Diff for /imach/src/imach.c between versions 1.199 and 1.204

version 1.199, 2015/09/07 14:09:23 version 1.204, 2015/10/01 16:20:26
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.204  2015/10/01 16:20:26  brouard
     Summary: Some new graphs of contribution to likelihood
   
     Revision 1.203  2015/09/30 17:45:14  brouard
     Summary: looking at better estimation of the hessian
   
     Also a better criteria for convergence to the period prevalence And
     therefore adding the number of years needed to converge. (The
     prevalence in any alive state shold sum to one
   
     Revision 1.202  2015/09/22 19:45:16  brouard
     Summary: Adding some overall graph on contribution to likelihood. Might change
   
     Revision 1.201  2015/09/15 17:34:58  brouard
     Summary: 0.98r0
   
     - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
   
     Revision 1.200  2015/09/09 16:53:55  brouard
     Summary: Big bug thanks to Flavia
   
     Even model=1+age+V2. did not work anymore
   
   Revision 1.199  2015/09/07 14:09:23  brouard    Revision 1.199  2015/09/07 14:09:23  brouard
   Summary: 0.98q6 changing default small png format for graph to vectorized svg.    Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   
Line 633 Line 657
   
 /* #define DEBUG */  /* #define DEBUG */
 /* #define DEBUGBRENT */  /* #define DEBUGBRENT */
   /* #define DEBUGLINMIN */
   /* #define DEBUGHESS */
   #define DEBUGHESSIJ
   /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 #define POWELLF1F3 /* Skip test */  #define POWELLF1F3 /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
Line 724  typedef struct { Line 752  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 791  char command[FILENAMELENGTH]; Line 819  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char fileresu[FILENAMELENGTH]; /* fileres without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
Line 881  double  idx; Line 909  double  idx;
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Tage;  int *Tage;
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 int **codtab; /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
Line 1587  void linmin(double p[], double xi[], int Line 1615  void linmin(double p[], double xi[], int
   double xx,xmin,bx,ax;     double xx,xmin,bx,ax; 
   double fx,fb,fa;    double fx,fb,fa;
   
   double scale=10., axs, xxs, xxss; /* Scale added for infinity */  #ifdef LINMINORIGINAL
    #else
     double scale=10., axs, xxs; /* Scale added for infinity */
   #endif
     
   ncom=n;     ncom=n; 
   pcom=vector(1,n);     pcom=vector(1,n); 
   xicom=vector(1,n);     xicom=vector(1,n); 
   nrfunc=func;     nrfunc=func; 
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     pcom[j]=p[j];       pcom[j]=p[j]; 
     xicom[j]=xi[j];       xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
   }     } 
   
   /* axs=0.0; */  #ifdef LINMINORIGINAL
   /* xxss=1; /\* 1 and using scale *\/ */    xx=1.;
   xxs=1;  #else
   /* do{ */    axs=0.0;
     ax=0.;    xxs=1.;
     do{
     xx= xxs;      xx= xxs;
   #endif
       ax=0.;
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
Line 1611  void linmin(double p[], double xi[], int Line 1645  void linmin(double p[], double xi[], int
     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
   /*   if (fx != fx){ */  #ifdef LINMINORIGINAL
   /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */  #else
   /*    printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx); */      if (fx != fx){
   /*   } */          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
   /* }while(fx != fx); */          printf("|");
           fprintf(ficlog,"|");
   #ifdef DEBUGLINMIN
           printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
   #endif
       }
     }while(fx != fx);
   #endif
     
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
     fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
 #endif  #endif
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
Line 1631  void linmin(double p[], double xi[], int Line 1673  void linmin(double p[], double xi[], int
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("linmin end ");    printf("linmin end ");
     fprintf(ficlog,"linmin end ");
 #endif  #endif
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     /* printf(" before xi[%d]=%12.8f", j,xi[j]); */  #ifdef LINMINORIGINAL
     xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */      xi[j] *= xmin; 
     /* if(xxs <1.0) */  #else
     /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */  #ifdef DEBUGLINMIN
       if(xxs <1.0)
         printf(" before xi[%d]=%12.8f", j,xi[j]);
   #endif
       xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
   #ifdef DEBUGLINMIN
       if(xxs <1.0)
         printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
   #endif
   #endif
     p[j] += xi[j]; /* Parameters values are updated accordingly */      p[j] += xi[j]; /* Parameters values are updated accordingly */
   }     } 
   /* printf("\n"); */  
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
     printf("\n");
   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);      printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
     if(j % ncovmodel == 0)      fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0){
       printf("\n");        printf("\n");
         fprintf(ficlog,"\n");
       }
   }    }
   #else
 #endif  #endif
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
Line 1680  void powell(double p[], double **xi, int Line 1737  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
     rcurr_time = time(NULL);      rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret); /* From former iteration or initial value */      fp=(*fret); /* From former iteration or initial value */
     ibig=0;       ibig=0; 
Line 1724  void powell(double p[], double **xi, int Line 1781  void powell(double p[], double **xi, int
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
           printf("%d",i);fflush(stdout); /* print direction (parameter) i */        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                                     /* Outputs are fret(new point p) p is updated and xit rescaled */                                      /* Outputs are fret(new point p) p is updated and xit rescaled */
Line 1825  void powell(double p[], double **xi, int Line 1882  void powell(double p[], double **xi, int
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       t= t- del*SQR(fp-fptt);        t= t- del*SQR(fp-fptt);
 #endif  #endif
       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
 #ifdef DEBUG  #ifdef DEBUG
       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
Line 1840  void powell(double p[], double **xi, int Line 1897  void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
         printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);          printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);          fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       }         } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
Line 1850  void powell(double p[], double **xi, int Line 1907  void powell(double p[], double **xi, int
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
         printf("Before linmin in direction P%d-P0\n",n);          printf("Before linmin in direction P%d-P0\n",n);
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           if(j % ncovmodel == 0)            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0){
             printf("\n");              printf("\n");
               fprintf(ficlog,"\n");
             }
         }          }
 #endif  #endif
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           if(j % ncovmodel == 0)            fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             if(j % ncovmodel == 0){
             printf("\n");              printf("\n");
               fprintf(ficlog,"\n");
             }
         }          }
 #endif  #endif
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
Line 1890  void powell(double p[], double **xi, int Line 1953  void powell(double p[], double **xi, int
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached with precision ftolpl */
       
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=100 ; /* Max number of years to converge */
     int ncvloop=0;
       
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 1910  double **prevalim(double **prlim, int nl Line 1974  double **prevalim(double **prlim, int nl
   cov[1]=1.;    cov[1]=1.;
       
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       ncvloop++;
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */        /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
     for (k=1; k<=cptcovprod;k++) /* Useless */      for (k=1; k<=cptcovprod;k++) /* Useless */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 1942  double **prevalim(double **prlim, int nl Line 2011  double **prevalim(double **prlim, int nl
         sumnew=0;          sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         prlim[i][j]= newm[i][j]/(1-sumnew);          prlim[i][j]= newm[i][j]/(1-sumnew);
         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/  
         max=FMAX(max,prlim[i][j]);          max=FMAX(max,prlim[i][j]);
         min=FMIN(min,prlim[i][j]);          min=FMIN(min,prlim[i][j]);
           /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */
       }        }
       maxmin=max-min;        maxmin=(max-min)/(max+min)*2;
       maxmax=FMAX(maxmax,maxmin);        maxmax=FMAX(maxmax,maxmin);
     } /* j loop */      } /* j loop */
       *ncvyear= (int)age- (int)agefin;
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
         /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* age loop */
     printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
   Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   return prlim; /* should not reach here */    return prlim; /* should not reach here */
 }  }
   
Line 2096  double ***hpxij(double ***po, int nhstep Line 2171  double ***hpxij(double ***po, int nhstep
       if(nagesqr==1)        if(nagesqr==1)
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=cptcovn;k++) 
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
           /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
           /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
Line 2525  double funcone( double *x) Line 2603  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\          fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],                  num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
Line 2559  void likelione(FILE *ficres,double p[], Line 2637  void likelione(FILE *ficres,double p[],
   int k;    int k;
   
   if(*globpri !=0){ /* Just counts and sums, no printings */    if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ilk");       strcpy(fileresilk,"ILK_"); 
     strcat(fileresilk,fileres);      strcat(fileresilk,fileresu);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }      }
     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");      fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
Line 2576  void likelione(FILE *ficres,double p[], Line 2654  void likelione(FILE *ficres,double p[],
   *fretone=(*funcone)(p);    *fretone=(*funcone)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle >= 1. You should at least run with mle >= 1 and starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fflush(fichtm);       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
      fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
   
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
   
       }
   }     } 
   return;    return;
 }  }
Line 2609  void mlikeli(FILE *ficres,double p[], in Line 2697  void mlikeli(FILE *ficres,double p[], in
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(filerespow,"pow");     strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);    strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", filerespow);      printf("Problem with resultfile: %s\n", filerespow);
Line 2652  void mlikeli(FILE *ficres,double p[], in Line 2740  void mlikeli(FILE *ficres,double p[], in
 #endif  #endif
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  /**** Computes Hessian and covariance matrix ***/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    /* double **hess; */
   int i, j;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);    double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double gompertz(double p[]);    double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    /* hess=matrix(1,npar,1,npar); */
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d-",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d-",i);fflush(ficlog);
         
      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           
Line 2688  void hesscov(double **matcov, double p[] Line 2776  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {      for (j=1;j<=npar;j++)  {
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d-%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j,func,npar);          hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
                   
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
Line 2724  void hesscov(double **matcov, double p[] Line 2812  void hesscov(double **matcov, double p[]
   fprintf(ficlog,"\n#Hessian matrix#\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=npar;i++) {     for (i=1;i<=npar;i++) { 
     for (j=1;j<=npar;j++) {       for (j=1;j<=npar;j++) { 
       printf("%.3e ",hess[i][j]);        printf("%.6e ",hess[i][j]);
       fprintf(ficlog,"%.3e ",hess[i][j]);        fprintf(ficlog,"%.6e ",hess[i][j]);
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   
     /* printf("\n#Covariance matrix#\n"); */
     /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
     /* for (i=1;i<=npar;i++) {  */
     /*   for (j=1;j<=npar;j++) {  */
     /*     printf("%.6e ",matcov[i][j]); */
     /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
   /* Recompute Inverse */    /* Recompute Inverse */
   for (i=1;i<=npar;i++)    /* for (i=1;i<=npar;i++) */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
   ludcmp(a,npar,indx,&pd);    /* ludcmp(a,npar,indx,&pd); */
   
     /*  printf("\n#Hessian matrix recomputed#\n"); */
   
     /* for (j=1;j<=npar;j++) { */
     /*   for (i=1;i<=npar;i++) x[i]=0; */
     /*   x[j]=1; */
     /*   lubksb(a,npar,indx,x); */
     /*   for (i=1;i<=npar;i++){  */
     /*     y[i][j]=x[i]; */
     /*     printf("%.3e ",y[i][j]); */
     /*     fprintf(ficlog,"%.3e ",y[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
     /* Verifying the inverse matrix */
   #ifdef DEBUGHESS
     y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
   
   /*  printf("\n#Hessian matrix recomputed#\n");     printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
      fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
   
   for (j=1;j<=npar;j++) {    for (j=1;j<=npar;j++) {
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){       for (i=1;i<=npar;i++){ 
       y[i][j]=x[i];        printf("%.2f ",y[i][j]);
       printf("%.3e ",y[i][j]);        fprintf(ficlog,"%.2f ",y[i][j]);
       fprintf(ficlog,"%.3e ",y[i][j]);  
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   */  #endif
   
   free_matrix(a,1,npar,1,npar);    free_matrix(a,1,npar,1,npar);
   free_matrix(y,1,npar,1,npar);    free_matrix(y,1,npar,1,npar);
   free_vector(x,1,npar);    free_vector(x,1,npar);
   free_ivector(indx,1,npar);    free_ivector(indx,1,npar);
   free_matrix(hess,1,npar,1,npar);    /* free_matrix(hess,1,npar,1,npar); */
   
   
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  { /* Around values of x, computes the function func and returns the scales delti and hessian */
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2, res, fx;
   double p2[MAXPARM+1]; /* identical to x */    double p2[MAXPARM+1]; /* identical to x */
   double res;  
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;  
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
   
Line 2786  double hessii(double x[], double delta, Line 2899  double hessii(double x[], double delta,
       p2[theta]=x[theta]-delt;        p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;        k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
               
 #ifdef DEBUGHESS  #ifdef DEBUGHESSII
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 #endif  #endif
Line 2802  double hessii(double x[], double delta, Line 2915  double hessii(double x[], double delta,
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
       }        }
     }      } /* End loop k */
   }    }
   delti[theta]=delts;    delti[theta]=delts;
   return res;     return res; 
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k, kmax=1;
     double v1, v2, cv12, lc1, lc2;
     
   fx=func(x);    fx=func(x);
   for (k=1; k<=2; k++) {    for (k=1; k<=kmax; k=k+10) {
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1;i<=npar;i++) p2[i]=x[i];
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k1=func(p2)-fx;      k1=func(p2)-fx;
       
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k2=func(p2)-fx;      k2=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k3=func(p2)-fx;      k3=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k4=func(p2)-fx;      k4=func(p2)-fx;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
 #ifdef DEBUG      if(k1*k2*k3*k4 <0.){
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        kmax=kmax+10;
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        if(kmax >=10){
         printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
         fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }
       }
   #ifdef DEBUGHESSIJ
       v1=hess[thetai][thetai];
       v2=hess[thetaj][thetaj];
       cv12=res;
       /* Computing eigen value of Hessian matrix */
       lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       if ((lc2 <0) || (lc1 <0) ){
         printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }
 #endif  #endif
   }    }
   return res;    return res;
 }  }
   
       /* Not done yet: Was supposed to fix if not exactly at the maximum */
   /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
   /* { */
   /*   int i; */
   /*   int l=1, lmax=20; */
   /*   double k1,k2,k3,k4,res,fx; */
   /*   double p2[MAXPARM+1]; */
   /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
   /*   int k=0,kmax=10; */
   /*   double l1; */
     
   /*   fx=func(x); */
   /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
   /*     l1=pow(10,l); */
   /*     delts=delt; */
   /*     for(k=1 ; k <kmax; k=k+1){ */
   /*       delt = delti*(l1*k); */
   /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k1=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k2=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k3=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k4=func(p2)-fx; */
   /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
   /* #ifdef DEBUGHESSIJ */
   /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /* #endif */
   /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
   /*      k=kmax; */
   /*       } */
   /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
   /*      k=kmax; l=lmax*10; */
   /*       } */
   /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
   /*      delts=delt; */
   /*       } */
   /*     } /\* End loop k *\/ */
   /*   } */
   /*   delti[theta]=delts; */
   /*   return res;  */
   /* } */
   
   
 /************** Inverse of matrix **************/  /************** Inverse of matrix **************/
 void ludcmp(double **a, int n, int *indx, double *d)   void ludcmp(double **a, int n, int *indx, double *d) 
 {   { 
Line 2936  void  freqsummary(char fileres[], int ia Line 3123  void  freqsummary(char fileres[], int ia
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileresp,"p");    strcpy(fileresp,"P_");
   strcat(fileresp,fileres);    strcat(fileresp,fileresu);
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
Line 3776  void cvevsij(double ***eij, double x[], Line 3963  void cvevsij(double ***eij, double x[],
 }  }
   
 /************ Variance ******************/  /************ 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])   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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {  {
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
Line 3805  void varevsij(char optionfilefiname[], d Line 3992  void varevsij(char optionfilefiname[], d
   
   if(popbased==1){    if(popbased==1){
     if(mobilav!=0)      if(mobilav!=0)
       strcpy(digitp,"-populbased-mobilav-");        strcpy(digitp,"-POPULBASED-MOBILAV_");
     else strcpy(digitp,"-populbased-nomobil-");      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
   }    }
   else     else 
     strcpy(digitp,"-stablbased-");      strcpy(digitp,"-STABLBASED_");
   
   if (mobilav!=0) {    if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 3819  void varevsij(char optionfilefiname[], d Line 4006  void varevsij(char optionfilefiname[], d
     }      }
   }    }
   
   strcpy(fileresprobmorprev,"prmorprev");     strcpy(fileresprobmorprev,"PRMORPREV-"); 
   sprintf(digit,"%-d",ij);    sprintf(digit,"%-d",ij);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcat(fileresprobmorprev,digit); /* Tvar to be done */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   strcat(fileresprobmorprev,fileres);    strcat(fileresprobmorprev,fileresu);
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobmorprev);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
Line 3842  void varevsij(char optionfilefiname[], d Line 4029  void varevsij(char optionfilefiname[], d
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");    fprintf(ficgp,"\n# Routine varevsij");
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/    fprintf(ficgp,"\nunset title \n");
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */  /*   } */
Line 3901  void varevsij(char optionfilefiname[], d Line 4089  void varevsij(char optionfilefiname[], d
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
   
       if (popbased==1) {        if (popbased==1) {
         if(mobilav ==0){          if(mobilav ==0){
Line 3932  void varevsij(char optionfilefiname[], d Line 4120  void varevsij(char optionfilefiname[], d
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
     
       if (popbased==1) {        if (popbased==1) {
         if(mobilav ==0){          if(mobilav ==0){
Line 4007  void varevsij(char optionfilefiname[], d Line 4195  void varevsij(char optionfilefiname[], d
     /* end ppptj */      /* end ppptj */
     /*  x centered again */      /*  x centered again */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
     
     if (popbased==1) {      if (popbased==1) {
       if(mobilav ==0){        if(mobilav ==0){
Line 4058  void varevsij(char optionfilefiname[], d Line 4246  void varevsij(char optionfilefiname[], d
   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
Line 4065  void varevsij(char optionfilefiname[], d Line 4254  void varevsij(char optionfilefiname[], d
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
 */  */
 /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
   fprintf(ficgp,"\nset out \"%s%s.svg\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);    free_matrix(doldm,1,nlstate,1,nlstate);
Line 4084  void varevsij(char optionfilefiname[], d Line 4273  void varevsij(char optionfilefiname[], d
 }  /* end varevsij */  }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyear, int ij, char strstart[])
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
Line 4123  void varprevlim(char fileres[], double * Line 4312  void varprevlim(char fileres[], double *
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
           
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
   
Line 4187  void varprob(char optionfilefiname[], do Line 4376  void varprob(char optionfilefiname[], do
   char fileresprobcor[FILENAMELENGTH];    char fileresprobcor[FILENAMELENGTH];
   double ***varpij;    double ***varpij;
   
   strcpy(fileresprob,"prob");     strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);    strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);      printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   strcpy(fileresprobcov,"probcov");     strcpy(fileresprobcov,"PROBCOV_"); 
   strcat(fileresprobcov,fileres);    strcat(fileresprobcov,fileresu);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);      printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }    }
   strcpy(fileresprobcor,"probcor");     strcpy(fileresprobcor,"PROBCOR_"); 
   strcat(fileresprobcor,fileres);    strcat(fileresprobcor,fileresu);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);      printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
Line 4242  void varprob(char optionfilefiname[], do Line 4431  void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 4294  To be simple, these graphs help to under Line 4483  To be simple, these graphs help to under
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= age*age;            cov[3]= age*age;
         for (k=1; k<=cptcovn;k++) {          for (k=1; k<=cptcovn;k++) {
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
             /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                          * 1  1 1 1 1                                                           * 1  1 1 1 1
                                                          * 2  2 1 1 1                                                           * 2  2 1 1 1
                                                          * 3  1 2 1 1                                                           * 3  1 2 1 1
Line 4302  To be simple, these graphs help to under Line 4492  To be simple, these graphs help to under
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         }          }
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         for (k=1; k<=cptcovprod;k++)          for (k=1; k<=cptcovprod;k++)
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                   
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
Line 4452  To be simple, these graphs help to under Line 4642  To be simple, these graphs help to under
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   if(first==1){                    if(first==1){
                     first=0;                      first=0;
                       fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                     fprintf(ficgp,"\nset parametric;unset label");                      fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter svg size 640, 480");                      fprintf(ficgp,"\nset ter svg size 640, 480");
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s%d%1d%1d-%1d%1d.svg\">\   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
 %s%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                      fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                      fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      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,"\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",\                      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",\
Line 4479  To be simple, these graphs help to under Line 4670  To be simple, these graphs help to under
                   }/* if first */                    }/* if first */
                 } /* age mod 5 */                  } /* age mod 5 */
               } /* end loop age */                } /* end loop age */
               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
               first=1;                first=1;
             } /*l12 */              } /*l12 */
           } /* k12 */            } /* k12 */
Line 4501  To be simple, these graphs help to under Line 4692  To be simple, these graphs help to under
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int estepm ,\                    int popforecast, int estepm ,\
Line 4514  void printinghtml(char fileres[], char t Line 4705  void printinghtml(char fileres[], char t
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n",     <a href=\"%s\">%s</a> <br>\n",
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));             estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Population projections by age and states: \   - Population projections by age and states: \
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
Line 4546  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4737  fprintf(fichtm," \n<ul><li><b>Graphs</b>
        }         }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model, for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
   <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.svg\">%s%d_1.svg</a><br> \       fprintf(fichtm,"<br>\n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
 <img src=\"%s%d_1.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.svg\">%s%d_2.svg</a><br> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
 <img src=\"%s%d_2.svg\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);    incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
        /* Period (stable) prevalence in each health state */  divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
        for(cpt=1; cpt<=nlstate;cpt++){  <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
          fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \       /* Survival functions (period) in state j */
 <img src=\"%s%d_%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);       for(cpt=1; cpt<=nlstate;cpt++){
        }         fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.\
    <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
        }
        /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s%d%d.svg\">%s%d%d.svg</a> <br> \
 <img src=\"%s%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }       }
    /* } /\* end i1 *\/ */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
Line 4569  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4776  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  fprintf(fichtm,"\   fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
 But because parameters are usually highly correlated (a higher incidence of disability \  But because parameters are usually highly correlated (a higher incidence of disability \
 and a higher incidence of recovery can give very close observed transition) it might \  and a higher incidence of recovery can give very close observed transition) it might \
 be very useful to look not only at linear confidence intervals estimated from the \  be very useful to look not only at linear confidence intervals estimated from the \
Line 4579  covariance matrix of the one-step probab Line 4786  covariance matrix of the one-step probab
 See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));           subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));           subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));           subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));           estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));           estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));           subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 4630  See page 'Matrix of variance-covariance Line 4837  See page 'Matrix of variance-covariance
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\  prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.svg <br>\
 <img src=\"%s%d_%d.svg\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences: %s%d.svg<br>\   observed and cahotic prevalences: %s_%d.svg<br>\
 <img src=\"%s%d.svg\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    /* } /\* end i1 *\/ */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
Line 4645  true period expectancies (those weighted Line 4852  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;    int ng=0;
     int vpopbased;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 4660  void printinggnuplot(char fileres[], cha Line 4868  void printinggnuplot(char fileres[], cha
     /*#endif */      /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* 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");
       fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
       /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
       fprintf(ficgp,"\nset ter png size 640, 480");
   /* nice for mle=4 plot by number of matrix products.
      replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
   /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
       /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
       fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
       fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
       fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
       fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
       for (i=1; i<= nlstate ; i ++) {
         fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
         fprintf(ficgp,"unset log;\n plot  \"%s\"",subdirf(fileresilk));
         fprintf(ficgp,"  u  2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable \\\n",i,1,i,1);
         for (j=2; j<= nlstate+ndeath ; j ++) {
           fprintf(ficgp,", \"\" u  2:($4 == %d && $5==%d ? $9 : 1/0):5 t \"p%d%d\" with points lc variable ",i,j,i,j);
         }
         fprintf(ficgp,";\nset out; unset ylabel;\n"); 
       }
       /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */              
       /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
       /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
       fprintf(ficgp,"\nset out;unset log\n");
       /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");    fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */      for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
      fprintf(ficgp,"\n#set out \"v%s%d_%d.svg\" \n",optionfilefiname,cpt,k1);       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
      fprintf(ficgp,"set xlabel \"Age\" \n\       fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n\  set ylabel \"Probability\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else        fprintf(ficgp," %%*lf (%%*lf)");         else        fprintf(ficgp," %%*lf (%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
    }       fprintf(ficgp,"\nset out \n");
   }      } /* k1 */
     } /* cpt */
   /*2 eme*/    /*2 eme*/
   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");    fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"%s%d.svg\" \n",subdirf2(optionfilefiname,"e"),k1);      fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);      for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             if(vpopbased==0)
     for (i=1; i<= nlstate+1 ; i ++) {          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
       k=2*i;        else
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);          fprintf(ficgp,"\nreplot ");
       for (j=1; j<= nlstate+1 ; j ++) {        for (i=1; i<= nlstate+1 ; i ++) {
         if (j==i) fprintf(ficgp," %%lf (%%lf)");          k=2*i;
         else fprintf(ficgp," %%*lf (%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            else fprintf(ficgp," %%*lf (%%*lf)");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);          }   
       for (j=1; j<= nlstate+1 ; j ++) {          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
         if (j==i) fprintf(ficgp," %%lf (%%lf)");          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
         else fprintf(ficgp," %%*lf (%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficgp,"\" t\"\" w l lt 0,");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);            else fprintf(ficgp," %%*lf (%%*lf)");
       for (j=1; j<= nlstate+1 ; j ++) {          }   
         if (j==i) fprintf(ficgp," %%lf (%%lf)");          fprintf(ficgp,"\" t\"\" w l lt 0,");
         else fprintf(ficgp," %%*lf (%%*lf)");          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
       }             for (j=1; j<= nlstate+1 ; j ++) {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
       else fprintf(ficgp,"\" t\"\" w l lt 0,");            else fprintf(ficgp," %%*lf (%%*lf)");
     }          }   
   }          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
             else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         } /* state */
       } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
     } /* k1 */
   /*3eme*/    /*3eme*/
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.svg\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       fprintf(ficgp,"set ter svg size 640, 480\n\        fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 4739  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4981  plot [%.f:%.f] \"%s\" every :::%d::%d u
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                   
       }         } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
   /* CV preval stable (period) */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;        k=3;
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate+ndeath ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         k=3;
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           if(j==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(cpt-1) +j;
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
           /* for (i=2; i<= nlstate+ndeath ; i ++) */
           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficgp,", '' ");
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           l=(nlstate+ndeath)*(cpt-1) +j;
           if(j < nlstate)
             fprintf(ficgp,"$%d +",k+l);
           else
             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
   
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
       fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n\
 unset log y\n\  unset log y\n\
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1)          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else          else
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1;
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=1; j<= (nlstate-1) ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
     
   /* proba elementaires */    /* proba elementaires */
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
Line 4790  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 5091  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
   
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
Line 4804  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 5105  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
      fprintf(ficgp,"# ng=%d\n",ng);       fprintf(ficgp,"# ng=%d\n",ng);
      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);       fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"#    jk=%d\n",jk);         fprintf(ficgp,"#    jk=%d\n",jk);
        fprintf(ficgp,"\nset out \"%s%d_%d.svg\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);          fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
        if (ng==2)         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 */
            fprintf(ficgp,"\nunset log y");
          }else if (ng==2){
            fprintf(ficgp,"\nset ylabel \"Probability\"\n");
            fprintf(ficgp,"\nset log y");
          }else if (ng==3){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else           fprintf(ficgp,"\nset log y");
          fprintf(ficgp,"\nset title \"Probability\"\n");         }else
        fprintf(ficgp,"\nset ter svg size 640, 480\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);           fprintf(ficgp,"\nunset title ");
          fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;         i=1;
        for(k2=1; k2<=nlstate; k2++) {         for(k2=1; k2<=nlstate; k2++) {
          k3=i;           k3=i;
          for(k=1; k<=(nlstate+ndeath); k++) {           for(k=1; k<=(nlstate+ndeath); k++) {
            if (k != k2){             if (k != k2){
              if(ng==2)               switch( ng) {
                case 1:
                if(nagesqr==0)                 if(nagesqr==0)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                else /* nagesqr =1 */                 else /* nagesqr =1 */
                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);                   fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
              else                 break;
                case 2: /* ng=2 */
                if(nagesqr==0)                 if(nagesqr==0)
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                else /* nagesqr =1 */                 else /* nagesqr =1 */
                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);                     fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                  break;
                case 3:
                  if(nagesqr==0)
                    fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                  else /* nagesqr =1 */
                    fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                  break;
                }
              ij=1;/* To be checked else nbcode[0][0] wrong */               ij=1;/* To be checked else nbcode[0][0] wrong */
              for(j=3; j <=ncovmodel-nagesqr; j++) {               for(j=3; j <=ncovmodel-nagesqr; j++) {
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                if(ij <=cptcovage) { /* Bug valgrind */                 if(ij <=cptcovage) { /* Bug valgrind */
                  if((j-2)==Tage[ij]) { /* Bug valgrind */                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);                     fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                    ij++;                     ij++;
                  }                   }
                }                 }
                else                 else
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
              }               }
              fprintf(ficgp,")/(1");               if(ng != 1){
                  fprintf(ficgp,")/(1");
                             
              for(k1=1; k1 <=nlstate; k1++){                  for(k1=1; k1 <=nlstate; k1++){ 
                if(nagesqr==0)                   if(nagesqr==0)
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                     fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                else /* nagesqr =1 */                   else /* nagesqr =1 */
                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                     fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                      
                ij=1;                   ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){                   for(j=3; j <=ncovmodel-nagesqr; j++){
                  if(ij <=cptcovage) { /* Bug valgrind */                     if(ij <=cptcovage) { /* Bug valgrind */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */                       if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);                         fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      ij++;                         /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                          ij++;
                        }
                    }                     }
                      else
                        fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                  }                   }
                  else                   fprintf(ficgp,")");
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);  
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
                  if(ng ==2)
                    fprintf(ficgp," t \"p%d%d\" ", k2,k);
                  else /* ng= 3 */
                    fprintf(ficgp," t \"i%d%d\" ", k2,k);
                }else{ /* end ng <> 1 */
                  fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
              }               }
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
              i=i+ncovmodel;               i=i+ncovmodel;
            }             }
          } /* end k */           } /* end k */
        } /* end k2 */         } /* end k2 */
          fprintf(ficgp,"\n set out\n");
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
  /* avoid: */   /* avoid: */
Line 4936  void prevforecast(char fileres[], double Line 5266  void prevforecast(char fileres[], double
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
   strcpy(fileresf,"f");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileresu);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
Line 5060  void populforecast(char fileres[], doubl Line 5390  void populforecast(char fileres[], doubl
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"POP_"); 
   strcat(filerespop,fileres);    strcat(filerespop,fileresu);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", filerespop);      printf("Problem with forecast resultfile: %s\n", filerespop);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
Line 5414  double gompertz_f(const gsl_vector *v, v Line 5744  double gompertz_f(const gsl_vector *v, v
 #endif  #endif
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,  double p[],double **matcov,double agemortsup){                    int imx,  double p[],double **matcov,double agemortsup){
   int i,k;    int i,k;
Line 5438  fprintf(fichtm,"<ul><li><h4>Life table</ Line 5768  fprintf(fichtm,"<ul><li><h4>Life table</
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   
Line 6145  void syscompilerinfo(int logged) Line 6475  void syscompilerinfo(int logged)
   
  }   }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    int i, j, k, i1 ;
   double ftolpl = 1.e-10;    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
     double tot;
   
     strcpy(filerespl,"pl");    strcpy(filerespl,"PL_");
     strcat(filerespl,fileres);    strcat(filerespl,fileresu);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     }    }
     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
     pstamp(ficrespl);    pstamp(ficrespl);
     fprintf(ficrespl,"# Period (stable) prevalence \n");    fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
       
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */      /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
Line 6179  int prevalence_limit(double *p, double * Line 6510  int prevalence_limit(double *p, double *
         k=k+1;          k=k+1;
         /* to clean */          /* to clean */
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));          //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"\n#******");          fprintf(ficrespl,"#******");
         printf("\n#******");          printf("#******");
         fprintf(ficlog,"\n#******");          fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 6193  int prevalence_limit(double *p, double * Line 6524  int prevalence_limit(double *p, double *
   
         fprintf(ficrespl,"#Age ");          fprintf(ficrespl,"#Age ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }          }
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
         fprintf(ficrespl,"\n");          fprintf(ficrespl,"Total Years_to_converge\n");
                   
         for (age=agebase; age<=agelim; age++){          for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
           fprintf(ficrespl,"%.0f ",age );            fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)            for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);              fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           for(i=1; i<=nlstate;i++)            tot=0.;
             for(i=1; i<=nlstate;i++){
               tot +=  prlim[i][i];
             fprintf(ficrespl," %.5f", prlim[i][i]);              fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");            }
             fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
         } /* Age */          } /* Age */
         /* was end of cptcod */          /* was end of cptcod */
     } /* cptcov */      } /* cptcov */
Line 6225  int hPijx(double *p, int bage, int fage) Line 6559  int hPijx(double *p, int bage, int fage)
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
   
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);      strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {      if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;        printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;        fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
Line 6299  int main(int argc, char *argv[]) Line 6633  int main(int argc, char *argv[])
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
     int ncvyearnp=0;
     int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int num_filled;    int num_filled;
Line 6347  int main(int argc, char *argv[]) Line 6682  int main(int argc, char *argv[])
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double  *p;
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
Line 6486  int main(int argc, char *argv[]) Line 6822  int main(int argc, char *argv[])
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
   /* Main ---------arguments file --------*/    /* Main ---------arguments file --------*/
   
Line 6501  int main(int argc, char *argv[]) Line 6839  int main(int argc, char *argv[])
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
Line 6551  int main(int argc, char *argv[]) Line 6889  int main(int argc, char *argv[])
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);      printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
   }    }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
   /* Third parameter line */    /* Third parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
Line 6564  int main(int argc, char *argv[]) Line 6903  int main(int argc, char *argv[])
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled != 1) {      if (num_filled == 0)
               model[0]='\0';
       else if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);        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);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
       model[0]='\0';        model[0]='\0';
Line 6575  int main(int argc, char *argv[]) Line 6916  int main(int argc, char *argv[])
       if (model[0]=='+'){        if (model[0]=='+'){
         for(i=1; i<=strlen(model);i++)          for(i=1; i<=strlen(model);i++)
           modeltemp[i-1]=model[i];            modeltemp[i-1]=model[i];
           strcpy(model,modeltemp); 
       }        }
       strcpy(model,modeltemp);   
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
       printf("model=1+age+%s\n",model);fflush(stdout);
   }    }
   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
   /* numlinepar=numlinepar+3; /\* In general *\/ */    /* numlinepar=numlinepar+3; /\* In general *\/ */
   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
   if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     model[strlen(model)-1]='\0';    fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);  
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);  
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
Line 6651  int main(int argc, char *argv[]) Line 6991  int main(int argc, char *argv[])
     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
   }    }
   else{    else{
     /* Read guessed parameters */      /* Read guessed parameters */
Line 6759  run imach with mle=-1 to get a correct t Line 7100  run imach with mle=-1 to get a correct t
     ungetc(c,ficpar);      ungetc(c,ficpar);
       
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;        for(j=1; j <=npar; j++) matcov[i][j]=0.;
               
Line 6810  Please run with mle=-1 to get a correct Line 7152  Please run with mle=-1 to get a correct
     strcat(rfileres,".");    /* */      strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */      strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {      if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
Line 6921  Please run with mle=-1 to get a correct Line 7263  Please run with mle=-1 to get a correct
      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */    /* 1 to ncodemax[j] is the maximum value of this jth covariate */
   
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    h=0;
Line 6954  Please run with mle=-1 to get a correct Line 7296  Please run with mle=-1 to get a correct
            *    15 i=8 1     2     2     2             *    15 i=8 1     2     2     2
            *    16     2     2     2     2             *    16     2     2     2     2
            */             */
   for(h=1; h <=100 ;h++){     /* /\* for(h=1; h <=100 ;h++){  *\/ */
     /* printf("h=%2d ", h); */    /*   /\* printf("h=%2d ", h); *\/ */
      for(k=1; k <=10; k++){    /*    /\* for(k=1; k <=10; k++){ *\/ */
        /* printf("k=%d %d ",k,codtabm(h,k)); */    /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
        codtab[h][k]=codtabm(h,k);    /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
      }    /*    /\* } *\/ */
      /* printf("\n"); */    /*    /\* printf("\n"); *\/ */
   }    /* } */
   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */    /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */    /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */    /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
Line 6994  Please run with mle=-1 to get a correct Line 7336  Please run with mle=-1 to get a correct
   /* Initialisation of ----------- gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-MORT_");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
   else{    else{
     fprintf(ficgp,"\n# %s\n", version);       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
     fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
     //fprintf(ficgp,"set missing 'NaNq'\n");      //fprintf(ficgp,"set missing 'NaNq'\n");
     fprintf(ficgp,"set datafile missing 'NaNq'\n");      fprintf(ficgp,"set datafile missing 'NaNq'\n");
Line 7013  Please run with mle=-1 to get a correct Line 7355  Please run with mle=-1 to get a correct
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
     strcat(optionfilehtm,"-mort");      strcat(optionfilehtm,"-MORT_");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm);      printf("Problem with %s \n",optionfilehtm);
Line 7028  Please run with mle=-1 to get a correct Line 7370  Please run with mle=-1 to get a correct
   else{    else{
   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br>  \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
Line 7129  Interval (in months) between two waves: Line 7473  Interval (in months) between two waves:
 #else  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif  #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"POW-MORT_"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileresu);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
Line 7226  Interval (in months) between two waves: Line 7570  Interval (in months) between two waves:
 #endif    #endif  
     fclose(ficrespow);      fclose(ficrespow);
           
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
     for(i=1; i <=NDIM; i++)      for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)        for(j=i+1;j<=NDIM;j++)
         matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
           
     printf("\nCovariance matrix\n ");      printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
     for(i=1; i <=NDIM; i++) {      for(i=1; i <=NDIM; i++) {
       for(j=1;j<=NDIM;j++){         for(j=1;j<=NDIM;j++){ 
         printf("%f ",matcov[i][j]);          printf("%f ",matcov[i][j]);
           fprintf(ficlog,"%f ",matcov[i][j]);
       }        }
       printf("\n ");        printf("\n ");  fprintf(ficlog,"\n ");
     }      }
           
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
Line 7284  Please run with mle=-1 to get a correct Line 7630  Please run with mle=-1 to get a correct
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }else
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);        printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \      printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
Line 7300  Please run with mle=-1 to get a correct Line 7646  Please run with mle=-1 to get a correct
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
   /* Standard maximisation */    /* Standard maximisation */
   else{ /* For mle >=1 */    else{ /* For mle !=- 3 */
     globpr=0;/* debug */      globpr=0;/* debug */
     /* Computes likelihood for initial parameters */      /* Computes likelihood for initial parameters */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
Line 7343  Please run with mle=-1 to get a correct Line 7689  Please run with mle=-1 to get a correct
         }          }
       }        }
     }      }
     if(mle!=0){      if(mle != 0){
       /* Computing hessian and covariance matrix */        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);        hesscov(matcov, hess, p, npar, delti, ftolhess, func);
     }        printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
     printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
     fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        for(i=1,jk=1; i <=nlstate; i++){
     for(i=1,jk=1; i <=nlstate; i++){          for(k=1; k <=(nlstate+ndeath); k++){
       for(k=1; k <=(nlstate+ndeath); k++){            if (k != i) {
         if (k != i) {              printf("%d%d ",i,k);
           printf("%d%d ",i,k);              fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);              for(j=1; j <=ncovmodel; j++){
           for(j=1; j <=ncovmodel; j++){                printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
             printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
             fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                jk++; 
             jk++;               }
               printf("\n");
               fprintf(ficlog,"\n");
           }            }
           printf("\n");  
           fprintf(ficlog,"\n");  
         }          }
       }        }
     }      } /* end of hesscov and Wald tests */
   
       /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 7389  Please run with mle=-1 to get a correct Line 7736  Please run with mle=-1 to get a correct
     }      }
           
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)      if(mle >= 1) /* To big for the screen */
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     /* # 121 Var(a12)\n\ */      /* # 121 Var(a12)\n\ */
Line 7452  Please run with mle=-1 to get a correct Line 7799  Please run with mle=-1 to get a correct
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{                        }else{
                         if(mle>=1)                          if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]);                             printf(" %.7e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]);                           fprintf(ficlog," %.7e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]);                           fprintf(ficres," %.7e",matcov[jj][ll]); 
                       }                        }
                     }                      }
                   }                    }
Line 7555  Please run with mle=-1 to get a correct Line 7902  Please run with mle=-1 to get a correct
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }else
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
           
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\                   model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                   jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
               
Line 7582  Please run with mle=-1 to get a correct Line 7929  Please run with mle=-1 to get a correct
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
     prevalence_limit(p, prlim,  ageminpar, agemaxpar);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  #ifdef FREEEXIT2
Line 7609  Please run with mle=-1 to get a correct Line 7956  Please run with mle=-1 to get a correct
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
       /*      }  */        /*      }  */
       /*      else{ */        /*      else{ */
Line 7639  Please run with mle=-1 to get a correct Line 7986  Please run with mle=-1 to get a correct
   
     /*---------- Health expectancies, no variances ------------*/      /*---------- Health expectancies, no variances ------------*/
   
     strcpy(filerese,"e");      strcpy(filerese,"E_");
     strcat(filerese,fileres);      strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
Line 7653  Please run with mle=-1 to get a correct Line 8000  Please run with mle=-1 to get a correct
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }          }
         fprintf(ficreseij,"******\n");          fprintf(ficreseij,"******\n");
   
Line 7670  Please run with mle=-1 to get a correct Line 8017  Please run with mle=-1 to get a correct
     /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
   
   
     strcpy(filerest,"t");      strcpy(filerest,"T_");
     strcat(filerest,fileres);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
Line 7680  Please run with mle=-1 to get a correct Line 8027  Please run with mle=-1 to get a correct
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
     strcpy(fileresstde,"stde");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileres);      strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
Line 7689  Please run with mle=-1 to get a correct Line 8036  Please run with mle=-1 to get a correct
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"cve");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileres);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
Line 7698  Please run with mle=-1 to get a correct Line 8045  Please run with mle=-1 to get a correct
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"v");      strcpy(fileresv,"V_");
     strcat(fileresv,fileres);      strcat(fileresv,fileresu);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
Line 7713  Please run with mle=-1 to get a correct Line 8060  Please run with mle=-1 to get a correct
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");          fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
   
         fprintf(ficresstdeij,"\n#****** ");          fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");          fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }          }
         fprintf(ficresstdeij,"******\n");          fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");          fprintf(ficrescveij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");          fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");          fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
Line 7744  Please run with mle=-1 to get a correct Line 8091  Please run with mle=-1 to get a correct
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms; /* ZZ Segmentation fault */            oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           cptcod= 0; /* To be deleted */            cptcod= 0; /* To be deleted */
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */            varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");            fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           if(vpopbased==1)            if(vpopbased==1)
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);              fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
           else            else
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");              fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
           fprintf(ficrest,"# Age e.. (std) ");            fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */            /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
           epj=vector(1,nlstate+1);            epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){            for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); /*ZZ Is it the correct prevalim */              prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
             if (vpopbased==1) {              if (vpopbased==1) {
               if(mobilav ==0){                if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)                  for(i=1; i<=nlstate;i++)
Line 7767  Please run with mle=-1 to get a correct Line 8114  Please run with mle=-1 to get a correct
               }                }
             }              }
                   
             fprintf(ficrest," %4.0f",age);              fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
             /* printf(" age %4.0f ",age); */              /* printf(" age %4.0f ",age); */
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {                for(i=1, epj[j]=0.;i <=nlstate;i++) {
Line 7809  Please run with mle=-1 to get a correct Line 8156  Please run with mle=-1 to get a correct
       
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
   
     strcpy(fileresvpl,"vpl");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileres);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
Line 7823  Please run with mle=-1 to get a correct Line 8170  Please run with mle=-1 to get a correct
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");          fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvpl,"******\n");          fprintf(ficresvpl,"******\n");
               
         varpl=matrix(1,nlstate,(int) bage, (int) fage);          varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
Line 7847  Please run with mle=-1 to get a correct Line 8194  Please run with mle=-1 to get a correct
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);      free_matrix(matcov,1,npar,1,npar);
       free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/      /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);      free_matrix(agev,1,maxwav,1,imx);
Line 7860  Please run with mle=-1 to get a correct Line 8208  Please run with mle=-1 to get a correct
     free_ivector(Tage,1,NCOVMAX);      free_ivector(Tage,1,NCOVMAX);
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);      /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       

Removed from v.1.199  
changed lines
  Added in v.1.204


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