc_t dev, void*userInfo); void (*newPage)(QuartzDesc_t dev, void*userInfo, int flags); void (*state)(QuartzDesc_t dev, void*userInfo, int state); void* (*par)(QuartzDesc_t dev, void*userInfo, int set, const char *key, void *value); void (*sync)(QuartzDesc_t dev, void*userInfo); void* (*cap)(QuartzDesc_t dev, void*userInfo); } QuartzBackend_t; /* parameters that are passed to functions that create backends */ typedef struct QuartzParameters_s { int size; /* structure size */ const char *type, *file, *title; double x, y, width, height, pointsize; const char *family; int flags; int connection; int bg, canvas; double *dpi; /* the following parameters can be used to pass custom parameters when desired */ double pard1, pard2; int pari1, pari2; const char *pars1, *pars2; void *parv; } QuartzParameters_t; /* all device implementations have to call this general Quartz device constructor at some point */ QuartzDesc_t QuartzDevice_Create(void *dd, QuartzBackend_t* def); typedef struct QuartzFunctons_s { void* (*Create)(void *, QuartzBackend_t *); /* create a new device */ int (*DevNumber)(QuartzDesc_t desc); /* returns device number */ void (*Kill)(QuartzDesc_t desc); /* call to close the device */ void (*ResetContext)(QuartzDesc_t desc); /* notifies Q back-end that the implementation has created a new context */ double (*GetWidth)(QuartzDesc_t desc); /* get device width (in inches) */ double (*GetHeight)(QuartzDesc_t desc); /* get device height (in inches) */ void (*SetSize)(QuartzDesc_t desc, double width, double height); /* set device size (in inches) */ double (*GetScaledWidth)(QuartzDesc_t desc); /* get device width (in pixels) */ double (*GetScaledHeight)(QuartzDesc_t desc); /* get device height (in pixels) */ void (*SetScaledSize)(QuartzDesc_t desc, double width, double height); /* set device size (in pixels) */ double (*GetXScale)(QuartzDesc_t desc); /* get x scale factor (px/pt ratio) */ double (*GetYScale)(QuartzDesc_t desc); /* get y scale factor (px/pt ratio) */ void (*SetScale)(QuartzDesc_t desc,double scalex, double scaley); /* sets both scale factors (px/pt ratio) */ void (*SetTextScale)(QuartzDesc_t desc,double scale); /* sets text scale factor */ double (*GetTextScale)(QuartzDesc_t desc); /* sets text scale factor */ void (*SetPointSize)(QuartzDesc_t desc,double ps); /* sets point size */ double (*GetPointSize)(QuartzDesc_t desc); /* gets point size */ int (*GetDirty)(QuartzDesc_t desc); /* sets dirty flag */ void (*SetDirty)(QuartzDesc_t desc,int dirty); /* gets dirty flag */ void (*ReplayDisplayList)(QuartzDesc_t desc); /* replay display list Note: it inhibits sync calls during repaint, the caller is responsible for calling sync if needed. Dirty flag is kept unmodified */ void* (*GetSnapshot)(QuartzDesc_t desc, int last); /* create a (replayable) snapshot of the device contents. when 'last' is set then the last stored display list is used, otherwise a new snapshot is created */ void (*RestoreSnapshot)(QuartzDesc_t desc,void* snapshot); /* restore a snapshot. also clears the dirty flag */ int (*GetAntialias)(QuartzDesc_t desc); /* get anti-alias flag */ void (*SetAntialias)(QuartzDesc_t desc, int aa); /* set anti-alias flag */ int (*GetBackground)(QuartzDesc_t desc); /* get background color */ void (*Activate)(QuartzDesc_t desc); /* activate/select the device */ /* get/set Quartz-specific parameters. desc can be NULL for global parameters */ void* (*SetParameter)(QuartzDesc_t desc, const char *key, void *value); void* (*GetParameter)(QuartzDesc_t desc, const char *key); } QuartzFunctions_t; #define QuartzParam_EmbeddingFlags "embeddeding flags" /* value: int[1] */ #define QP_Flags_CFLoop 0x0001 /* drives application event loop */ #define QP_Flags_Cocoa 0x0002 /* Cocoa is fully initialized */ #define QP_Flags_Front 0x0004 /* is front application */ /* from unix/aqua.c - loads grDevices if necessary and returns NULL on failure */ QuartzFunctions_t *getQuartzFunctions(); /* type of a Quartz contructor */ typedef QuartzDesc_t (*quartz_create_fn_t)(void *dd, QuartzFunctions_t *fn, QuartzParameters_t *par); /* grDevices currently supply following constructors: QuartzCocoa_DeviceCreate, QuartzCarbon_DeviceCreate, QuartzBitmap_DeviceCreate, QuartzPDF_DeviceCreate */ /* embedded Quartz support hook (defined in unix/aqua.c): dd = should be passed-through to QuartzDevice_Create fn = Quartz API functions par = parameters (see above) */ #ifndef IN_AQUA_C extern #endif QuartzDesc_t (*ptr_QuartzBackend)(void *dd, QuartzFunctions_t *fn, QuartzParameters_t *par); /* C version of the Quartz call (experimental) returns 0 on success, error code on failure */ QuartzDesc_t Quartz_C(QuartzParameters_t *par, quartz_create_fn_t q_create, int *errorCode); #ifdef __cplusplus } #endif #endif ./BNW/src/localscore/Parse.h0000775000076600007660000000240012074111132015746 0ustar abhatta3abhatta3/* * R : A Computer Language for Statistical Data Analysis * Copyright (C) 1998-2006 R Core Team * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, a copy is available at * http://www.r-project.org/Licenses/ */ /* NOTE: This file exports a part of the current internal parse interface. It is subject to change at any minor (x.y.0) version of R. */ #ifndef R_EXT_PARSE_H_ #define R_EXT_PARSE_H_ #ifdef __cplusplus extern "C" { #endif /* PARSE_NULL will not be returned by R_ParseVector */ typedef enum { PARSE_NULL, PARSE_OK, PARSE_INCOMPLETE, PARSE_ERROR, PARSE_EOF } ParseStatus; SEXP R_ParseVector(SEXP, int, ParseStatus *, SEXP); #ifdef __cplusplus } #endif #endif ./BNW/README.txt0000775000076600007660000001421412133065300013313 0ustar abhatta3abhatta3===================== README ===================== BNW_src.tar contains a standalone version the structure learning method that is implemented in the Bayesian Network Webserver (BNW). This readme focuses on the use of the package. A more compete description of the method is given on the BNW website: http://compbio.uthsc.edu/BNW Requirements ============ bash, gcc Compile ======= To compile the package, change to the /src directory and type: sh build.sh Test examples ============= To test the installation, type: sh run.sh example1 sh run.sh example2 These commands should create the model_structure.txt and model_averaging_probabilities.txt files in the example1 and example2 directories. The output in these files should match test_model_structure.txt and test_model_averaging_probabilites.txt in each directory. Further description of the examples is given in Example Description section. Running the BNW structure learning package ========================================== The BNW structure learning package is run with the command sh run.sh dir where dir is the name of a directory containing the 3 files described below. The dir directory should be a subdirectory within the BNW/src directory. Structure search parameters =========================== Users can set 3 parameters that will affect the properties of the structure search by modifying the run.sh file. 'maxparent' sets the maximum number of parents that any node in the network can have in a network. By default, the value is set to 4, and each node in the network can have a maximum of 4 direct parents. 'k' sets the number of high scoring networks to include in model averaging. By default, k=100, and the 100 highest scoring networks are included in model averaging. If k=1, no model averaging is performed. 'THR' sets the probability threshold when selecting edges to include in the final network structure after model averaging. By default, THR is set to 0.5, and all edges with a model averaging posterior probability greater than 0.5 are included in the the model_structure.txt file. Input file format ================= (Example input files are in ./src/example1 and ./src/example2 directories) The package requires three tab-delimited text files. input.txt Data file that contains sample values for each variables. Variables are listed in the columns and samples are listed in the rows. Variable names are in the first row. The second row describes the type of each variable. In the second row,enter '1' for each continuous variable and the number of discrete states for each discrete variable. For example, Geno1 and Geno2 in the example1 directory are discrete variables with two states (1 and 2) and the remaining variables are continuous variables. Therefore, the second row contains a '2' for Geno1 and Geno2 and a '1' for the other variables. The remaining rows are the sample values of the variables in each column. Also note that discrete variables should be the leftmost columns of the input data file. banlist.txt This input file lists edges that should be excluded from structure learning. The first row of the file should always contain "From" and "To", while the remaining rows contain the names of the variables that should be excluded from structure learning. A row containing VariableA followed by VariableB will not allow edges from VariableA to VariableB in the network. If no edges are to be excluded from network structure learning, banlist.txt should still exist and contain a header row. The example1 directory contains a sample empty banlist file, while example2 contains an example with edges that should be banned from the network. whitelist.txt This input file lists edges that should be required during structure learning. The format of the file is the same as the banlist.txt file. If an edge is present in whitelist.txt, only those networks that contain the edge will be considered. If no edges are required in the network, whitelist.txt should still exist and contain an header row. Output file format ================= model_structure.txt A structure file with the variable names on the first row. The remainder of the file should be an n x n matrix of 0's and 1's, where n is the number of variables in the network. A '1' in row i and column j in this matrix indicates that there is a directed edge connecting variables i and j, (i.e., there is an edge from i to j in the network). '0' indicate that there is not a directed edge from variable i to variable j. This file can be loaded into BNW using the "Make predictions using a known structure" link on the BNW homepage. model_averaging_probabilities.txt The format of the model_averaging_probability file is similar to model_structure.txt. It is an n x n matrix of values between '0' and '1', where the value gives the posterior probability of the edge after model averaging over the k-best network structures. A value close to '1' in the matrix indicates that the edge was present in most or all of the k-best networks, while a value close to '0' indicates that it was present in few or none of the k-best networks. Example Description =================== The example folders contain data from a synthetic genetic network containing two genotypes (Geno1 and Geno2) and 6 quantitative traits. In the example1 directory, no structural constraints have been added to the structure search (i.e. the banlist.txt and whitelist.txt files contain only a file header). The example2 directory contains several structural constraints. First, we do not allow the genotype nodes to be be the parents of each other (Geno1 to Geno2 and Geno2 to Geno1 are in banlist.txt). Second, Trait5 and Trait6 are not allowed to be the parents of the other variables in the network. This type of structural constraint might be relevant if Trait5 and Trait6 had trans-QTLs at Geno1 and/or Geno2, while the other traits had cis-QTLs at these loci or if Trait5 and Trait6 were higher order phenotypes that were explained by cellular or gene-level Traits1, 2, 3, and 4. Finally, whitelist.txt contains two interactions between Trait2 and Trait4 and Trait3 and Trait6 that are required to be in the network, indicating that a known regulatory relationships exist between these variables. Contact ======= ycui2@uthsc.edu