--- imach/src/imach.c 2017/06/27 11:06:02 1.273 +++ imach/src/imach.c 2017/07/17 08:53:49 1.277 @@ -1,6 +1,18 @@ -/* $Id: imach.c,v 1.273 2017/06/27 11:06:02 brouard Exp $ +/* $Id: imach.c,v 1.277 2017/07/17 08:53:49 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.277 2017/07/17 08:53:49 brouard + Summary: BOM files can be read now + + Revision 1.276 2017/06/30 15:48:31 brouard + Summary: Graphs improvements + + Revision 1.275 2017/06/30 13:39:33 brouard + Summary: Saito's color + + Revision 1.274 2017/06/29 09:47:08 brouard + Summary: Version 0.99r14 + Revision 1.273 2017/06/27 11:06:02 brouard Summary: More documentation on projections @@ -1022,12 +1034,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.273 2017/06/27 11:06:02 brouard Exp $ */ +/* $Id: imach.c,v 1.277 2017/07/17 08:53:49 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; -char fullversion[]="$Revision: 1.273 $ $Date: 2017/06/27 11:06:02 $"; +char fullversion[]="$Revision: 1.277 $ $Date: 2017/07/17 08:53:49 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -3854,7 +3866,7 @@ void likelione(FILE *ficres,double p[], else if(mle >=1) fprintf(fichtm,"\n
File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: %s
\n",subdirf(fileresilk),subdirf(fileresilk)); - + fprintf(fichtm,"\n
Equation of the model: model=1+age+%s
\n",model); for (k=1; k<= nlstate ; k++) { fprintf(fichtm,"
- Probability p%dj by origin %d and destination j. Dot's sizes are related to corresponding weight: %s-p%dj.png
\ @@ -6963,6 +6975,20 @@ void printinggnuplot(char fileresu[], ch /*#endif */ m=pow(2,cptcoveff); + /* diagram of the model */ + fprintf(ficgp,"\n#Diagram of the model \n"); + fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n"); + fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate); + fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + + fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + fprintf(ficgp,"\n#show arrow\nunset label\n"); + fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate); + fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n"); + fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_")); + fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n"); + /* Contribution to likelihood */ /* Plot the probability implied in the likelihood */ fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); @@ -7032,7 +7058,8 @@ void printinggnuplot(char fileresu[], ch fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres); fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres); - fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */ + fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */ /* k1-1 error should be nres-1*/ @@ -7117,15 +7144,16 @@ void printinggnuplot(char fileresu[], ch if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"95%% CI\" w l lt 5,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); + fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l lt 5"); + fprintf(ficgp,"\" t\"\" w l lt 4"); } /* end if backprojcast */ } /* end if backcast */ - fprintf(ficgp,"\nset out ;unset label;\n"); + /* fprintf(ficgp,"\nset out ;unset label;\n"); */ + fprintf(ficgp,"\nset out ;unset title;\n"); } /* nres */ } /* k1 */ } /* cpt */ @@ -7739,7 +7767,7 @@ set ter svg size 640, 480\nunset log y\n continue; fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); strcpy(gplotlabel,"("); - sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1); + /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/ for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -7756,7 +7784,9 @@ set ter svg size 640, 480\nunset log y\n strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres); - fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); + fprintf(ficgp,"\nset key outside "); + /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */ + fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel); fprintf(ficgp,"\nset ter svg size 640, 480 "); if (ng==1){ fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */ @@ -7876,12 +7906,12 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficgp,")"); if(ng ==2) - fprintf(ficgp," t \"p%d%d\" ", k2,k); + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); else /* ng= 3 */ - fprintf(ficgp," t \"i%d%d\" ", k2,k); + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); }else{ /* end ng <> 1 */ if( k !=k2) /* logit p11 is hard to draw */ - fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); + fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); } if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) fprintf(ficgp,","); @@ -7890,7 +7920,8 @@ set ter svg size 640, 480\nunset log y\n i=i+ncovmodel; } /* end k */ } /* end k2 */ - fprintf(ficgp,"\n set out; unset label;\n"); + /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */ + fprintf(ficgp,"\n set out; unset title;set key default;\n"); } /* end k1 */ } /* end ng */ /* avoid: */ @@ -10585,7 +10616,9 @@ int main(int argc, char *argv[]) int vpopbased=0; int nres=0; int endishere=0; - + int noffset=0; + int ncurrv=0; /* Temporary variable */ + char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ @@ -10812,11 +10845,32 @@ int main(int argc, char *argv[]) /* Reads comments: lines beginning with '#' */ numlinepar=0; - - /* First parameter line */ + /* Is it a BOM UTF-8 Windows file? */ + /* First parameter line */ while(fgets(line, MAXLINE, ficpar)) { + noffset=0; + if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */ + { + noffset=noffset+3; + printf("# File is an UTF8 Bom.\n"); // 0xBF + } + else if( line[0] == (char)0xFE && line[1] == (char)0xFF) + { + noffset=noffset+2; + printf("# File is an UTF16BE BOM file\n"); + } + else if( line[0] == 0 && line[1] == 0) + { + if( line[2] == (char)0xFE && line[3] == (char)0xFF){ + noffset=noffset+4; + printf("# File is an UTF16BE BOM file\n"); + } + } else{ + ;/*printf(" Not a BOM file\n");*/ + } + /* If line starts with a # it is a comment */ - if (line[0] == '#') { + if (line[noffset] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); @@ -11470,10 +11524,31 @@ Title=%s
Datafile=%s Firstpass=%d La firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); - fprintf(fichtm,"
Total number of observations=%d
\n\ + fprintf(fichtm,"

Parameter line 2

\n", \ + nlstate, ndeath, maxwav, mle, weightopt); + + fprintf(fichtm,"

Diagram of states %s_.svg

\n\ +", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_")); + + + fprintf(fichtm,"\n

Some descriptive statistics

\n
Total number of observations=%d
\n\ Youngest age at first (selected) pass %.2f, oldest age %.2f
\n\ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n",\ - imx,agemin,agemax,jmin,jmax,jmean); + imx,agemin,agemax,jmin,jmax,jmean); pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */