--- imach/src/imach.c 2017/06/30 15:48:31 1.276
+++ imach/src/imach.c 2018/02/27 19:25:23 1.281
@@ -1,6 +1,23 @@
-/* $Id: imach.c,v 1.276 2017/06/30 15:48:31 brouard Exp $
+/* $Id: imach.c,v 1.281 2018/02/27 19:25:23 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ Revision 1.281 2018/02/27 19:25:23 brouard
+ Summary: Adding second argument for quitting
+
+ Revision 1.280 2018/02/21 07:58:13 brouard
+ Summary: 0.99r15
+
+ New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
+
+ Revision 1.279 2017/07/20 13:35:01 brouard
+ Summary: temporary working
+
+ Revision 1.278 2017/07/19 14:09:02 brouard
+ Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+
+ 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
@@ -1031,12 +1048,12 @@ typedef struct {
#define ODIRSEPARATOR '\\'
#endif
-/* $Id: imach.c,v 1.276 2017/06/30 15:48:31 brouard Exp $ */
+/* $Id: imach.c,v 1.281 2018/02/27 19:25:23 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: 1.276 $ $Date: 2017/06/30 15:48:31 $";
+char fullversion[]="$Revision: 1.281 $ $Date: 2018/02/27 19:25:23 $";
char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
@@ -2510,15 +2527,18 @@ void powell(double p[], double **xi, int
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
{
- /* Computes the prevalence limit in each live state at age x and for covariate combination ij
- (and selected quantitative values in nres)
- by left multiplying the unit
- matrix by transitions matrix until convergence is reached with precision ftolpl */
- /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
- /* Wx is row vector: population in state 1, population in state 2, population dead */
- /* or prevalence in state 1, prevalence in state 2, 0 */
- /* newm is the matrix after multiplications, its rows are identical at a factor */
- /* Initial matrix pimij */
+ /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
+ * (and selected quantitative values in nres)
+ * by left multiplying the unit
+ * matrix by transitions matrix until convergence is reached with precision ftolpl
+ * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
+ * Wx is row vector: population in state 1, population in state 2, population dead
+ * or prevalence in state 1, prevalence in state 2, 0
+ * newm is the matrix after multiplications, its rows are identical at a factor.
+ * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+ * Output is prlim.
+ * Initial matrix pimij
+ */
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
/* 0, 0 , 1} */
@@ -5766,10 +5786,11 @@ void concatwav(int wav[], int **dh, int
/************ Variance ******************/
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
{
- /* Variance of health expectancies */
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- /* double **newm;*/
- /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+ /** Variance of health expectancies
+ * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
+ * double **newm;
+ * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
+ */
/* int movingaverage(); */
double **dnewm,**doldm;
@@ -5777,11 +5798,11 @@ void concatwav(int wav[], int **dh, int
int i, j, nhstepm, hstepm, h, nstepm ;
int k;
double *xp;
- double **gp, **gm; /* for var eij */
- double ***gradg, ***trgradg; /*for var eij */
- double **gradgp, **trgradgp; /* for var p point j */
- double *gpp, *gmp; /* for var p point j */
- double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+ double **gp, **gm; /**< for var eij */
+ double ***gradg, ***trgradg; /**< for var eij */
+ double **gradgp, **trgradgp; /**< for var p point j */
+ double *gpp, *gmp; /**< for var p point j */
+ double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
double ***p3mat;
double age,agelim, hf;
/* double ***mobaverage; */
@@ -5842,7 +5863,7 @@ void concatwav(int wav[], int **dh, int
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
\n");
fprintf(fichtm,"\n
%s
\n",digitp);
- /* } */
+
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
@@ -5897,9 +5918,12 @@ void concatwav(int wav[], int **dh, int
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
-
+ /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
+ * returns into prlim .
+ */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
-
+
+ /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
@@ -5909,23 +5933,28 @@ void concatwav(int wav[], int **dh, int
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
-
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+ /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
+ */
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
+ /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
+ * at horizon h in state j including mortality.
+ */
for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
- /* Next for computing probability of death (h=1 means
+ /* Next for computing shifted+ probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
+ as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
+ }
+
+ /* Again with minus shift */
for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
@@ -5958,19 +5987,23 @@ void concatwav(int wav[], int **dh, int
for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
- /* end probability of death */
-
+ /* end shifting computations */
+
+ /**< Computing gradient matrix at horizon h
+ */
for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}
-
- for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+ /**< Gradient of overall mortality p.3 (or p.j)
+ */
+ for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}
} /* End theta */
-
+
+ /* We got the gradient matrix for each theta and state j */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
for(h=0; h<=nhstepm; h++) /* veij */
@@ -5981,13 +6014,19 @@ void concatwav(int wav[], int **dh, int
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];
-
+ /**< as well as its transposed matrix
+ */
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;
-
+
+ /* Computing trgradg by matcov by gradg at age and summing over h
+ * and k (nhstepm) formula 15 of article
+ * Lievre-Brouard-Heathcote
+ */
+
for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
@@ -5998,7 +6037,11 @@ void concatwav(int wav[], int **dh, int
}
}
- /* pptj */
+ /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
+ * p.j overall mortality formula 49 but computed directly because
+ * we compute the grad (wix pijx) instead of grad (pijx),even if
+ * wix is independent of theta.
+ */
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)
@@ -6607,7 +6650,12 @@ To be simple, these graphs help to under
}
/* Eigen vectors */
- v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+ if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+ printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+ }else
+ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
v21=(lc1-v1)/cv12*v11;
v12=-v21;
@@ -6638,8 +6686,8 @@ To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
- mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
- mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */
+ mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
+ mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{
first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
@@ -7942,8 +7990,8 @@ set ter svg size 640, 480\nunset log y\n
double *agemingoodr, *agemaxgoodr;
- /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
- /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
+ /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
+ /* a covariate has 2 modalities, should be equal to ncovcombmax */
sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);
@@ -8267,11 +8315,11 @@ set ter svg size 640, 480\nunset log y\n
for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;
for(i=1; i<=nlstate;i++) {
- /* if (mobilav>=1) */
- ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
- /* else { */ /* even if mobilav==-1 we use mobaverage */
- /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
- /* } */
+ if (mobilav>=1)
+ ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+ else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+ ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+ }
fprintf(ficresf," %.3f", p3mat[i][j][h]);
} /* end i */
fprintf(ficresf," %.3f", ppij);
@@ -10613,7 +10661,7 @@ 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];
@@ -10750,8 +10798,13 @@ int main(int argc, char *argv[])
if(pathr[0] == '\0') break; /* Dirty */
}
}
+ else if (argc<=2){
+ strcpy(pathtot,argv[1]);
+ }
else{
strcpy(pathtot,argv[1]);
+ strcpy(z,argv[2]);
+ printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
}
/*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
/*cygwin_split_path(pathtot,path,optionfile);
@@ -10829,8 +10882,6 @@ int main(int argc, char *argv[])
exit(70);
}
-
-
strcpy(filereso,"o");
strcat(filereso,fileresu);
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
@@ -10839,17 +10890,52 @@ int main(int argc, char *argv[])
fflush(ficlog);
goto end;
}
+ /*-------- Rewriting parameter file ----------*/
+ strcpy(rfileres,"r"); /* "Rparameterfile */
+ strcat(rfileres,optionfilefiname); /* Parameter file first name */
+ strcat(rfileres,"."); /* */
+ strcat(rfileres,optionfilext); /* Other files have txt extension */
+ if((ficres =fopen(rfileres,"w"))==NULL) {
+ printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+ fflush(ficlog);
+ goto end;
+ }
+ fprintf(ficres,"#IMaCh %s\n",version);
+
/* 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);
+ fputs(line,ficres);
fputs(line,ficlog);
continue;
}else
@@ -10870,6 +10956,7 @@ int main(int argc, char *argv[])
numlinepar++;
fputs(line,stdout);
fputs(line,ficparo);
+ fputs(line,ficres);
fputs(line,ficlog);
continue;
}else
@@ -10892,20 +10979,16 @@ int main(int argc, char *argv[])
numlinepar++;
fputs(line,stdout);
fputs(line,ficparo);
+ fputs(line,ficres);
fputs(line,ficlog);
continue;
}else
break;
}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
- if (num_filled == 0){
- printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
- fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
- model[0]='\0';
- goto end;
- } else if (num_filled != 1){
- printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
- fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+ if (num_filled != 1){
+ printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
+ fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
model[0]='\0';
goto end;
}
@@ -10927,11 +11010,11 @@ int main(int argc, char *argv[])
fflush(ficlog);
/* if(model[0]=='#'|| model[0]== '\0'){ */
if(model[0]=='#'){
- printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
- 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
- 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
+ printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
+ 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
+ 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
if(mle != -1){
- printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+ printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
exit(1);
}
}
@@ -11153,16 +11236,6 @@ Please run with mle=-1 to get a correct
fflush(ficlog);
- /*-------- Rewriting parameter file ----------*/
- strcpy(rfileres,"r"); /* "Rparameterfile */
- strcat(rfileres,optionfilefiname); /* Parameter file first name*/
- strcat(rfileres,"."); /* */
- strcat(rfileres,optionfilext); /* Other files have txt extension */
- if((ficres =fopen(rfileres,"w"))==NULL) {
- printf("Problem writing new parameter file: %s\n", rfileres);goto end;
- fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
- }
- fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */
/* Main data
@@ -12594,6 +12667,8 @@ Please run with mle=-1 to get a correct
fclose(ficlog);
/*------ End -----------*/
+
+/* Executes gnuplot */
printf("Before Current directory %s!\n",pathcd);
#ifdef WIN32