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Diff for /imach/src/imach.c between versions 1.220 and 1.224

version 1.220, 2016/02/15 23:22:02 version 1.224, 2016/07/01 13:16:01
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
   Revision 1.220  2016/02/15 23:22:02  brouard    Revision 1.224  2016/07/01 13:16:01  brouard
   Summary: 0.99r2    Summary: Fixes
   
     Revision 1.223  2016/02/19 09:23:35  brouard
     Summary: temporary
   
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
     Revision 1.221  2016/02/15 23:35:36  brouard
     Summary: minor bug
   
   Revision 1.219  2016/02/15 00:48:12  brouard    Revision 1.219  2016/02/15 00:48:12  brouard
   *** empty log message ***    *** empty log message ***
Line 739  Back prevalence and projections: Line 748  Back prevalence and projections:
 /* #define DEBUGLINMIN */  /* #define DEBUGLINMIN */
 /* #define DEBUGHESS */  /* #define DEBUGHESS */
 #define DEBUGHESSIJ  #define DEBUGHESSIJ
 #define LINMINORIGINAL  /* Don't use loop on scale in linmin (accepting nan)*/  /* #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 POWELLNOF3INFF1TEST /* 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 *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
Line 835  typedef struct { Line 844  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 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 copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 848  int cptcovs=0; /**< cptcovs number of si Line 857  int cptcovs=0; /**< cptcovs number of si
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int ncoveff=0; /* Total number of effective covariates in the model */
   int nqveff=0; /**< nqveff number of effective quantitative variables */
   int ntveff=0; /**< ntveff number of effective time varying variables */
   int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
Line 992  double *agedc; Line 1006  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * covar=matrix(0,NCOVMAX,1,n);                     * covar=matrix(0,NCOVMAX,1,n); 
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   double **coqvar; /* Fixed quantitative covariate */
   double ***cotvar; /* Time varying covariate */
   double ***cotqvar; /* Time varying quantitative covariate */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Tage;  int *Tage;
Line 1539  double brent(double ax, double bx, doubl Line 1556  double brent(double ax, double bx, doubl
       etemp=e;         etemp=e; 
       e=d;         e=d; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));                                   d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       else {         else { 
         d=p/q;                                   d=p/q; 
         u=x+d;                                   u=x+d; 
         if (u-a < tol2 || b-u < tol2)                                   if (u-a < tol2 || b-u < tol2) 
           d=SIGN(tol1,xm-x);                                           d=SIGN(tol1,xm-x); 
       }         } 
     } else {       } else { 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
Line 1558  double brent(double ax, double bx, doubl Line 1575  double brent(double ax, double bx, doubl
     } else {       } else { 
       if (u < x) a=u; else b=u;         if (u < x) a=u; else b=u; 
       if (fu <= fw || w == x) {         if (fu <= fw || w == x) { 
         v=w;                                   v=w; 
         w=u;                                   w=u; 
         fv=fw;                                   fv=fw; 
         fw=fu;                                   fw=fu; 
       } else if (fu <= fv || v == x || v == w) {         } else if (fu <= fv || v == x || v == w) { 
         v=u;                                   v=u; 
         fv=fu;                                   fv=fu; 
       }         } 
     }       } 
   }     } 
Line 1605  values at the three points, fa, fb , and Line 1622  values at the three points, fa, fb , and
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
 #ifdef DEBUG  #ifdef DEBUG
   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
 #endif  #endif
   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
     r=(*bx-*ax)*(*fb-*fc);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
Line 1621  values at the three points, fa, fb , and Line 1638  values at the three points, fa, fb , and
       double A, fparabu;         double A, fparabu; 
       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       fparabu= *fa - A*(*ax-u)*(*ax-u);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);        printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);        fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       /* And thus,it can be that fu > *fc even if fparabu < *fc */        /* And thus,it can be that fu > *fc even if fparabu < *fc */
       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
Line 1655  values at the three points, fa, fb , and Line 1672  values at the three points, fa, fb , and
 /*      fu = *fc; */  /*      fu = *fc; */
 /*      *fc =dum; */  /*      *fc =dum; */
 /*       } */  /*       } */
 #ifdef DEBUG  #ifdef DEBUGMNBRAK
       printf("mnbrak34  fu < or >= fc \n");                   double A, fparabu; 
       fprintf(ficlog, "mnbrak34 fu < fc\n");       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
        printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
        fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
 #endif  #endif
       dum=u; /* Shifting c and u */        dum=u; /* Shifting c and u */
       u = *cx;        u = *cx;
Line 1668  values at the three points, fa, fb , and Line 1688  values at the three points, fa, fb , and
 #endif  #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim\n");        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
 #endif  #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim AND fu < fc\n");                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");                            fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
   #endif
                             SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                                   SHFT(*fb,*fc,fu,(*func)(u)) 
   #ifdef DEBUG
                                           printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
 #endif  #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   
         SHFT(*fb,*fc,fu,(*func)(u))   
       }         } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");        fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
 #endif  #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else { /* u could be left to b (if r > q parabola has a maximum) */      } else { /* u could be left to b (if r > q parabola has a maximum) */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
 #endif  #endif
       u=(*cx)+GOLD*(*cx-*bx);         u=(*cx)+GOLD*(*cx-*bx); 
       fu=(*func)(u);         fu=(*func)(u); 
   #ifdef DEBUG
         printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
         fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
   #endif
     } /* end tests */      } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
     SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
 #endif  #endif
   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
Line 1714  int ncom; Line 1741  int ncom;
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
     
   #ifdef LINMINORIGINAL
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   #else
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
   #endif
 {   { 
   double brent(double ax, double bx, double cx,     double brent(double ax, double bx, double cx, 
                double (*f)(double), double tol, double *xmin);                  double (*f)(double), double tol, double *xmin); 
Line 1758  void linmin(double p[], double xi[], int Line 1789  void linmin(double p[], double xi[], int
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
     if (fx != fx){      if (fx != fx){
         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */                          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
         printf("|");                          printf("|");
         fprintf(ficlog,"|");                          fprintf(ficlog,"|");
 #ifdef DEBUGLINMIN  #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);                          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  #endif
     }      }
   }while(fx != fx);    }while(fx != fx && xxs > 1.e-5);
 #endif  #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);    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
   #ifdef LINMINORIGINAL
   #else
           if(fb == fx){ /* Flat function in the direction */
                   xmin=xx;
       *flat=1;
           }else{
       *flat=0;
   #endif
                   /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
   *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]) */
   /* fmin = f(p[j] + xmin * xi[j]) */    /* fmin = f(p[j] + xmin * xi[j]) */
   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
 #ifdef DEBUG  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   #endif
   #ifdef LINMINORIGINAL
   #else
                           }
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("linmin end ");    printf("linmin end ");
Line 1829  such that failure to decrease by more th Line 1873  such that failure to decrease by more th
 output, p is set to the best point found, xi is the then-current direction set, fret is the returned  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 function value at p , and iter is the number of iterations taken. The routine linmin is used.  function value at p , and iter is the number of iterations taken. The routine linmin is used.
  */   */
   #ifdef LINMINORIGINAL
   #else
           int *flatdir; /* Function is vanishing in that direction */
           int flat=0; /* Function is vanishing in that direction */
   #endif
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
   void linmin(double p[], double xi[], int n, double *fret,   #ifdef LINMINORIGINAL
    void linmin(double p[], double xi[], int n, double *fret, 
               double (*func)(double []));                 double (*func)(double [])); 
   #else 
    void linmin(double p[], double xi[], int n, double *fret, 
                                                    double (*func)(double []),int *flat); 
   #endif
   int i,ibig,j;     int i,ibig,j; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double directest;    double directest;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
   #ifdef LINMINORIGINAL
   #else
   
     flatdir=ivector(1,n); 
     for (j=1;j<=n;j++) flatdir[j]=0; 
   #endif
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
Line 1873  void powell(double p[], double **xi, int Line 1933  void powell(double p[], double **xi, int
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';                                  strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);                                  rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         forecast_time = *localtime(&rforecast_time);                                  forecast_time = *localtime(&rforecast_time);
         strcpy(strfor,asctime(&forecast_time));                                  strcpy(strfor,asctime(&forecast_time));
         itmp = strlen(strfor);                                  itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')                                  if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';                                          strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);                                  printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);                                  fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i */
Line 1896  void powell(double p[], double **xi, int Line 1956  void powell(double p[], double **xi, int
 #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);
   #ifdef LINMINORIGINAL
       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 */  #else
         linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                           flatdir[i]=flat; /* Function is vanishing in that direction i */
   #endif
                           /* Outputs are fret(new point p) p is updated and xit rescaled */
       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
         /* because that direction will be replaced unless the gain del is small */                                  /* because that direction will be replaced unless the gain del is small */
         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */                                  /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
         /* Unless the n directions are conjugate some gain in the determinant may be obtained */                                  /* Unless the n directions are conjugate some gain in the determinant may be obtained */
         /* with the new direction. */                                  /* with the new direction. */
         del=fabs(fptt-(*fret));                                   del=fabs(fptt-(*fret)); 
         ibig=i;                                   ibig=i; 
       }         } 
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %.12e",i,(*fret));        printf("%d %.12e",i,(*fret));
       fprintf(ficlog,"%d %.12e",i,(*fret));        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         printf(" x(%d)=%.12e",j,xit[j]);                                  printf(" x(%d)=%.12e",j,xit[j]);
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p(%d)=%.12e",j,p[j]);                          printf(" p(%d)=%lf ",j,p[j]);
         fprintf(ficlog," p(%d)=%.12e",j,p[j]);                          fprintf(ficlog," p(%d)=%lf ",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
Line 1925  void powell(double p[], double **xi, int Line 1990  void powell(double p[], double **xi, int
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
     /* New value of last point Pn is not computed, P(n-1) */      /* New value of last point Pn is not computed, P(n-1) */
         for(j=1;j<=n;j++) {
                             printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                             fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
         }
         printf("\n");
         fprintf(ficlog,"\n");
   
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
Line 1933  void powell(double p[], double **xi, int Line 2005  void powell(double p[], double **xi, int
       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
       /* By adding 10 parameters more the gain should be 18.31 */        /* By adding 10 parameters more the gain should be 18.31 */
                           
       /* Starting the program with initial values given by a former maximization will simply change */        /* Starting the program with initial values given by a former maximization will simply change */
       /* the scales of the directions and the directions, because the are reset to canonical directions */        /* the scales of the directions and the directions, because the are reset to canonical directions */
       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
Line 1961  void powell(double p[], double **xi, int Line 2033  void powell(double p[], double **xi, int
       }        }
 #endif  #endif
   
   #ifdef LINMINORIGINAL
   #else
         free_ivector(flatdir,1,n); 
   #endif
       free_vector(xit,1,n);         free_vector(xit,1,n); 
       free_vector(xits,1,n);         free_vector(xits,1,n); 
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
Line 1975  void powell(double p[], double **xi, int Line 2050  void powell(double p[], double **xi, int
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt); /* f_3 */      fptt=(*func)(ptt); /* f_3 */
 #ifdef POWELLF1F3  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   if (*iter <=4) {
   #else                   
   #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
 #else  #else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
 #endif  #endif
Line 1984  void powell(double p[], double **xi, int Line 2062  void powell(double p[], double **xi, int
       /* Let f"(x2) be the 2nd derivative equal everywhere.  */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
         /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
         /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         /*  Even if f3 <f1, directest can be negative and t >0 */
         /* mu² and del² are equal when f3=f1 */
                           /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                           /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                           /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                           /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
 #ifdef NRCORIGINAL  #ifdef NRCORIGINAL
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
 #else  #else
Line 2007  void powell(double p[], double **xi, int Line 2093  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 (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("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 (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,"directest= %.12lf (if directest<0 or t<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 */
 #endif  #endif
 #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]);
           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);                                          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           if(j % ncovmodel == 0){                                          if(j % ncovmodel == 0){
             printf("\n");                                                  printf("\n");
             fprintf(ficlog,"\n");                                                  fprintf(ficlog,"\n");
           }                                          }
         }                                  }
 #endif  #endif
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/  #ifdef LINMINORIGINAL
 #ifdef DEBUGLINMIN                                  linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
         for (j=1;j<=n;j++) {   #else
           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);                                  linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);                                  flatdir[i]=flat; /* Function is vanishing in that direction i */
           if(j % ncovmodel == 0){  
             printf("\n");  
             fprintf(ficlog,"\n");  
           }  
         }  
 #endif  #endif
         for (j=1;j<=n;j++) {   
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */  
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */  
         }  
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);  
         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);  
   
   #ifdef DEBUGLINMIN
                                   for (j=1;j<=n;j++) { 
                                           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           if(j % ncovmodel == 0){
                                                   printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
   #endif
                                   for (j=1;j<=n;j++) { 
                                           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                   }
   #ifdef LINMINORIGINAL
   #else
                                   printf("Flat directions\n");
                                   fprintf(ficlog,"Flat directions\n");
                                   for (j=1;j<=n;j++) { 
                                           printf("flatdir[%d]=%d ",j,flatdir[j]);
                                           fprintf(ficlog,"flatdir[%d]=%d ",j,flatdir[j]);
           }
                                   printf("\n");
                                   fprintf(ficlog,"\n");
   #endif
                                   printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for(j=1;j<=n;j++){                                  for(j=1;j<=n;j++){
           printf(" %.12e",xit[j]);                                          printf(" %lf",xit[j]);
           fprintf(ficlog," %.12e",xit[j]);                                          fprintf(ficlog," %lf",xit[j]);
         }                                  }
         printf("\n");                                  printf("\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t or directest negative */        } /* end of t or directest negative */
 #ifdef POWELLF1F3  #ifdef POWELLNOF3INFF1TEST
 #else  #else
     } /* end if (fptt < fp)  */      } /* end if (fptt < fp)  */
 #endif  #endif
                   } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
   #endif
   } /* loop iteration */     } /* loop iteration */ 
 }   } 
   
Line 2331  double **pmij(double **ps, double *cov, Line 2436  double **pmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 for(j=1; j<i;j++){      for(j=1; j<i;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                 }      }
         }    }
       
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 s1=0;      s1=0;
                 for(j=1; j<i; j++){      for(j=1; j<i; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                 ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
                 /* Computing other pijs */      /* Computing other pijs */
                 for(j=1; j<i; j++)      for(j=1; j<i; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 for(j=i+1; j<=nlstate+ndeath; j++)      for(j=i+1; j<=nlstate+ndeath; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         } /* end i */    } /* end i */
       
         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                 for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
                         ps[ii][jj]=0;        ps[ii][jj]=0;
                         ps[ii][ii]=1;        ps[ii][ii]=1;
                 }      }
         }    }
       
       
         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         /*   } */    /*   } */
         /*   printf("\n "); */    /*   printf("\n "); */
         /* } */    /* } */
         /* printf("\n ");printf("%lf ",cov[2]);*/    /* printf("\n ");printf("%lf ",cov[2]);*/
         /*    /*
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 goto end;*/                  goto end;*/
         return ps;    return ps;
 }  }
   
 /*************** backward transition probabilities ***************/   /*************** backward transition probabilities ***************/ 
Line 2398  double **pmij(double **ps, double *cov, Line 2503  double **pmij(double **ps, double *cov,
 /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
         /* Computes the backward probability at age agefin and covariate ij    /* Computes the backward probability at age agefin and covariate ij
          * and returns in **ps as well as **bmij.     * and returns in **ps as well as **bmij.
          */     */
   int i, ii, j,k;    int i, ii, j,k;
     
         double **out, **pmij();    double **out, **pmij();
         double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
     
         double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
         double **bbmij;    double **bbmij;
     
   doldm=ddoldms; /* global pointers */    doldm=ddoldms; /* global pointers */
         dnewm=ddnewms;    dnewm=ddnewms;
         dsavm=ddsavms;    dsavm=ddsavms;
     
         agefin=cov[2];    agefin=cov[2];
         /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
                  the observed prevalence (with this covariate ij) */       the observed prevalence (with this covariate ij) */
         dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);    dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
         /* We do have the matrix Px in savm  and we need pij */    /* We do have the matrix Px in savm  and we need pij */
         for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
                 sumnew=0.; /* w1 p11 + w2 p21 only on live states */      sumnew=0.; /* w1 p11 + w2 p21 only on live states */
                 for (ii=1;ii<=nlstate;ii++){      for (ii=1;ii<=nlstate;ii++){
                         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];        sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
                 } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
                 for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
                         if(sumnew >= 1.e-10){        if(sumnew >= 1.e-10){
                                 /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
                                 /* }else if(agefin >= agemaxpar+stepm/YEARM){ */          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
                                 /* }else */          /* }else */
                                         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);          doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
                         }else{        }else{
                                 printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);          printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
                         }        }
                 } /*End ii */      } /*End ii */
         } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
                 /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */    /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
         bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */    bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
         /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */    /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
         /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */    /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
         /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */    /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
         /* left Product of this matrix by diag matrix of prevalences (savm) */    /* left Product of this matrix by diag matrix of prevalences (savm) */
         for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
                 for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
                         dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);        dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
                 }      }
         } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
         ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */    ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
         /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */    /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
         /* end bmij */    /* end bmij */
         return ps;     return ps; 
 }  }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
Line 2657  double ***hpxij(double ***po, int nhstep Line 2762  double ***hpxij(double ***po, int nhstep
   
 /************* Higher Back Matrix Product ***************/  /************* Higher Back Matrix Product ***************/
 /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
 {  {
   /* Computes the transition matrix starting at age 'age' over    /* Computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
Line 2669  double ***hpxij(double ***po, int nhstep Line 2774  double ***hpxij(double ***po, int nhstep
      Model is determined by parameters x and covariates have to be       Model is determined by parameters x and covariates have to be
      included manually here.       included manually here.
   
      */    */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
         double **oldm, **savm;    double **oldm, **savm;
   
         oldm=oldms;savm=savms;    oldm=oldms;savm=savms;
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2695  double ***hpxij(double ***po, int nhstep Line 2800  double ***hpxij(double ***po, int nhstep
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
       cov[2]=agexact;        cov[2]=agexact;
       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,k)];          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[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,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]; */        /* 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,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          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])]; */        /* 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);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       /* Careful transposed matrix */        /* Careful transposed matrix */
                         /* age is in cov[2] */        /* age is in cov[2] */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
                         /*                                               1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                                                                          1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
       /*        for(i=1; i<=nlstate+ndeath; i++) { */        /*        for(i=1; i<=nlstate+ndeath; i++) { */
Line 2735  double ***hpxij(double ***po, int nhstep Line 2840  double ***hpxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
                                 po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
         /*     printf("\n H=%d \n",h); */    /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
Line 2768  double ***hpxij(double ***po, int nhstep Line 2873  double ***hpxij(double ***po, int nhstep
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;          int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];          int ioffset=0;
   double **out;          double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double sw; /* Sum of weights */          double **out;
   double lli; /* Individual log likelihood */          double sw; /* Sum of weights */
   int s1, s2;          double lli; /* Individual log likelihood */
   double bbh, survp;          int s1, s2;
   long ipmx;          int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   double agexact;          double bbh, survp;
   /*extern weight */          long ipmx;
   /* We are differentiating ll according to initial status */          double agexact;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          /*extern weight */
   /*for(i=1;i<imx;i++)           /* We are differentiating ll according to initial status */
     printf(" %d\n",s[4][i]);          /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   */          /*for(i=1;i<imx;i++) 
                   printf(" %d\n",s[4][i]);
           */
   
   ++countcallfunc;          ++countcallfunc;
   
   cov[1]=1.;          cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;          for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
           if(mle==1){
                   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                           /* Computes the values of the ncovmodel covariates of the model
                                    depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
                                    Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                                    to be observed in j being in i according to the model.
                           */
                           ioffset=2+nagesqr+cptcovage;
                           /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
                           for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
                                   cov[++ioffset]=covar[Tvar[k]][i];
                           }
                           for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
                                   cov[++ioffset]=coqvar[iqv][i];
                           }
   
   if(mle==1){                          /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){                                   is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       /* Computes the values of the ncovmodel covariates of the model                                   has been calculated etc */
          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]                          /* For an individual i, wav[i] gives the number of effective waves */
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability                          /* We compute the contribution to Likelihood of each effective transition
          to be observed in j being in i according to the model.                                   mw[mi][i] is real wave of the mi th effectve wave */
        */                          /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */                                   s2=s[mw[mi+1][i]][i];
           cov[2+nagesqr+k]=covar[Tvar[k]][i];                                   And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
       }                                   But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]                                    meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]                           */
          has been calculated etc */                          for(mi=1; mi<= wav[i]-1; mi++){
       for(mi=1; mi<= wav[i]-1; mi++){                                  for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
         for (ii=1;ii<=nlstate+ndeath;ii++)                                          cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
           for (j=1;j<=nlstate+ndeath;j++){                                  }
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                  for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
             savm[ii][j]=(ii==j ? 1.0 : 0.0);                                          cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
           }                                  }
         for(d=0; d<dh[mi][i]; d++){                                  /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
           newm=savm;                                  for (ii=1;ii<=nlstate+ndeath;ii++)
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                          for (j=1;j<=nlstate+ndeath;j++){
           cov[2]=agexact;                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(nagesqr==1)                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
             cov[3]= agexact*agexact;                                          }
           for (kk=1; kk<=cptcovage;kk++) {                                  for(d=0; d<dh[mi][i]; d++){
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */                                          newm=savm;
           }                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                          cov[2]=agexact;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                          if(nagesqr==1)
           savm=oldm;                                                  cov[3]= agexact*agexact;  /* Should be changed here */
           oldm=newm;                                          for (kk=1; kk<=cptcovage;kk++) {
         } /* end mult */                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
                                                 }
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         /* But now since version 0.9 we anticipate for bias at large stepm.                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          * If stepm is larger than one month (smallest stepm) and if the exact delay                                           savm=oldm;
          * (in months) between two waves is not a multiple of stepm, we rounded to                                           oldm=newm;
          * the nearest (and in case of equal distance, to the lowest) interval but now                                  } /* end mult */
          * we keep into memory the bias bh[mi][i] and also the previous matrix product                                  
          * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the                                          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          * probability in order to take into account the bias as a fraction of the way                                  /* But now since version 0.9 we anticipate for bias at large stepm.
          * from savm to out if bh is negative or even beyond if bh is positive. bh varies                                   * If stepm is larger than one month (smallest stepm) and if the exact delay 
          * -stepm/2 to stepm/2 .                                   * (in months) between two waves is not a multiple of stepm, we rounded to 
          * For stepm=1 the results are the same as for previous versions of Imach.                                   * the nearest (and in case of equal distance, to the lowest) interval but now
          * For stepm > 1 the results are less biased than in previous versions.                                    * we keep into memory the bias bh[mi][i] and also the previous matrix product
          */                                   * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         s1=s[mw[mi][i]][i];                                   * probability in order to take into account the bias as a fraction of the way
         s2=s[mw[mi+1][i]][i];                                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         bbh=(double)bh[mi][i]/(double)stepm;                                    * -stepm/2 to stepm/2 .
         /* bias bh is positive if real duration                                   * For stepm=1 the results are the same as for previous versions of Imach.
          * is higher than the multiple of stepm and negative otherwise.                                   * For stepm > 1 the results are less biased than in previous versions. 
          */                                   */
         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/                                  s1=s[mw[mi][i]][i];
         if( s2 > nlstate){                                   s2=s[mw[mi+1][i]][i];
           /* i.e. if s2 is a death state and if the date of death is known                                   bbh=(double)bh[mi][i]/(double)stepm; 
              then the contribution to the likelihood is the probability to                                   /* bias bh is positive if real duration
              die between last step unit time and current  step unit time,                                    * is higher than the multiple of stepm and negative otherwise.
              which is also equal to probability to die before dh                                    */
              minus probability to die before dh-stepm .                                   /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
              In version up to 0.92 likelihood was computed                                  if( s2 > nlstate){ 
         as if date of death was unknown. Death was treated as any other                                          /* i.e. if s2 is a death state and if the date of death is known 
         health state: the date of the interview describes the actual state                                                   then the contribution to the likelihood is the probability to 
         and not the date of a change in health state. The former idea was                                                   die between last step unit time and current  step unit time, 
         to consider that at each interview the state was recorded                                                   which is also equal to probability to die before dh 
         (healthy, disable or death) and IMaCh was corrected; but when we                                                   minus probability to die before dh-stepm . 
         introduced the exact date of death then we should have modified                                                   In version up to 0.92 likelihood was computed
         the contribution of an exact death to the likelihood. This new                                                   as if date of death was unknown. Death was treated as any other
         contribution is smaller and very dependent of the step unit                                                   health state: the date of the interview describes the actual state
         stepm. It is no more the probability to die between last interview                                                   and not the date of a change in health state. The former idea was
         and month of death but the probability to survive from last                                                   to consider that at each interview the state was recorded
         interview up to one month before death multiplied by the                                                   (healthy, disable or death) and IMaCh was corrected; but when we
         probability to die within a month. Thanks to Chris                                                   introduced the exact date of death then we should have modified
         Jackson for correcting this bug.  Former versions increased                                                   the contribution of an exact death to the likelihood. This new
         mortality artificially. The bad side is that we add another loop                                                   contribution is smaller and very dependent of the step unit
         which slows down the processing. The difference can be up to 10%                                                   stepm. It is no more the probability to die between last interview
         lower mortality.                                                   and month of death but the probability to survive from last
           */                                                   interview up to one month before death multiplied by the
         /* If, at the beginning of the maximization mostly, the                                                   probability to die within a month. Thanks to Chris
            cumulative probability or probability to be dead is                                                   Jackson for correcting this bug.  Former versions increased
            constant (ie = 1) over time d, the difference is equal to                                                   mortality artificially. The bad side is that we add another loop
            0.  out[s1][3] = savm[s1][3]: probability, being at state                                                   which slows down the processing. The difference can be up to 10%
            s1 at precedent wave, to be dead a month before current                                                   lower mortality.
            wave is equal to probability, being at state s1 at                                          */
            precedent wave, to be dead at mont of the current                                          /* If, at the beginning of the maximization mostly, the
            wave. Then the observed probability (that this person died)                                                   cumulative probability or probability to be dead is
            is null according to current estimated parameter. In fact,                                                   constant (ie = 1) over time d, the difference is equal to
            it should be very low but not zero otherwise the log go to                                                   0.  out[s1][3] = savm[s1][3]: probability, being at state
            infinity.                                                   s1 at precedent wave, to be dead a month before current
         */                                                   wave is equal to probability, being at state s1 at
                                                    precedent wave, to be dead at mont of the current
                                                    wave. Then the observed probability (that this person died)
                                                    is null according to current estimated parameter. In fact,
                                                    it should be very low but not zero otherwise the log go to
                                                    infinity.
                                           */
 /* #ifdef INFINITYORIGINAL */  /* #ifdef INFINITYORIGINAL */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #else */  /* #else */
Line 2888  double func( double *x) Line 3017  double func( double *x)
 /*        else */  /*        else */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */  /* #endif */
           lli=log(out[s1][s2] - savm[s1][s2]);                                          lli=log(out[s1][s2] - savm[s1][s2]);
                       
         } else if  ( s2==-1 ) { /* alive */                                  } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++)                                           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           /*survp += out[s1][j]; */                                          /*survp += out[s1][j]; */
           lli= log(survp);                                          lli= log(survp);
         }                                  }
         else if  (s2==-4) {                                   else if  (s2==-4) { 
           for (j=3,survp=0. ; j<=nlstate; j++)                                            for (j=3,survp=0. ; j<=nlstate; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);                                           lli= log(survp); 
         }                                   } 
         else if  (s2==-5) {                                   else if  (s2==-5) { 
           for (j=1,survp=0. ; j<=2; j++)                                            for (j=1,survp=0. ; j<=2; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];                                                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);                                           lli= log(survp); 
         }                                   } 
         else{                                  else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */                                          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */                                          /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         }                                   } 
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/                                  /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         /*if(lli ==000.0)*/                                  /*if(lli ==000.0)*/
         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */                                  /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         ipmx +=1;                                  ipmx +=1;
         sw += weight[i];                                  sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /* if (lli < log(mytinydouble)){ */                                  /* if (lli < log(mytinydouble)){ */
         /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */                                  /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
         /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */                                  /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
         /* } */                                  /* } */
       } /* end of wave */                          } /* end of wave */
     } /* end of individual */                  } /* end of individual */
   }  else if(mle==2){          }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){                          for(mi=1; mi<= wav[i]-1; mi++){
         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++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }                                          }
         for(d=0; d<=dh[mi][i]; d++){                                  for(d=0; d<=dh[mi][i]; d++){
           newm=savm;                                          newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;                                          cov[2]=agexact;
           if(nagesqr==1)                                          if(nagesqr==1)
             cov[3]= agexact*agexact;                                                  cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {                                          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }                                          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;                                          savm=oldm;
           oldm=newm;                                          oldm=newm;
         } /* end mult */                                  } /* end mult */
               
         s1=s[mw[mi][i]][i];                                  s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];                                  s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm;                                   bbh=(double)bh[mi][i]/(double)stepm; 
         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */                                  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         ipmx +=1;                                  ipmx +=1;
         sw += weight[i];                                  sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       } /* end of wave */                          } /* end of wave */
     } /* end of individual */                  } /* end of individual */
   }  else if(mle==3){  /* exponential inter-extrapolation */          }  else if(mle==3){  /* exponential inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){                          for(mi=1; mi<= wav[i]-1; mi++){
         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++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }                                          }
         for(d=0; d<dh[mi][i]; d++){                                  for(d=0; d<dh[mi][i]; d++){
           newm=savm;                                          newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;                                          cov[2]=agexact;
           if(nagesqr==1)                                          if(nagesqr==1)
             cov[3]= agexact*agexact;                                                  cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {                                          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }                                          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;                                          savm=oldm;
           oldm=newm;                                          oldm=newm;
         } /* end mult */                                  } /* end mult */
               
         s1=s[mw[mi][i]][i];                                  s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];                                  s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm;                                   bbh=(double)bh[mi][i]/(double)stepm; 
         lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */                                  lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         ipmx +=1;                                  ipmx +=1;
         sw += weight[i];                                  sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;                                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       } /* end of wave */                          } /* end of wave */
     } /* end of individual */                  } /* end of individual */
   }else if (mle==4){  /* ml=4 no inter-extrapolation */          }else if (mle==4){  /* ml=4 no inter-extrapolation */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){                          for(mi=1; mi<= wav[i]-1; mi++){
         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++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }                                          }
         for(d=0; d<dh[mi][i]; d++){                                  for(d=0; d<dh[mi][i]; d++){
           newm=savm;                                          newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;                                          cov[2]=agexact;
           if(nagesqr==1)                                          if(nagesqr==1)
             cov[3]= agexact*agexact;                                                  cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {                                          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }                                          }
                   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;                                          savm=oldm;
           oldm=newm;                                          oldm=newm;
         } /* end mult */                                  } /* end mult */
               
         s1=s[mw[mi][i]][i];                                  s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];                                  s2=s[mw[mi+1][i]][i];
         if( s2 > nlstate){                                   if( s2 > nlstate){ 
           lli=log(out[s1][s2] - savm[s1][s2]);                                          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  ( s2==-1 ) { /* alive */                                  } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++)                                           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += out[s1][j];                                                  survp += out[s1][j];
           lli= log(survp);                                          lli= log(survp);
         }else{                                  }else{
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */                                          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }                                  }
         ipmx +=1;                                  ipmx +=1;
         sw += weight[i];                                  sw += weight[i];
         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]); */
       } /* end of wave */                          } /* end of wave */
     } /* end of individual */                  } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */          }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){                  for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];                          for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){                          for(mi=1; mi<= wav[i]-1; mi++){
         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++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);                                                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }                                          }
         for(d=0; d<dh[mi][i]; d++){                                  for(d=0; d<dh[mi][i]; d++){
           newm=savm;                                          newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;                                          cov[2]=agexact;
           if(nagesqr==1)                                          if(nagesqr==1)
             cov[3]= agexact*agexact;                                                  cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {                                          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;                                                  cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           }                                          }
                   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                                                                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;                                          savm=oldm;
           oldm=newm;                                          oldm=newm;
         } /* end mult */                                  } /* end mult */
               
         s1=s[mw[mi][i]][i];                                  s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];                                  s2=s[mw[mi+1][i]][i];
         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */                                  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         ipmx +=1;                                  ipmx +=1;
         sw += weight[i];                                  sw += weight[i];
         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]);*/
       } /* end of wave */                          } /* end of wave */
     } /* end of individual */                  } /* end of individual */
   } /* End of if */          } /* End of if */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   return -l;          return -l;
 }  }
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
Line 3076  double funcone( double *x) Line 3205  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
           int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
   int s1, s2;    int s1, s2;
           int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
Line 3093  double funcone( double *x) Line 3224  double funcone( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];                  ioffset=2+nagesqr+cptcovage;
       /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
                   for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
                           cov[++ioffset]=covar[Tvar[k]][i];
                   }
                   for(iqv=1; iqv <= nqveff; iqv++){ /* Quantitatives covariates */
                           cov[++ioffset]=coqvar[iqv][i];
                   }
   
     for(mi=1; mi<= wav[i]-1; mi++){      for(mi=1; mi<= wav[i]-1; mi++){
                           for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
                                   cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
                           }
                           for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
                                   cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
                           }
       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++){
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);                                          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           savm[ii][j]=(ii==j ? 1.0 : 0.0);                                          savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }                                  }
               
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]                                  /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           and mw[mi+1][i]. dh depends on stepm.*/                                          and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;                                  newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;                                  agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         cov[2]=agexact;                                  cov[2]=agexact;
         if(nagesqr==1)                                  if(nagesqr==1)
           cov[3]= agexact*agexact;                                          cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {                                  for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;                                          cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         }                                  }
                                   
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */                                  /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                                                                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */                                  /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */                                  /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         savm=oldm;                                  savm=oldm;
         oldm=newm;                                  oldm=newm;
       } /* end mult */        } /* end mult */
               
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
Line 3137  double funcone( double *x) Line 3282  double funcone( double *x)
        * is higher than the multiple of stepm and negative otherwise.         * is higher than the multiple of stepm and negative otherwise.
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);                                  lli=log(out[s1][s2] - savm[s1][s2]);
       } else if  ( s2==-1 ) { /* alive */        } else if  ( s2==-1 ) { /* alive */
         for (j=1,survp=0. ; j<=nlstate; j++)                                   for (j=1,survp=0. ; j<=nlstate; j++) 
           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];                                          survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         lli= log(survp);                                  lli= log(survp);
       }else if (mle==1){        }else if (mle==1){
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */                                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       } else if(mle==2){        } else if(mle==2){
         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */                                  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       } else if(mle==3){  /* exponential inter-extrapolation */        } else if(mle==3){  /* exponential inter-extrapolation */
         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */                                  lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       } else if (mle==4){  /* mle=4 no inter-extrapolation */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         lli=log(out[s1][s2]); /* Original formula */                                  lli=log(out[s1][s2]); /* Original formula */
       } else{  /* mle=0 back to 1 */        } else{  /* mle=0 back to 1 */
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */                                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         /*lli=log(out[s1][s2]); */ /* Original formula */                                  /*lli=log(out[s1][s2]); */ /* Original formula */
       } /* End of if */        } /* End of if */
       ipmx +=1;        ipmx +=1;
       sw += weight[i];        sw += weight[i];
       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 %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\                                  fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                                                                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 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;
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);                                          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         }                                  }
         fprintf(ficresilk," %10.6f\n", -llt);                                  fprintf(ficresilk," %10.6f\n", -llt);
       }        }
     } /* end of wave */      } /* end of wave */
   } /* end of individual */    } /* end of individual */
Line 3684  void pstamp(FILE *fichier) Line 3829  void pstamp(FILE *fichier)
          int mi; /* Effective wave */           int mi; /* Effective wave */
          int first;           int first;
          double ***freq; /* Frequencies */           double ***freq; /* Frequencies */
            double *meanq;
            double **meanqt;
          double *pp, **prop, *posprop, *pospropt;           double *pp, **prop, *posprop, *pospropt;
          double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;           double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];           char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
Line 3694  void pstamp(FILE *fichier) Line 3841  void pstamp(FILE *fichier)
          posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */            posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
          pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */            pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
          /* prop=matrix(1,nlstate,iagemin,iagemax+3); */           /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
            meanq=vector(1,nqveff);
            meanqt=matrix(1,lastpass,1,nqtveff);
          strcpy(fileresp,"P_");           strcpy(fileresp,"P_");
          strcat(fileresp,fileresu);           strcat(fileresp,fileresu);
          /*strcat(fileresphtm,fileresu);*/           /*strcat(fileresphtm,fileresu);*/
Line 3736  Title=%s <br>Datafile=%s Firstpass=%d La Line 3885  Title=%s <br>Datafile=%s Firstpass=%d La
          freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);           freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
          j1=0;           j1=0;
       
          j=cptcoveff;           j=ncoveff;
          if (cptcovn<1) {j=1;ncodemax[1]=1;}           if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
          first=1;           first=1;
Line 3748  Title=%s <br>Datafile=%s Firstpass=%d La Line 3897  Title=%s <br>Datafile=%s Firstpass=%d La
                         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff                           Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
          */           */
   
          for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */           for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */
                  posproptt=0.;                   posproptt=0.;
                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);                   /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                          scanf("%d", i);*/                           scanf("%d", i);*/
Line 3763  Title=%s <br>Datafile=%s Firstpass=%d La Line 3912  Title=%s <br>Datafile=%s Firstpass=%d La
                          posprop[i]=0;                           posprop[i]=0;
                          pospropt[i]=0;                           pospropt[i]=0;
                  }                   }
                    for (z1=1; z1<= nqveff; z1++) {  
                            meanq[z1]+=0.;
                            for(m=1;m<=lastpass;m++){
                                    meanqt[m][z1]=0.;
                            }
                    }
               
                  dateintsum=0;                   dateintsum=0;
                  k2cpt=0;                   k2cpt=0;
        /* For that comination of covariate j1, we count and print the frequencies */
                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */                   for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                          bool=1;                           bool=1;
                          if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */                           if (nqveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                                  for (z1=1; z1<=cptcoveff; z1++) {                                         for (z1=1; z1<= nqveff; z1++) {  
                                            meanq[z1]+=coqvar[Tvar[z1]][iind];
                                    }
                                    for (z1=1; z1<=ncoveff; z1++) {  
                                            /* if(Tvaraff[z1] ==-20){ */
                                            /*      /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                                            /* }else  if(Tvaraff[z1] ==-10){ */
                                            /*      /\* sumnew+=coqvar[z1][iind]; *\/ */
                                            /* }else  */
                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){                                           if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                                                  /* Tests if the value of each of the covariates of i is equal to filter j1 */                                                   /* Tests if this individual i responded to j1 (V4=1 V3=0) */
                                                  bool=0;                                                   bool=0;
                                                  /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",                                                    /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
Line 3782  Title=%s <br>Datafile=%s Firstpass=%d La Line 3945  Title=%s <br>Datafile=%s Firstpass=%d La
                                  } /* end z1 */                                   } /* end z1 */
                          } /* cptcovn > 0 */                           } /* cptcovn > 0 */
   
                          if (bool==1){                           if (bool==1){ /* We selected an individual iin satisfying combination j1 */
                                  /* for(m=firstpass; m<=lastpass; m++){ */                                   /* for(m=firstpass; m<=lastpass; m++){ */
                                  for(mi=1; mi<wav[iind];mi++){                                   for(mi=1; mi<wav[iind];mi++){
                                          m=mw[mi][iind];                                           m=mw[mi][iind];
Line 3822  Title=%s <br>Datafile=%s Firstpass=%d La Line 3985  Title=%s <br>Datafile=%s Firstpass=%d La
   
                  /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/                   /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                  pstamp(ficresp);                   pstamp(ficresp);
                  if  (cptcovn>0) {                   if  (ncoveff>0) {
                          fprintf(ficresp, "\n#********** Variable ");                            fprintf(ficresp, "\n#********** Variable "); 
                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");                            fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");                            fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                          for (z1=1; z1<=cptcoveff; z1++){                           for (z1=1; z1<=ncoveff; z1++){
                                  fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                                   fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                  fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                                   fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                  fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                                   fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
Line 3835  Title=%s <br>Datafile=%s Firstpass=%d La Line 3998  Title=%s <br>Datafile=%s Firstpass=%d La
                          fprintf(ficresphtm, "**********</h3>\n");                           fprintf(ficresphtm, "**********</h3>\n");
                          fprintf(ficresphtmfr, "**********</h3>\n");                           fprintf(ficresphtmfr, "**********</h3>\n");
                          fprintf(ficlog, "\n#********** Variable ");                            fprintf(ficlog, "\n#********** Variable "); 
                          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                           for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                          fprintf(ficlog, "**********\n");                           fprintf(ficlog, "**********\n");
                  }                   }
                  fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");                   fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
Line 3962  Title=%s <br>Datafile=%s Firstpass=%d La Line 4125  Title=%s <br>Datafile=%s Firstpass=%d La
                  fprintf(ficresphtm,"<tr><th>Tot</th>");                   fprintf(ficresphtm,"<tr><th>Tot</th>");
                  for(jk=1; jk <=nlstate ; jk++){                   for(jk=1; jk <=nlstate ; jk++){
                          if(posproptt < 1.e-5){                           if(posproptt < 1.e-5){
                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);                                      fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);  
                          }else{                           }else{
                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);                                      fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);   
                          }                           }
                  }                   }
                  fprintf(ficresphtm,"</tr>\n");                   fprintf(ficresphtm,"</tr>\n");
Line 3986  Title=%s <br>Datafile=%s Firstpass=%d La Line 4149  Title=%s <br>Datafile=%s Firstpass=%d La
          fclose(ficresp);           fclose(ficresp);
          fclose(ficresphtm);           fclose(ficresphtm);
          fclose(ficresphtmfr);           fclose(ficresphtmfr);
            free_vector(meanq,1,nqveff);
            free_matrix(meanqt,1,lastpass,1,nqtveff);
          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);           free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
          free_vector(pospropt,1,nlstate);           free_vector(pospropt,1,nlstate);
          free_vector(posprop,1,nlstate);           free_vector(posprop,1,nlstate);
          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);           free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
          free_vector(pp,1,nlstate);           free_vector(pp,1,nlstate);
          /* End of Freq */           /* End of freqsummary */
  }   }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {     {  
   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      in each health status at the date of interview (if between dateprev1 and dateprev2).        in each health status at the date of interview (if between dateprev1 and dateprev2).
      We still use firstpass and lastpass as another selection.        We still use firstpass and lastpass as another selection.
   */     */
     
   int i, m, jk, j1, bool, z1,j;     int i, m, jk, j1, bool, z1,j;
   int mi; /* Effective wave */     int mi; /* Effective wave */
   int iage;     int iage;
   double agebegin, ageend;     double agebegin, ageend;
   
   double **prop;     double **prop;
   double posprop;      double posprop; 
   double  y2; /* in fractional years */     double  y2; /* in fractional years */
   int iagemin, iagemax;     int iagemin, iagemax;
   int first; /** to stop verbosity which is redirected to log file */     int first; /** to stop verbosity which is redirected to log file */
   
   iagemin= (int) agemin;     iagemin= (int) agemin;
   iagemax= (int) agemax;     iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/     /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);      prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;     j1=0;
       
   /*j=cptcoveff;*/     /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;     first=1;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */     for(j1=1; j1<= (int) pow(2,nqveff);j1++){ /* For each combination of covariate */
     for (i=1; i<=nlstate; i++)         for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)         for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
                                 prop[i][iage]=0.0;           prop[i][iage]=0.0;
           
     for (i=1; i<=imx; i++) { /* Each individual */       for (i=1; i<=imx; i++) { /* Each individual */
       bool=1;         bool=1;
       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */         if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                                 for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/           for (z1=1; z1<=nqveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
                                         if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
                                                 bool=0;               bool=0;
       }          } 
       if (bool==1) { /* For this combination of covariates values, this individual fits */         if (bool==1) { /* For this combination of covariates values, this individual fits */
                                 /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */           /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
                                 for(mi=1; mi<wav[i];mi++){           for(mi=1; mi<wav[i];mi++){
                                         m=mw[mi][i];             m=mw[mi][i];
                                         agebegin=agev[m][i]; /* Age at beginning of wave before transition*/             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                                         /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                                         if(m >=firstpass && m <=lastpass){             if(m >=firstpass && m <=lastpass){
                                                 y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                                                 if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                                                         if(agev[m][i]==0) agev[m][i]=iagemax+1;                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                                                         if(agev[m][i]==1) agev[m][i]=iagemax+2;                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                                                         if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
                                                                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);                    printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                                                                 exit(1);                   exit(1);
                                                         }                 }
                                                         if (s[m][i]>0 && s[m][i]<=nlstate) {                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
                                                                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                                                                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                                                                 prop[s[m][i]][iagemax+3] += weight[i];                    prop[s[m][i]][iagemax+3] += weight[i]; 
                                                         } /* end valid statuses */                  } /* end valid statuses */ 
                                                 } /* end selection of dates */               } /* end selection of dates */
                                         } /* end selection of waves */             } /* end selection of waves */
                                 } /* end effective waves */           } /* end effective waves */
       } /* end bool */         } /* end bool */
     }       }
     for(i=iagemin; i <= iagemax+3; i++){         for(i=iagemin; i <= iagemax+3; i++){  
       for(jk=1,posprop=0; jk <=nlstate ; jk++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                                 posprop += prop[jk][i];            posprop += prop[jk][i]; 
       }          } 
               
       for(jk=1; jk <=nlstate ; jk++){                for(jk=1; jk <=nlstate ; jk++){      
                                 if( i <=  iagemax){            if( i <=  iagemax){ 
                                         if(posprop>=1.e-5){              if(posprop>=1.e-5){ 
                                                 probs[i][jk][j1]= prop[jk][i]/posprop;               probs[i][jk][j1]= prop[jk][i]/posprop;
                                         } else{             } else{
                                                 if(first==1){               if(first==1){
                                                         first=0;                 first=0;
                                                         printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                                                 }               }
                                         }             }
                                 }            } 
       }/* end jk */          }/* end jk */ 
     }/* end i */        }/* end i */ 
     /*} *//* end i1 */       /*} *//* end i1 */
   } /* end j1 */     } /* end j1 */
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/     /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);     free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
 }  /* End of prevalence */   }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
Line 4098  void  concatwav(int wav[], int **dh, int Line 4263  void  concatwav(int wav[], int **dh, int
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */       */
   
   int i, mi, m;    int i=0, mi=0, m=0, mli=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/       double sum=0., jmean=0.;*/
   int first, firstwo, firsthree, firstfour;    int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
Line 4111  void  concatwav(int wav[], int **dh, int Line 4276  void  concatwav(int wav[], int **dh, int
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   
   /* Treating live states */
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;      mi=0;  /* First valid wave */
                   mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state */
       if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */                          if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
         mw[++mi][i]=m;                                  mli=m-1;/* mw[++mi][i]=m-1; */
                           }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
                                   mw[++mi][i]=m;
                                   mli=m;
         } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
         if(m < lastpass){ /* m < lastpass, standard case */
                                   m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
       if(m >=lastpass){                          else{ /* m >= lastpass, eventual special issue with warning */
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
           if(firsthree == 0){                                  break;
             printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);  #else
             firsthree=1;                                  if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           }                                          if(firsthree == 0){
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);                                                  printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
           mw[++mi][i]=m;                                                  firsthree=1;
         }                                          }
         if(s[m][i]==-2){ /* Vital status is really unknown */                                          fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
           nbwarn++;                                          mw[++mi][i]=m;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */                                          mli=m;
             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);                                  }
             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);                                  if(s[m][i]==-2){ /* Vital status is really unknown */
           }                                          nbwarn++;
           break;                                          if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
         }                                                  printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
         break;                                                  fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
       }                                          }
       else                                          break;
         m++;                                  }
                                   break;
   #endif
                           }/* End m >= lastpass */
     }/* end while */      }/* end while */
       
           /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
     /* After last pass */      /* After last pass */
   /* Treating death states */
     if (s[m][i] > nlstate){  /* In a death state */      if (s[m][i] > nlstate){  /* In a death state */
                           /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                           /* } */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
          /* Only death is a correct wave */                          /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */      }
   #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
                   else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
       /* m++; */        /* m++; */
       /* mi++; */        /* mi++; */
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
       /* mw[mi][i]=m; */        /* mw[mi][i]=m; */
       nberr++;  
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if(firstwo==0){                                  if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
           printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                          nbwarn++;
           firstwo=1;                                          if(firstfiv==0){
         }                                                  printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                                  firstfiv=1;
                                           }else{
                                                   fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                           }
                                   }else{ /* Death occured afer last wave potential bias */
                                           nberr++;
                                           if(firstwo==0){
                                                   printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                                   firstwo=1;
                                           }
                                           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                   }
       }else{ /* end date of interview is known */        }else{ /* end date of interview is known */
         /* death is known but not confirmed by death status at any wave */                                  /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){                                  if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                          printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
           firstfour=1;                                          firstfour=1;
         }                                  }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                  fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }        }
     }      } /* end if date of death is known */
     wav[i]=mi;  #endif
       wav[i]=mi; /* mi should be the last effective wave (or mli) */
       /* wav[i]=mw[mi][i]; */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);                                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;                                  first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);                                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
   /* wav and mw are no more changed */    /* wav and mw are no more changed */
           
       
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;                                  dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */                                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           if (agedc[i] < 2*AGESUP) {                                          if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                                                   j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */                                                  if(j==0) j=1;  /* Survives at least one month after exam */
             else if(j<0){                                                  else if(j<0){
               nberr++;                                                          nberr++;
               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                          printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               j=1; /* Temporary Dangerous patch */                                                          j=1; /* Temporary Dangerous patch */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                                                          printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                          fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                                                          fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }                                                  }
             k=k+1;                                                  k=k+1;
             if (j >= jmax){                                                  if (j >= jmax){
               jmax=j;                                                          jmax=j;
               ijmax=i;                                                          ijmax=i;
             }                                                  }
             if (j <= jmin){                                                  if (j <= jmin){
               jmin=j;                                                          jmin=j;
               ijmin=i;                                                          ijmin=i;
             }                                                  }
             sum=sum+j;                                                  sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/                                                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/                                                  /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }                                          }
         }                                  }
         else{                                  else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                                          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                           
           k=k+1;                                          k=k+1;
           if (j >= jmax) {                                          if (j >= jmax) {
             jmax=j;                                                  jmax=j;
             ijmax=i;                                                  ijmax=i;
           }                                          }
           else if (j <= jmin){                                          else if (j <= jmin){
             jmin=j;                                                  jmin=j;
             ijmin=i;                                                  ijmin=i;
           }                                          }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                                          /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/                                          /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           if(j<0){                                          if(j<0){
             nberr++;                                                  nberr++;
             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                  printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                  fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                                          }
           sum=sum+j;                                          sum=sum+j;
         }                                  }
         jk= j/stepm;                                  jk= j/stepm;
         jl= j -jk*stepm;                                  jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;                                  ju= j -(jk+1)*stepm;
         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */                                  if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           if(jl==0){                                          if(jl==0){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=0;                                                  bh[mi][i]=0;
           }else{ /* We want a negative bias in order to only have interpolation ie                                          }else{ /* We want a negative bias in order to only have interpolation ie
                   * to avoid the price of an extra matrix product in likelihood */                                                                          * to avoid the price of an extra matrix product in likelihood */
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
         }else{                                  }else{
           if(jl <= -ju){                                          if(jl <= -ju){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=jl;       /* bias is positive if real duration                                                  bh[mi][i]=jl;   /* bias is positive if real duration
                                  * is higher than the multiple of stepm and negative otherwise.                                                                                                           * is higher than the multiple of stepm and negative otherwise.
                                  */                                                                                                           */
           }                                          }
           else{                                          else{
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
           if(dh[mi][i]==0){                                          if(dh[mi][i]==0){
             dh[mi][i]=1; /* At least one step */                                                  dh[mi][i]=1; /* At least one step */
             bh[mi][i]=ju; /* At least one step */                                                  bh[mi][i]=ju; /* At least one step */
             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/                                                  /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }                                          }
         } /* end if mle */                                  } /* end if mle */
       }        }
     } /* end wave */      } /* end wave */
   }    }
Line 4279  void  concatwav(int wav[], int **dh, int Line 4474  void  concatwav(int wav[], int **dh, int
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    * Boring subroutine which should only output nbcode[Tvar[j]][k]     * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
    * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
   */    */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 4290  void  concatwav(int wav[], int **dh, int Line 4485  void  concatwav(int wav[], int **dh, int
   
   
   /* cptcoveff=0;  */    /* cptcoveff=0;  */
         *cptcov=0;          /* *cptcov=0; */
     
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* Loop on covariates without age and products and no quantitative variable */
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
     for (j=1; j<=(*cptcov); j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
     for (k=-1; k < maxncov; k++) Ndum[k]=0;      for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the       for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                                                                                                                 modality of this covariate Vj*/                                                                                                                                   modality of this covariate Vj*/
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i                          if(Tvar[j]  >=1 && Tvar[j]  <= *cptcov){ /* A real fixed covariate */
                                                                                                                                                 * If product of Vn*Vm, still boolean *:                                  ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                                                                                                                                 * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables                                                                                                                                                          * If product of Vn*Vm, still boolean *:
                                                                                                                                                 * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */                                                                                                                                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the                                                                                                                                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                                       modality of the nth covariate of individual i. */                                  /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
       if (ij > modmaxcovj)                                           modality of the nth covariate of individual i. */
         modmaxcovj=ij;                                   if (ij > modmaxcovj)
       else if (ij < modmincovj)                                           modmaxcovj=ij; 
                                 modmincovj=ij;                                   else if (ij < modmincovj) 
       if ((ij < -1) && (ij > NCOVMAX)){                                          modmincovj=ij; 
                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );                                  if ((ij < -1) && (ij > NCOVMAX)){
                                 exit(1);                                          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       }else                                          exit(1);
       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/                                  }else
                                           Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       /* getting the maximum value of the modality of the covariate        /* getting the maximum value of the modality of the covariate
          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and                                   (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
          female is 1, then modmaxcovj=1.*/                                   female ies 1, then modmaxcovj=1.*/
     } /* end for loop on individuals i */                          }
                   } /* end for loop on individuals i */
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);      fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     cptcode=modmaxcovj;      cptcode=modmaxcovj;
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    /*for (i=0; i<=cptcode; i++) {*/                  /*for (i=0; i<=cptcode; i++) {*/
     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */      for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
Line 4339  void  concatwav(int wav[], int **dh, int Line 4537  void  concatwav(int wav[], int **dh, int
                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */                                                                                                                                  undefined. Usually 3: -1, 0 and 1. */
       }        }
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
                                  historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */                           * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
                                   
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
Line 4360  void  concatwav(int wav[], int **dh, int Line 4558  void  concatwav(int wav[], int **dh, int
         if (Ndum[i] == 0) { /* If nobody responded to this modality k */          if (Ndum[i] == 0) { /* If nobody responded to this modality k */
                                 break;                                  break;
                         }                          }
         ij++;                          ij++;
         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/                          nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
         cptcode = ij; /* New max modality for covar j */                          cptcode = ij; /* New max modality for covar j */
     } /* end of loop on modality i=-1 to 1 or more */      } /* end of loop on modality i=-1 to 1 or more */
                         
     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
     /*  /\*recode from 0 *\/ */      /*  /\*recode from 0 *\/ */
     /*                               k is a modality. If we have model=V1+V1*sex  */      /*                               k is a modality. If we have model=V1+V1*sex  */
Line 4386  void  concatwav(int wav[], int **dh, int Line 4584  void  concatwav(int wav[], int **dh, int
                 /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/                   /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
                 ij=Tvar[i]; /* Tvar might be -1 if status was unknown */                   ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
                 Ndum[ij]++; /* Might be supersed V1 + V1*age */                  Ndum[ij]++; /* Might be supersed V1 + V1*age */
         }           } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
                   
         ij=0;          ij=0;
         for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */          for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
                 /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/                  /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
                 if((Ndum[i]!=0) && (i<=ncovcol)){                  if((Ndum[i]!=0) && (i<=ncovcol)){
                         ij++;  
                         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/                          /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                         Tvaraff[ij]=i; /*For printing (unclear) */                          Tvaraff[++ij]=i; /*For printing (unclear) */
                 }else{                  }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
                         /* Tvaraff[ij]=0; */                          Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
                   }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
                           Tvaraff[++ij]=i; /*For printing (unclear) */
                   }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
                    Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
                 }                  }
         }          } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
         /* ij--; */          /* ij--; */
         /* cptcoveff=ij; /\*Number of total covariates*\/ */          /* cptcoveff=ij; /\*Number of total covariates*\/ */
         *cptcov=ij; /*Number of total covariates*/          *cptcov=ij; /*Number of total real effective covariates: effective
                                                                    * because they can be excluded from the model and real
                                                            * if in the model but excluded because missing values*/
 }  }
   
   
Line 4520  void cvevsij(double ***eij, double x[], Line 4722  void cvevsij(double ***eij, double x[],
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .       to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
Line 4626  void cvevsij(double ***eij, double x[], Line 4828  void cvevsij(double ***eij, double x[],
        decrease memory allocation */         decrease memory allocation */
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
                                 xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                                 xm[i] = x[i] - (i==theta ?delti[theta]:0);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                                                   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
                                 for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
                                         for(h=0; h<=nhstepm-1; h++){            for(h=0; h<=nhstepm-1; h++){
                                                 gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                                                 gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                                         }            }
                                 }          }
       }        }
                                                   
       for(ij=1; ij<= nlstate*nlstate; ij++)        for(ij=1; ij<= nlstate*nlstate; ij++)
                                 for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
                                         gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                                 }          }
     }/* End theta */      }/* End theta */
           
           
     for(h=0; h<=nhstepm-1; h++)      for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
                                 for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
                                         trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
           
                                   
                 for(ij=1;ij<=nlstate*nlstate;ij++)      for(ij=1;ij<=nlstate*nlstate;ij++)
       for(ji=1;ji<=nlstate*nlstate;ji++)        for(ji=1;ji<=nlstate*nlstate;ji++)
                                 varhe[ij][ji][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
                                   
                 printf("%d|",(int)age);fflush(stdout);      printf("%d|",(int)age);fflush(stdout);
                 fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                 for(h=0;h<=nhstepm-1;h++){      for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
                                 matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                                 matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                                 for(ij=1;ij<=nlstate*nlstate;ij++)          for(ij=1;ij<=nlstate*nlstate;ij++)
                                         for(ji=1;ji<=nlstate*nlstate;ji++)            for(ji=1;ji<=nlstate*nlstate;ji++)
                                                 varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                                   
Line 4674  void cvevsij(double ***eij, double x[], Line 4876  void cvevsij(double ***eij, double x[],
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
                                 for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                                         eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                                                                                   
                                         /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                                                                   
                                 }          }
                                   
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
       vip=0.;        vip=0.;
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
                                 eip += eij[i][j][(int)age];          eip += eij[i][j][(int)age];
                                 for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                                         vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                                 fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       }        }
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
Line 4698  void cvevsij(double ***eij, double x[], Line 4900  void cvevsij(double ***eij, double x[],
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
                                 cptj= (j-1)*nlstate+i;          cptj= (j-1)*nlstate+i;
                                 for(i2=1; i2<=nlstate;i2++)          for(i2=1; i2<=nlstate;i2++)
                                         for(j2=1; j2<=nlstate;j2++){            for(j2=1; j2<=nlstate;j2++){
                                                 cptj2= (j2-1)*nlstate+i2;              cptj2= (j2-1)*nlstate+i2;
                                                 if(cptj2 <= cptj)              if(cptj2 <= cptj)
                                                         fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                                         }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                                   
Line 5161  void cvevsij(double ***eij, double x[], Line 5363  void cvevsij(double ***eij, double x[],
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {   {
   int i, j=0,  k1, l1, tj;     int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;     int k2, l2, j1,  z1;
   int k=0, l;     int k=0, l;
   int first=1, first1, first2;     int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;     double **dnewm,**doldm;
   double *xp;     double *xp;
   double *gp, *gm;     double *gp, *gm;
   double **gradg, **trgradg;     double **gradg, **trgradg;
   double **mu;     double **mu;
   double age, cov[NCOVMAX+1];     double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;     int theta;
   char fileresprob[FILENAMELENGTH];     char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];     char fileresprobcov[FILENAMELENGTH];
   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,fileresu);     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,fileresu);     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);
   }     }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   pstamp(ficresprob);     pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");     fprintf(ficresprob,"# Age");
   pstamp(ficresprobcov);     pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");     fprintf(ficresprobcov,"# Age");
   pstamp(ficresprobcor);     pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcor,"# Age");     fprintf(ficresprobcor,"# Age");
   
   
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }    
  /* fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  
  */  
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;  
   fprintf(ficgp,"\n# Routine varprob");  
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  
   fprintf(fichtm,"\n");  
   
   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);     for(i=1; i<=nlstate;i++)
   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);       for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   
      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,"\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.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
 It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
 standard deviations wide on each axis. <br>\  standard deviations wide on each axis. <br>\
Line 5248  standard deviations wide on each axis. < Line 5450  standard deviations wide on each axis. <
  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   cov[1]=1;     cov[1]=1;
   /* tj=cptcoveff; */     /* tj=cptcoveff; */
   tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,nqveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;     j1=0;
   for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
                 if  (cptcovn>0) {       if  (cptcovn>0) {
                         fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprob, "**********\n#\n");         fprintf(ficresprob, "**********\n#\n");
                         fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficresprobcov, "**********\n#\n");
                                                   
                         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=nqveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficgp, "**********\n#\n");         fprintf(ficgp, "**********\n#\n");
                                                   
                                                   
                         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=nqveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                                                   
                         fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "\n#********** Variable ");    
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=nqveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprobcor, "**********\n#");             fprintf(ficresprobcor, "**********\n#");    
                         if(invalidvarcomb[j1]){         if(invalidvarcomb[j1]){
                           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
                           fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);            fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                           continue;           continue;
                         }         }
                 }       }
                 gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                 trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                 gp=vector(1,(nlstate)*(nlstate+ndeath));       gp=vector(1,(nlstate)*(nlstate+ndeath));
                 gm=vector(1,(nlstate)*(nlstate+ndeath));       gm=vector(1,(nlstate)*(nlstate+ndeath));
                 for (age=bage; age<=fage; age ++){        for (age=bage; age<=fage; age ++){ 
                         cov[2]=age;         cov[2]=age;
                         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,k)];           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           /*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
                                                                                                                                                                                                                                                                          */                                                                      */
                                 /* 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,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,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];           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++){
                                 for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
                                         xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                                                   
                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);           pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                                                   
                                 k=0;           k=0;
                                 for(i=1; i<= (nlstate); i++){           for(i=1; i<= (nlstate); i++){
                                         for(j=1; j<=(nlstate+ndeath);j++){             for(j=1; j<=(nlstate+ndeath);j++){
                                                 k=k+1;               k=k+1;
                                                 gp[k]=pmmij[i][j];               gp[k]=pmmij[i][j];
                                         }             }
                                 }           }
                                                                   
                                 for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
                                         xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                                                                   
                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);           pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                 k=0;           k=0;
                                 for(i=1; i<=(nlstate); i++){           for(i=1; i<=(nlstate); i++){
                                         for(j=1; j<=(nlstate+ndeath);j++){             for(j=1; j<=(nlstate+ndeath);j++){
                                                 k=k+1;               k=k+1;
                                                 gm[k]=pmmij[i][j];               gm[k]=pmmij[i][j];
                                         }             }
                                 }           }
                                                                   
                                 for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                                         gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                         }         }
   
                         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                                 for(theta=1; theta <=npar; theta++)           for(theta=1; theta <=npar; theta++)
                                         trgradg[j][theta]=gradg[theta][j];             trgradg[j][theta]=gradg[theta][j];
                                                   
                         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                                                   
                         pmij(pmmij,cov,ncovmodel,x,nlstate);         pmij(pmmij,cov,ncovmodel,x,nlstate);
                                                   
                         k=0;         k=0;
                         for(i=1; i<=(nlstate); i++){         for(i=1; i<=(nlstate); i++){
                                 for(j=1; j<=(nlstate+ndeath);j++){           for(j=1; j<=(nlstate+ndeath);j++){
                                         k=k+1;             k=k+1;
                                         mu[k][(int) age]=pmmij[i][j];             mu[k][(int) age]=pmmij[i][j];
                                 }           }
                         }         }
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                                 for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                                         varpij[i][j][(int)age] = doldm[i][j];             varpij[i][j][(int)age] = doldm[i][j];
                                                   
                         /*printf("\n%d ",(int)age);         /*printf("\n%d ",(int)age);
                                 for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                                 printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                                 fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                                 }*/           }*/
                                                   
                         fprintf(ficresprob,"\n%d ",(int)age);         fprintf(ficresprob,"\n%d ",(int)age);
                         fprintf(ficresprobcov,"\n%d ",(int)age);         fprintf(ficresprobcov,"\n%d ",(int)age);
                         fprintf(ficresprobcor,"\n%d ",(int)age);         fprintf(ficresprobcor,"\n%d ",(int)age);
                                                   
                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                                 fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                                 fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                                 fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                         }         }
                         i=0;         i=0;
                         for (k=1; k<=(nlstate);k++){         for (k=1; k<=(nlstate);k++){
                                 for (l=1; l<=(nlstate+ndeath);l++){            for (l=1; l<=(nlstate+ndeath);l++){ 
                                         i++;             i++;
                                         fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                                         fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                                         for (j=1; j<=i;j++){             for (j=1; j<=i;j++){
                                                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                                                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                                                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                                         }             }
                                 }           }
                         }/* end of loop for state */         }/* end of loop for state */
                 } /* end of loop for age */       } /* end of loop for age */
                 free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                 free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                 free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           
                 /* Confidence intervalle of pij  */       /* Confidence intervalle of pij  */
                 /*       /*
                         fprintf(ficgp,"\nunset parametric;unset label");         fprintf(ficgp,"\nunset parametric;unset label");
                         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                 */       */
                                   
                 /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                 first1=1;first2=2;       first1=1;first2=2;
                 for (k2=1; k2<=(nlstate);k2++){       for (k2=1; k2<=(nlstate);k2++){
                         for (l2=1; l2<=(nlstate+ndeath);l2++){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                                 if(l2==k2) continue;           if(l2==k2) continue;
                                 j=(k2-1)*(nlstate+ndeath)+l2;           j=(k2-1)*(nlstate+ndeath)+l2;
                                 for (k1=1; k1<=(nlstate);k1++){           for (k1=1; k1<=(nlstate);k1++){
                                         for (l1=1; l1<=(nlstate+ndeath);l1++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                                                 if(l1==k1) continue;               if(l1==k1) continue;
                                                 i=(k1-1)*(nlstate+ndeath)+l1;               i=(k1-1)*(nlstate+ndeath)+l1;
                                                 if(i<=j) continue;               if(i<=j) continue;
                                                 for (age=bage; age<=fage; age ++){                for (age=bage; age<=fage; age ++){ 
                                                         if ((int)age %5==0){                 if ((int)age %5==0){
                                                                 v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 mu1=mu[i][(int) age]/stepm*YEARM ;                   mu1=mu[i][(int) age]/stepm*YEARM ;
                                                                 mu2=mu[j][(int) age]/stepm*YEARM;                   mu2=mu[j][(int) age]/stepm*YEARM;
                                                                 c12=cv12/sqrt(v1*v2);                   c12=cv12/sqrt(v1*v2);
                                                                 /* Computing eigen value of matrix of covariance */                   /* Computing eigen value of matrix of covariance */
                                                                 lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                   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.;                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                                                                 if ((lc2 <0) || (lc1 <0) ){                   if ((lc2 <0) || (lc1 <0) ){
                                                                         if(first2==1){                     if(first2==1){
                                                                                 first1=0;                       first1=0;
                                                                                 printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                                                                         }                     }
                                                                         fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                                                                         /* lc1=fabs(lc1); */ /* If we want to have them positive */                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
                                                                         /* lc2=fabs(lc2); */                     /* lc2=fabs(lc2); */
                                                                 }                   }
                                                                                                                                   
                                                                 /* Eigen vectors */                   /* Eigen vectors */
                                                                 v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                                                                 /*v21=sqrt(1.-v11*v11); *//* error */                   /*v21=sqrt(1.-v11*v11); *//* error */
                                                                 v21=(lc1-v1)/cv12*v11;                   v21=(lc1-v1)/cv12*v11;
                                                                 v12=-v21;                   v12=-v21;
                                                                 v22=v11;                   v22=v11;
                                                                 tnalp=v21/v11;                   tnalp=v21/v11;
                                                                 if(first1==1){                   if(first1==1){
                                                                         first1=0;                     first1=0;
                                                                         printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                                                                 }                   }
                                                                 fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                                                                 /*printf(fignu*/                   /*printf(fignu*/
                                                                 /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                                                                 /* 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,"\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",      \
                                                                 mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                            \                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
                                                                 mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                                                                 }else{                   }else{
                                                                         first=0;                     first=0;
                                                                         fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                                                                         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,"\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,"\nreplot %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,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                                                                                                         mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                    \                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
                                                                                                         mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                                                                 }/* if first */                   }/* if first */
                                                         } /* age mod 5 */                 } /* age mod 5 */
                                                 } /* end loop age */               } /* end loop age */
                                                 fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",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 */
                         } /*l1 */         } /*l1 */
                 }/* k1 */       }/* k1 */
         }  /* loop on combination of covariates j1 */     }  /* loop on combination of covariates j1 */
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_vector(xp,1,npar);     free_vector(xp,1,npar);
   fclose(ficresprob);     fclose(ficresprob);
   fclose(ficresprobcov);     fclose(ficresprobcov);
   fclose(ficresprobcor);     fclose(ficresprobcor);
   fflush(ficgp);     fflush(ficgp);
   fflush(fichtmcov);     fflush(fichtmcov);
 }   }
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
Line 5536  void printinghtml(char fileresu[], char Line 5738  void printinghtml(char fileresu[], char
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"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>");
   
  m=pow(2,cptcoveff);     m=pow(2,nqveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
   
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
          jj1++;       jj1++;
          if (cptcovn > 0) {       if (cptcovn > 0) {
                  fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                  for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=nqveff;cpt++){ 
                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
                          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
                  }         }
                  fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                  if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
                          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
                          printf("\nCombination (%d) ignored because no cases \n",k1);            printf("\nCombination (%d) ignored because no cases \n",k1); 
                          continue;           continue;
                  }         }
          }       }
          /* aij, bij */       /* aij, bij */
          fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), 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> \       fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), 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\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
          /* Pij */       /* Pij */
          fprintf(fichtm,"<br>\n- P<sub>ij</sub> 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> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> 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-2.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>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> 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, \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
 divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
 <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);   <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
          /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
          for(cpt=1; cpt<=nlstate;cpt++){       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> \         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);  <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) */       /* State specific survival functions (period) */
          for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
                  fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\         fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   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);   <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 */       /* 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);  
          }  
          if(backcast==1){  
      /* Period (stable) back prevalence in each health state */  
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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> \         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);
        }
        if(backcast==1){
          /* Period (stable) back prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
          }
      }       }
          }       if(prevfcast==1){
          if(prevfcast==1){         /* Projection of prevalence up to period (stable) prevalence in each health state */
                  /* Projection of prevalence up to period (stable) prevalence in each health state */         for(cpt=1; cpt<=nlstate;cpt++){
                  for(cpt=1; cpt<=nlstate;cpt++){           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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> \
                          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),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) (or area under each survival functions): <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 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
  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 if optimization has been done (mle != 0).<br> \   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
Line 5622  variances but at the covariance matrix. Line 5824  variances but at the covariance matrix.
 covariance matrix of the one-step probabilities. \  covariance matrix of the one-step probabilities. \
 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(fileresu,"PROB_"),subdirf2(fileresu,"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(fileresu,"PROBCOV_"),subdirf2(fileresu,"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(fileresu,"PROBCOR_"),subdirf2(fileresu,"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(fileresu,"CVE_"),subdirf2(fileresu,"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(fileresu,"STDE_"),subdirf2(fileresu,"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(fileresu,"V_"),subdirf2(fileresu,"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(fileresu,"T_"),subdirf2(fileresu,"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(fileresu,"VPL_"),subdirf2(fileresu,"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 5655  See page 'Matrix of variance-covariance Line 5857  See page 'Matrix of variance-covariance
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
  fflush(fichtm);     fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,nqveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
   /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                  jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=nqveff;cpt++) 
                                                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
                          if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
                                  fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
                                  continue;           continue;
                          }         }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
Line 5687  true period expectancies (those weighted Line 5889  true period expectancies (those weighted
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
 <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
  fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
         char gplotcondition[132];    char gplotcondition[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 lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
         int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 5711  true period expectancies (those weighted Line 5913  true period expectancies (those weighted
   
   /*#ifdef windows */    /*#ifdef windows */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,nqveff);
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the 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# 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,"\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 svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");    fprintf(ficgp,"\nset ter pngcairo size 640, 480");
 /* nice for mle=4 plot by number of matrix products.  /* 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  "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)"  */  /* 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.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));    fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));    fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 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 out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));    fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {    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,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));      fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);      fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {      for (j=2; j<= nlstate+ndeath ; j ++) {
                                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);        fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }      }
       fprintf(ficgp,";\nset out; unset ylabel;\n");       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 */                  /* 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,"\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,"\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;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */    /* 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*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */        for (k=1; k<=nqveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */          lv= decodtabm(k1,k,nqveff); /* Should be the value of the covariate corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
                         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;          continue;
                         }        }
   
                         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(fileresu,"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(fileresu,"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(fileresu,"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(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
                         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */        if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
                                 /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */          /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
                                 fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */          fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
                                 kl=0;          if(nqveff ==0){
                                 for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          }else{
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            kl=0;
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            for (k=1; k<=nqveff; k++){    /* For each combination of covariate  */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */              lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                         vlv= nbcode[Tvaraff[k]][lv];              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         kl++;              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */               vlv= nbcode[Tvaraff[k]][lv];
                                         /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               kl++;
                                         /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                         if(k==cptcoveff){              /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                                                                         6+(cpt-1),  cpt );              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                         }else{              if(k==nqveff){
                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                                                 kl++;                        6+(cpt-1),  cpt );
                                         }              }else{
                                 } /* end covariate */                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                         }                kl++;
                         fprintf(ficgp,"\nset out \n");              }
             } /* end covariate */
           } /* end if no covariate */
         } /* end if backcast */
         fprintf(ficgp,"\nset out \n");
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
   
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");      fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */      for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */        lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];        vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }      }
       fprintf(ficgp,"\n#\n");      fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){      if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;        continue;
                         }      }
                                                   
                         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);      fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
                         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*/
                                 if(vpopbased==0)        if(vpopbased==0)
                                         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
                                 else        else
                                         fprintf(ficgp,"\nreplot ");          fprintf(ficgp,"\nreplot ");
                                 for (i=1; i<= nlstate+1 ; i ++) {        for (i=1; i<= nlstate+1 ; i ++) {
                                         k=2*i;          k=2*i;
                                         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);          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 ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
                                         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
                                         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);          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 ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         fprintf(ficgp,"\" t\"\" w l lt 0,");          fprintf(ficgp,"\" t\"\" w l lt 0,");
                                         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);          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 ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                                         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");          else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
                                 } /* state */        } /* state */
                         } /* vpopbased */      } /* vpopbased */
                         fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */      fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
   } /* k1 */    } /* k1 */
                   
                   
Line 5871  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6077  plot [%.f:%.f] \"%s\" every :::%d::%d u
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;          continue;
                         }        }
                                                   
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
Line 5891  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6097  plot [%.f:%.f] \"%s\" every :::%d::%d u
       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(fileresu,"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);
                                 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);
                                                                   
       */        */
       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(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(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(fileresu,"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);
     }      }
   }    }
       
         /* 4eme */    /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* 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 */
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                         continue;          continue;
                         }        }
                                                   
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);        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\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 5934  unset log y\n Line 6140  unset log y\n
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3;        k=3;
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
                                 if(i==1){          if(i==1){
                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"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/($%d",k1,k+l+(cpt-1),k+l);
                                 for (j=2; j<= nlstate+ndeath ; j ++)          for (j=2; j<= nlstate+ndeath ; j ++)
                                         fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
                                 fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
Line 5953  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6159  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   /* Survival functions (period) from state i in state j by final state j */    /* 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 (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
                           
       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,"\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);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                  lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 5964  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6170  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;                                  continue;
                         }        }
                                                   
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);        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\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 6003  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6209  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */    for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                           
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                  lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 6014  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6220  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;                                  continue;
                         }        }
                           
       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);
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
Line 6039  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6245  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
           
           
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(backcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);                                  fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */                                  for (k=1; k<=nqveff; k++){    /* For each covariate and each value */
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate number corresponding to k1 combination */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];                                          vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }                                  }
                                 fprintf(ficgp,"\n#\n");                                  fprintf(ficgp,"\n#\n");
                                 if(invalidvarcomb[k1]){                                  if(invalidvarcomb[k1]){
                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                                 continue;                                          continue;
                                 }                                  }
                                                                   
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
Line 6087  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6293  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
       
         /* 8eme */    /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to stable (period) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);                                  fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                 for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */                                  for (k=1; k<=nqveff; k++){    /* For each correspondig covariate value  */
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                                          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 6104  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6310  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 }                                  }
                                 fprintf(ficgp,"\n#\n");                                  fprintf(ficgp,"\n#\n");
                                 if(invalidvarcomb[k1]){                                  if(invalidvarcomb[k1]){
                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                                 continue;                                          continue;
                                 }                                  }
                                                                   
                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");                                  fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\                                  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \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+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */                                  for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
Line 6124  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6330  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                         }else{                                          }else{
                                                 fprintf(ficgp,",\\\n '' ");                                                  fprintf(ficgp,",\\\n '' ");
                                         }                                          }
                                         if(cptcoveff ==0){ /* No covariate */                                          if(nqveff ==0){ /* No covariate */
                                                 ioffset=2; /* Age is in 2 */                                                  ioffset=2; /* Age is in 2 */
                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/                                                  /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */                                                  /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
Line 6138  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6344  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \                                                          fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                         }else{ /* more than 2 covariates */                                          }else{ /* more than 2 covariates */
                                                 if(cptcoveff ==1){                                                  if(nqveff ==1){
                                                         ioffset=4; /* Age is in 4 */                                                          ioffset=4; /* Age is in 4 */
                                                 }else{                                                  }else{
                                                         ioffset=6; /* Age is in 6 */                                                          ioffset=6; /* Age is in 6 */
                                                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/                                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                 /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */                                                          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                 }                                                     }   
                                                 fprintf(ficgp," u %d:(",ioffset);                                                   fprintf(ficgp," u %d:(",ioffset); 
                                                 kl=0;                                                  kl=0;
                                                 strcpy(gplotcondition,"(");                                                  strcpy(gplotcondition,"(");
                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */                                                  for (k=1; k<=nqveff; k++){    /* For each covariate writing the chain of conditions */
                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                                                          lv= decodtabm(k1,k,nqveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                                          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                                                          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 6157  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6363  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                         kl++;                                                          kl++;
                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                                                          sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                         kl++;                                                          kl++;
                                                         if(k <cptcoveff && cptcoveff>1)                                                          if(k <nqveff && nqveff>1)
                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                                                                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                 }                                                  }
                                                 strcpy(gplotcondition+strlen(gplotcondition),")");                                                  strcpy(gplotcondition+strlen(gplotcondition),")");
Line 6169  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6375  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                 }else{                                                  }else{
                                                                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                 }                                                  }
                                         } /* end if covariate */                                          } /* end if covariate */
                                 } /* nlstate */                                  } /* nlstate */
                                 fprintf(ficgp,"\nset out\n");                                  fprintf(ficgp,"\nset out\n");
                         } /* end cpt state*/        } /* end cpt state*/
                 } /* end covariate */      } /* end covariate */
         } /* End if prevfcast */    } /* End if prevfcast */
                   
                   
         /* 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++){
     fprintf(ficgp,"# initial state %d\n",i);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
         fprintf(ficgp,"#   current state %d\n",k);                                  fprintf(ficgp,"#   current state %d\n",k);
         for(j=1; j <=ncovmodel; j++){                                  for(j=1; j <=ncovmodel; j++){
           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);                                          fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
           jk++;                                           jk++; 
         }                                  }
         fprintf(ficgp,"\n");                                  fprintf(ficgp,"\n");
       }        }
     }      }
    }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
           
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics 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");
Line 6212  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6418  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<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences 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",nqveff,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\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
        fprintf(ficgp,"\nset ter svg size 640, 480 ");        fprintf(ficgp,"\nset ter svg size 640, 480 ");
        if (ng==1){        if (ng==1){
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
          fprintf(ficgp,"\nunset log y");          fprintf(ficgp,"\nunset log y");
        }else if (ng==2){        }else if (ng==2){
          fprintf(ficgp,"\nset ylabel \"Probability\"\n");          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
          fprintf(ficgp,"\nset log y");          fprintf(ficgp,"\nset log y");
        }else if (ng==3){        }else if (ng==3){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          fprintf(ficgp,"\nset log y");          fprintf(ficgp,"\nset log y");
        }else        }else
          fprintf(ficgp,"\nunset title ");          fprintf(ficgp,"\nunset title ");
        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        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){
              switch( ng) {              switch( ng) {
              case 1:              case 1:
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp," p%d+p%d*x",i,i+1);                  fprintf(ficgp," p%d+p%d*x",i,i+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                break;                break;
              case 2: /* ng=2 */              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;                break;
              case 3:              case 3:
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,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," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                break;                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,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])]); */                    /* 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)]);
              }              }
            }else{            }else{
              i=i-ncovmodel;              i=i-ncovmodel;
              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                fprintf(ficgp," (1.");                fprintf(ficgp," (1.");
            }            }
                         
            if(ng != 1){            if(ng != 1){
              fprintf(ficgp,")/(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,j-2)]);                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      /* 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,Tvar[j-2])]); */
                      ij++;                      ij++;
                    }                    }
                  }                  }
                  else                  else
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                    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,")");
              }              }
              fprintf(ficgp,")");              fprintf(ficgp,")");
              if(ng ==2)              if(ng ==2)
                fprintf(ficgp," t \"p%d%d\" ", k2,k);                fprintf(ficgp," t \"p%d%d\" ", k2,k);
              else /* ng= 3 */              else /* ng= 3 */
                fprintf(ficgp," t \"i%d%d\" ", k2,k);                fprintf(ficgp," t \"i%d%d\" ", k2,k);
            }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
              if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
            }            }
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
              fprintf(ficgp,",");              fprintf(ficgp,",");
            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
              fprintf(ficgp,",");              fprintf(ficgp,",");
            i=i+ncovmodel;            i=i+ncovmodel;
          } /* end k */          } /* end k */
        } /* end k2 */        } /* end k2 */
        fprintf(ficgp,"\n set out\n");        fprintf(ficgp,"\n set out\n");
      } /* end jk */      } /* end jk */
    } /* end ng */    } /* end ng */
  /* avoid: */    /* avoid: */
    fflush(ficgp);     fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */  /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
 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, cpt, cptcod;     int i, cpt, cptcod;
   int modcovmax =1;     int modcovmax =1;
   int mobilavrange, mob;     int mobilavrange, mob;
   int iage=0;     int iage=0;
   
   double sum=0.;     double sum=0.;
   double age;     double age;
   double *sumnewp, *sumnewm;     double *sumnewp, *sumnewm;
   double *agemingood, *agemaxgood; /* Currently identical for all covariates */     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
       
       
   /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */     /* modcovmax=2*nqveff;/\* Max number of modalities. We suppose  */
         /*                 a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */     /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
   
   sumnewp = vector(1,ncovcombmax);     sumnewp = vector(1,ncovcombmax);
   sumnewm = vector(1,ncovcombmax);     sumnewm = vector(1,ncovcombmax);
   agemingood = vector(1,ncovcombmax);        agemingood = vector(1,ncovcombmax);  
   agemaxgood = vector(1,ncovcombmax);     agemaxgood = vector(1,ncovcombmax);
   
   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                 sumnewm[cptcod]=0.;       sumnewm[cptcod]=0.;
                 sumnewp[cptcod]=0.;       sumnewp[cptcod]=0.;
                 agemingood[cptcod]=0;       agemingood[cptcod]=0;
                 agemaxgood[cptcod]=0;       agemaxgood[cptcod]=0;
         }     }
   if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
       
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if(mobilav==1) mobilavrange=5; /* default */       if(mobilav==1) mobilavrange=5; /* default */
     else mobilavrange=mobilav;       else mobilavrange=mobilav;
     for (age=bage; age<=fage; age++)       for (age=bage; age<=fage; age++)
       for (i=1; i<=nlstate;i++)         for (i=1; i<=nlstate;i++)
                                 for (cptcod=1;cptcod<=ncovcombmax;cptcod++)           for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
                                         mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     /* We keep the original values on the extreme ages bage, fage and for        /* We keep the original values on the extreme ages bage, fage and for 
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
        we use a 5 terms etc. until the borders are no more concerned.           we use a 5 terms etc. until the borders are no more concerned. 
     */        */ 
     for (mob=3;mob <=mobilavrange;mob=mob+2){       for (mob=3;mob <=mobilavrange;mob=mob+2){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                                 for (i=1; i<=nlstate;i++){           for (i=1; i<=nlstate;i++){
                                         for (cptcod=1;cptcod<=ncovcombmax;cptcod++){             for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                                                 mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                                                 for (cpt=1;cpt<=(mob-1)/2;cpt++){               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                                                 }               }
                                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                                         }             }
                                 }           }
       }/* end age */         }/* end age */
     }/* end mob */       }/* end mob */
   }else     }else
     return -1;       return -1;
   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
     /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
     agemingood[cptcod]=fage-(mob-1)/2;       if(invalidvarcomb[cptcod]){
     for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */         printf("\nCombination (%d) ignored because no cases \n",cptcod); 
       sumnewm[cptcod]=0.;         continue;
       for (i=1; i<=nlstate;i++){       }
         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];  
       }       agemingood[cptcod]=fage-(mob-1)/2;
       if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */       for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
                                 agemingood[cptcod]=age;         sumnewm[cptcod]=0.;
       }else{ /* bad */         for (i=1; i<=nlstate;i++){
                                 for (i=1; i<=nlstate;i++){           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                                         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];         }
                                 } /* i */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
       } /* end bad */           agemingood[cptcod]=age;
     }/* age */         }else{ /* bad */
     sum=0.;           for (i=1; i<=nlstate;i++){
     for (i=1; i<=nlstate;i++){             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];           } /* i */
     }         } /* end bad */
     if(fabs(sum - 1.) > 1.e-3) { /* bad */       }/* age */
       printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);       sum=0.;
       /* for (i=1; i<=nlstate;i++){ */       for (i=1; i<=nlstate;i++){
       /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       /* } /\* i *\/ */       }
     } /* end bad */       if(fabs(sum - 1.) > 1.e-3) { /* bad */
     /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
                 /* From youngest, finding the oldest wrong */         /* for (i=1; i<=nlstate;i++){ */
                 agemaxgood[cptcod]=bage+(mob-1)/2;         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                 for (age=bage+(mob-1)/2; age<=fage; age++){         /* } /\* i *\/ */
                         sumnewm[cptcod]=0.;       } /* end bad */
                         for (i=1; i<=nlstate;i++){       /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
                                 sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];       /* From youngest, finding the oldest wrong */
                         }       agemaxgood[cptcod]=bage+(mob-1)/2;
                         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */       for (age=bage+(mob-1)/2; age<=fage; age++){
                                 agemaxgood[cptcod]=age;         sumnewm[cptcod]=0.;
                         }else{ /* bad */         for (i=1; i<=nlstate;i++){
                                 for (i=1; i<=nlstate;i++){           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                                         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         }
                                 } /* i */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                         } /* end bad */           agemaxgood[cptcod]=age;
                 }/* age */         }else{ /* bad */
                 sum=0.;           for (i=1; i<=nlstate;i++){
                 for (i=1; i<=nlstate;i++){             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                         sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];           } /* i */
                 }         } /* end bad */
                 if(fabs(sum - 1.) > 1.e-3) { /* bad */       }/* age */
                         printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);       sum=0.;
                         /* for (i=1; i<=nlstate;i++){ */       for (i=1; i<=nlstate;i++){
                         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                         /* } /\* i *\/ */       }
                 } /* end bad */       if(fabs(sum - 1.) > 1.e-3) { /* bad */
                          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
                 for (age=bage; age<=fage; age++){         /* for (i=1; i<=nlstate;i++){ */
                         printf("%d %d ", cptcod, (int)age);         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                         sumnewp[cptcod]=0.;         /* } /\* i *\/ */
                         sumnewm[cptcod]=0.;       } /* end bad */
                         for (i=1; i<=nlstate;i++){                  
                                 sumnewp[cptcod]+=probs[(int)age][i][cptcod];       for (age=bage; age<=fage; age++){
                                 sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];         printf("%d %d ", cptcod, (int)age);
                                 /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */         sumnewp[cptcod]=0.;
                         }         sumnewm[cptcod]=0.;
                         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */         for (i=1; i<=nlstate;i++){
                 }           sumnewp[cptcod]+=probs[(int)age][i][cptcod];
                 /* printf("\n"); */           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
     /* } */           /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
     /* brutal averaging */         }
     for (i=1; i<=nlstate;i++){         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
       for (age=1; age<=bage; age++){       }
                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       /* printf("\n"); */
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /* } */
       }        /* brutal averaging */
       for (age=fage; age<=AGESUP; age++){       for (i=1; i<=nlstate;i++){
                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         for (age=1; age<=bage; age++){
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       }           /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
     } /* end i status */         }        
     for (i=nlstate+1; i<=nlstate+ndeath;i++){         for (age=fage; age<=AGESUP; age++){
       for (age=1; age<=AGESUP; age++){           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                                 /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/           /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
                                 mobaverage[(int)age][i][cptcod]=0.;         }
       }       } /* end i status */
     }       for (i=nlstate+1; i<=nlstate+ndeath;i++){
   }/* end cptcod */         for (age=1; age<=AGESUP; age++){
   free_vector(sumnewm,1, ncovcombmax);           /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
   free_vector(sumnewp,1, ncovcombmax);           mobaverage[(int)age][i][cptcod]=0.;
   free_vector(agemaxgood,1, ncovcombmax);         }
   free_vector(agemingood,1, ncovcombmax);       }
   return 0;     }/* end cptcod */
 }/* End movingaverage */     free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
     
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int nqveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
Line 6504  void prevforecast(char fileres[], double Line 6715  void prevforecast(char fileres[], double
   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);    printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);    fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (nqveff==0) ncodemax[nqveff]=1;
   
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 6525  void prevforecast(char fileres[], double Line 6736  void prevforecast(char fileres[], double
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
   
   i1=cptcoveff;    i1=nqveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
Line 6534  void prevforecast(char fileres[], double Line 6745  void prevforecast(char fileres[], double
   
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");        fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=nqveff;j++) {
                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficresf," yearproj age");        fprintf(ficresf," yearproj age");
Line 6559  void prevforecast(char fileres[], double Line 6770  void prevforecast(char fileres[], double
                                         for (h=0; h<=nhstepm; h++){                                          for (h=0; h<=nhstepm; h++){
                                                 if (h*hstepm/YEARM*stepm ==yearp) {                                                  if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");                fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++)                 for(j=1;j<=nqveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);                                                          fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                                                 }                                                   } 
Line 6593  void prevforecast(char fileres[], double Line 6804  void prevforecast(char fileres[], double
 }  }
   
 /* /\************** Back Forecasting ******************\/ */  /* /\************** Back Forecasting ******************\/ */
 /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */  /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int nqveff){ */
 /*   /\* back1, year, month, day of starting backection  */  /*   /\* back1, year, month, day of starting backection  */
 /*      agemin, agemax range of age */  /*      agemin, agemax range of age */
 /*      dateprev1 dateprev2 range of dates during which prevalence is computed */  /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
Line 6625  void prevforecast(char fileres[], double Line 6836  void prevforecast(char fileres[], double
 /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
 /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
                   
 /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */  /*   if (nqveff==0) ncodemax[nqveff]=1; */
                   
 /*   /\* if (mobilav!=0) { *\/ */  /*   /\* if (mobilav!=0) { *\/ */
 /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */  /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
Line 6653  void prevforecast(char fileres[], double Line 6864  void prevforecast(char fileres[], double
 /*   if(jprojmean==0) jprojmean=1; */  /*   if(jprojmean==0) jprojmean=1; */
 /*   if(mprojmean==0) jprojmean=1; */  /*   if(mprojmean==0) jprojmean=1; */
                   
 /*   i1=cptcoveff; */  /*   i1=nqveff; */
 /*   if (cptcovn < 1){i1=1;} */  /*   if (cptcovn < 1){i1=1;} */
       
 /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */  /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
Line 6662  void prevforecast(char fileres[], double Line 6873  void prevforecast(char fileres[], double
                   
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */  /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */  /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */  /*     for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){ */
 /*       k=k+1; */  /*       k=k+1; */
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */  /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
 /*       for(j=1;j<=cptcoveff;j++) { */  /*       for(j=1;j<=nqveff;j++) { */
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */  /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
 /*       } */  /*       } */
 /*       fprintf(ficresfb," yearbproj age"); */  /*       fprintf(ficresfb," yearbproj age"); */
Line 6687  void prevforecast(char fileres[], double Line 6898  void prevforecast(char fileres[], double
 /*                                      for (h=0; h<=nhstepm; h++){ */  /*                                      for (h=0; h<=nhstepm; h++){ */
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */  /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
 /*               fprintf(ficresfb,"\n"); */  /*               fprintf(ficresfb,"\n"); */
 /*               for(j=1;j<=cptcoveff;j++)  */  /*               for(j=1;j<=nqveff;j++)  */
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */  /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */  /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
 /*                                              }  */  /*                                              }  */
Line 6750  void populforecast(char fileres[], doubl Line 6961  void populforecast(char fileres[], doubl
   printf("Computing forecasting: result on file '%s' \n", filerespop);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (nqveff==0) ncodemax[nqveff]=1;
   
   /* if (mobilav!=0) { */    /* if (mobilav!=0) { */
   /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
Line 6785  void populforecast(char fileres[], doubl Line 6996  void populforecast(char fileres[], doubl
   }    }
       
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[nqveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficrespop,"\n#******");        fprintf(ficrespop,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=nqveff;j++) {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficrespop,"******\n");        fprintf(ficrespop,"******\n");
Line 7148  int readdata(char datafile[], int firsto Line 7359  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0;    int i=0, j=0, n=0, iv=0;
     int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;  
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
Line 7180  int readdata(char datafile[], int firsto Line 7392  int readdata(char datafile[], int firsto
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     strcpy(line, linetmp);      strcpy(line, linetmp);
         
       /* Loops on waves */
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           /* what_kind_of_number(strb); */
                                           dval=strtod(strb,&endptr); 
                                           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
                                           /* if(strb != endptr && *endptr == '\0') */
                                           /*    dval=dlval; */
                                           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                           cotqvar[j][iv][i]=dval; 
                                   }
                                   strcpy(line,stra);
         }/* end loop ntqv */
                           
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           lval=strtol(strb,&endptr,10); 
                                           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                   }
                                   if(lval <-1 || lval >1){
                                           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                                                                                                                \
    Exiting.\n",lval,linei, i,line,j);
                                           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                                           return 1;
                                   }
                                   cotvar[j][iv][i]=(double)(lval);
                                   strcpy(line,stra);
         }/* end loop ntv */
   
         /* Statuses  at wave */
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing value */
         lval=-1;                                  lval=-1;
       }else{        }else{
         errno=0;                                  errno=0;
         lval=strtol(strb,&endptr,10);                                   lval=strtol(strb,&endptr,10); 
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/                                  /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){                                  if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);                                          printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);                                          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
           return 1;                                          return 1;
         }                                  }
       }        }
        
       s[j][i]=lval;        s[j][i]=lval;
         
         /* Date of Interview */
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }        }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;                                  month=99;
         year=9999;                                  year=9999;
       }else{        }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);                                  printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);                                  fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
         return 1;                                  return 1;
       }        }
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month; 
       strcpy(line,stra);        strcpy(line,stra);
     } /* ENd Waves */      } /* End loop on waves */
       
       /* Date of death */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 7223  int readdata(char datafile[], int firsto Line 7500  int readdata(char datafile[], int firsto
       year=9999;        year=9999;
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);                          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
     }      }
     andc[i]=(double) year;       andc[i]=(double) year; 
     moisdc[i]=(double) month;       moisdc[i]=(double) month; 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Date of birth */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 7239  int readdata(char datafile[], int firsto Line 7517  int readdata(char datafile[], int firsto
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
     }      }
     if (year==9999) {      if (year==9999) {
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
   
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
     strcpy(line,stra);      strcpy(line,stra);
       
       /* Sample weight */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     dval=strtod(strb,&endptr);       dval=strtod(strb,&endptr); 
Line 7262  int readdata(char datafile[], int firsto Line 7541  int readdata(char datafile[], int firsto
     }      }
     weight[i]=dval;       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
   
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
                                   lval=-1;
         }else{
                                   errno=0;
                                   /* what_kind_of_number(strb); */
                                   dval=strtod(strb,&endptr);
                                   /* if(strb != endptr && *endptr == '\0') */
                                   /*   dval=dlval; */
                                   /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                   if( strb[0]=='\0' || (*endptr != '\0')){
                                           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
                                           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
                                           return 1;
                                   }
                                   coqvar[iv][i]=dval; 
         }
         strcpy(line,stra);
       }/* end loop nqv */
           
       /* Covariate values */
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing covariate value */
         lval=-1;                                  lval=-1;
       }else{        }else{
         errno=0;                                  errno=0;
         lval=strtol(strb,&endptr,10);                                   lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){                                  if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);                                          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);                                          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
           return 1;                                          return 1;
         }                                  }
       }        }
       if(lval <-1 || lval >1){        if(lval <-1 || lval >1){
         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \                                  printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n \
Line 7286  int readdata(char datafile[], int firsto Line 7587  int readdata(char datafile[], int firsto
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n \   output of IMaCh is often meaningless.\n \
  Exiting.\n",lval,linei, i,line,j);   Exiting.\n",lval,linei, i,line,j);
         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \                                  fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n \
Line 7295  int readdata(char datafile[], int firsto Line 7596  int readdata(char datafile[], int firsto
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n \   output of IMaCh is often meaningless.\n \
  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
         return 1;                                  return 1;
       }        }
       covar[j][i]=(double)(lval);        covar[j][i]=(double)(lval);
       strcpy(line,stra);        strcpy(line,stra);
Line 7319  int readdata(char datafile[], int firsto Line 7620  int readdata(char datafile[], int firsto
     
   return (0);    return (0);
   /* endread: */    /* endread: */
     printf("Exiting readdata: ");          printf("Exiting readdata: ");
     fclose(fic);          fclose(fic);
     return (1);          return (1);
   
   
   
 }  }
   
 void removespace(char *str) {  void removespace(char *str) {
   char *p1 = str, *p2 = str;    char *p1 = str, *p2 = str;
   do    do
Line 7334  void removespace(char *str) { Line 7633  void removespace(char *str) {
   while (*p1++ == *p2++);    while (*p1++ == *p2++);
 }  }
   
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:  int decodemodel ( char model[], int lastobs)
    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age   /**< This routine decode the model and returns:
    * - nagesqr = 1 if age*age in the model, otherwise 0.          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age          * - nagesqr = 1 if age*age in the model, otherwise 0.
    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
    * - cptcovage number of covariates with age*products =2          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
    * - cptcovs number of simple covariates          * - cptcovage number of covariates with age*products =2
    * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10          * - cptcovs number of simple covariates
    *     which is a new column after the 9 (ncovcol) variables.           * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual          *     which is a new column after the 9 (ncovcol) variables. 
    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage          * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
  */          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
           */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int  j1, k1, k2;    int  j1, k1, k2;
Line 7372  int decodemodel ( char model[], int last Line 7672  int decodemodel ( char model[], int last
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \                                  printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \                                  fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
       return 1;                                  return 1;
     }                          }
   
       nagesqr=1;        nagesqr=1;
       if (strstr(model,"+age*age") !=0)        if (strstr(model,"+age*age") !=0)
         substrchaine(modelsav, model, "+age*age");                                  substrchaine(modelsav, model, "+age*age");
       else if (strstr(model,"age*age+") !=0)        else if (strstr(model,"age*age+") !=0)
         substrchaine(modelsav, model, "age*age+");                                  substrchaine(modelsav, model, "age*age+");
       else         else 
         substrchaine(modelsav, model, "age*age");                                  substrchaine(modelsav, model, "age*age");
     }else      }else
       nagesqr=0;        nagesqr=0;
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){
       j=nbocc(modelsav,'+'); /**< j=Number of '+' */        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */        cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
       cptcovt= j+1; /* Number of total covariates in the model, not including        cptcovt= j+1; /* Number of total covariates in the model, not including
                    * cst, age and age*age                                                                                    * cst, age and age*age 
                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/                                                                                   * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                   /* including age products which are counted in cptcovage.                          /* including age products which are counted in cptcovage.
                   * but the covariates which are products must be treated                            * but the covariates which are products must be treated 
                   * separately: ncovn=4- 2=2 (V1+V3). */                           * separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
   
Line 7411  int decodemodel ( char model[], int last Line 7711  int decodemodel ( char model[], int last
        *   k=  1    2      3       4     5       6      7        8         *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:         *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k         *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1         *       if products, new covar are created after ncovcol with k1
Line 7456  int decodemodel ( char model[], int last Line 7756  int decodemodel ( char model[], int last
         Tvar[k]=0;          Tvar[k]=0;
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'                                   cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */                                                                                                                                                                    modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */                                  if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                                  /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/                                  /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */                                  if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */                                          cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */                                          if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */                                                  /* covar is not filled and then is empty */
             cptcovprod--;                                                  cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */                                                  cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */                                                  Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             cptcovage++; /* Sums the number of covariates which include age as a product */                                                  cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */                                                  Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/                                                  /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */                                          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;                                                  cptcovprod--;
             cutl(stre,strb,strc,'V');                                                  cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);                                                  Tvar[k]=atoi(stre);
             cptcovage++;                                                  cptcovage++;
             Tage[cptcovage]=k;                                                  Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/                                          } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */                                                  /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;                                                  cptcovn++;
             cptcovprodnoage++;k1++;                                                  cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/                                                  cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but                                                  Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                    because this model-covariate is a construction we invent a new column                                                                                                                                           because this model-covariate is a construction we invent a new column
                                    ncovcol + k1                                                                                                                                           ncovcol + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                                                                                                           If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                                                                                                           Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */                                                  cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */                                                  Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/                                                  Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/                                                  Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;                                                  k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */                                                  Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */                                                  Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){                                                  for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of                                                          /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                                                                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];                                                          covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }                                                  }
           } /* End age is not in the model */                                          } /* End age is not in the model */
         } /* End if model includes a product */                                  } /* End if model includes a product */
         else { /* no more sum */                                  else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                                          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/                                          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');                                          cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */                                          ks++; /**< Number of simple covariates */
           cptcovn++;                                          cptcovn++;
           Tvar[k]=atoi(strd);                                          Tvar[k]=atoi(strd);
         }                                  }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */                                   strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/                                          scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* end if strlen(model == 0) */
Line 7520  int decodemodel ( char model[], int last Line 7820  int decodemodel ( char model[], int last
     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);                   printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
   scanf("%d ",i);*/                   scanf("%d ",i);*/
   /* Dispatching in quantitative and time varying covariates */
   
           for(k=1, ncoveff=0, nqveff=0, ntveff=0, nqtveff=0;k<=cptcovn; k++){ /* or cptocvt */
                   if (Tvar[k] <=ncovcol){
                           ncoveff++;
                   }else if( Tvar[k] <=ncovcol+nqv){
                           nqveff++;
                   }else if( Tvar[k] <=ncovcol+nqv+ntv){
                           ntveff++;
                   }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
                           nqtveff++;
                   }else
                           printf("Error in effective covariates \n");
           }
   
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
     printf("Exiting decodemodel: ");          printf("Exiting decodemodel: ");
     return (1);          return (1);
 }  }
   
 int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
Line 7864  int prevalence_limit(double *p, double * Line 8177  int prevalence_limit(double *p, double *
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   
   i1=pow(2,cptcoveff);    i1=pow(2,ncoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){
Line 7877  int prevalence_limit(double *p, double * Line 8190  int prevalence_limit(double *p, double *
     fprintf(ficrespl,"#******");      fprintf(ficrespl,"#******");
     printf("#******");      printf("#******");
     fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=nqveff;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)]);
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 7893  int prevalence_limit(double *p, double * Line 8206  int prevalence_limit(double *p, double *
                 }                  }
   
     fprintf(ficrespl,"#Age ");      fprintf(ficrespl,"#Age ");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=nqveff;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);
Line 7903  int prevalence_limit(double *p, double * Line 8216  int prevalence_limit(double *p, double *
       /* for (age=agebase; age<=agebase; age++){ */        /* for (age=agebase; age<=agebase; age++){ */
       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);        prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
       fprintf(ficrespl,"%.0f ",age );        fprintf(ficrespl,"%.0f ",age );
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=nqveff;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)]);
       tot=0.;        tot=0.;
       for(i=1; i<=nlstate;i++){        for(i=1; i<=nlstate;i++){
Line 7951  int back_prevalence_limit(double *p, dou Line 8264  int back_prevalence_limit(double *p, dou
   agelim=agemaxpar;    agelim=agemaxpar;
       
       
   i1=pow(2,cptcoveff);    i1=pow(2,nqveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
         for(k=1; k<=i1;k++){           for(k=1; k<=i1;k++){ 
Line 7964  int back_prevalence_limit(double *p, dou Line 8277  int back_prevalence_limit(double *p, dou
     fprintf(ficresplb,"#******");      fprintf(ficresplb,"#******");
     printf("#******");      printf("#******");
     fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=nqveff;j++) {
       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresplb," 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)]);
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 7980  int back_prevalence_limit(double *p, dou Line 8293  int back_prevalence_limit(double *p, dou
                 }                  }
           
     fprintf(ficresplb,"#Age ");      fprintf(ficresplb,"#Age ");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=nqveff;j++) {
       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     }      }
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);      for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
Line 8002  int back_prevalence_limit(double *p, dou Line 8315  int back_prevalence_limit(double *p, dou
                                 bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);                                  bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
       }        }
       fprintf(ficresplb,"%.0f ",age );        fprintf(ficresplb,"%.0f ",age );
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=nqveff;j++)
                                 fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       tot=0.;        tot=0.;
       for(i=1; i<=nlstate;i++){        for(i=1; i<=nlstate;i++){
Line 8050  int hPijx(double *p, int bage, int fage) Line 8363  int hPijx(double *p, int bage, int fage)
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);      i1= pow(2,nqveff);
                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,nqveff); k++){
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=nqveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
Line 8122  int hPijx(double *p, int bage, int fage) Line 8435  int hPijx(double *p, int bage, int fage)
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   pstamp(ficrespijb);    pstamp(ficrespijb);
   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");    fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
   i1= pow(2,cptcoveff);    i1= pow(2,nqveff);
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for (k=1; k <= (int) pow(2,cptcoveff); k++){    for (k=1; k <= (int) pow(2,nqveff); k++){
     fprintf(ficrespijb,"\n#****** ");      fprintf(ficrespijb,"\n#****** ");
     for(j=1;j<=cptcoveff;j++)      for(j=1;j<=nqveff;j++)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     fprintf(ficrespijb,"******\n");      fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
           
     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */      /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */      for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
Line 8445  int main(int argc, char *argv[]) Line 8762  int main(int argc, char *argv[])
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \    if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){                          &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
     if (num_filled != 8) {      if (num_filled != 11) {
       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       printf("but line=%s\n",line);        printf("but line=%s\n",line);
     }      }
     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 nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, 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*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 8489  int main(int argc, char *argv[]) Line 8806  int main(int argc, char *argv[])
   /* 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); */
   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(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, 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);    fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, 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 8519  int main(int argc, char *argv[]) Line 8836  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     coqvar=matrix(1,nqv,1,n);  /**< used in readdata */
     cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< used in readdata */
     cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< used in readdata */
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
Line 8786  Please run with mle=-1 to get a correct Line 9106  Please run with mle=-1 to get a correct
 /* Main decodemodel */  /* Main decodemodel */
   
   
   if(decodemodel(model, lastobs) == 1)    if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
     goto end;      goto end;
   
   if((double)(lastobs-imx)/(double)imx > 1.10){    if((double)(lastobs-imx)/(double)imx > 1.10){
Line 9014  Title=%s <br>Datafile=%s Firstpass=%d La Line 9334  Title=%s <br>Datafile=%s Firstpass=%d La
                  and for any valid combination of covariates                   and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
               firstpass, lastpass,  stepm,  weightopt, model);                                                          firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 9043  Interval (in months) between two waves: Line 9363  Interval (in months) between two waves:
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
     dcwave=ivector(1,n);      dcwave=ivector(1,n);
                    
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
Line 9288  Please run with mle=-1 to get a correct Line 9608  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 9543  Please run with mle=-1 to get a correct Line 9863  Please run with mle=-1 to get a correct
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);      fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
     fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
           
Line 9635  Please run with mle=-1 to get a correct Line 9955  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(fileresu, 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, nqveff);
     }      }
     if(backcast==1){      if(backcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
Line 9648  Please run with mle=-1 to get a correct Line 9968  Please run with mle=-1 to get a correct
       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
       fclose(ficresplb);        fclose(ficresplb);
   
       /* hBijx(p, bage, fage, mobaverage); */        hBijx(p, bage, fage, mobaverage);
       /* fclose(ficrespijb); */        fclose(ficrespijb);
       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */        free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,        /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */           bage, fage, firstpass, lastpass, anback2, p, nqveff); */
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
Line 9679  Please run with mle=-1 to get a correct Line 9999  Please run with mle=-1 to get a correct
     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
                                   
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,nqveff); k++){
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=nqveff;j++) {
                                 fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
Line 9739  Please run with mle=-1 to get a correct Line 10059  Please run with mle=-1 to get a correct
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,nqveff); k++){
       fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=nqveff;j++) 
                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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<=nqveff;j++) {
                                 fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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]][codtabm(k,j)]);                                  fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
Line 9755  Please run with mle=-1 to get a correct Line 10075  Please run with mle=-1 to get a correct
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
               
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=nqveff;j++) 
                                 fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
Line 9865  Please run with mle=-1 to get a correct Line 10185  Please run with mle=-1 to get a correct
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,nqveff); k++){
         fprintf(ficresvpl,"\n#****** ");          fprintf(ficresvpl,"\n#****** ");
                         for(j=1;j<=cptcoveff;j++)                           for(j=1;j<=nqveff;j++) 
                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                         fprintf(ficresvpl,"******\n");                          fprintf(ficresvpl,"******\n");
               
Line 9893  Please run with mle=-1 to get a correct Line 10213  Please run with mle=-1 to get a correct
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
       free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
       free_matrix(coqvar,1,maxwav,1,n);
     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_matrix(hess,1,npar,1,npar);
Removed from v.1.220  
changed lines
  Added in v.1.224

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