Diff for /imach/src/imach.c between versions 1.286 and 1.303

version 1.286, 2018/04/27 14:27:04 version 1.303, 2021/02/11 19:50:15
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.303  2021/02/11 19:50:15  brouard
     *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
   
     Revision 1.302  2020/02/22 21:00:05  brouard
     *  (Module): imach.c Update mle=-3 (for computing Life expectancy
     and life table from the data without any state)
   
     Revision 1.301  2019/06/04 13:51:20  brouard
     Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
   
     Revision 1.300  2019/05/22 19:09:45  brouard
     Summary: version 0.99r19 of May 2019
   
     Revision 1.299  2019/05/22 18:37:08  brouard
     Summary: Cleaned 0.99r19
   
     Revision 1.298  2019/05/22 18:19:56  brouard
     *** empty log message ***
   
     Revision 1.297  2019/05/22 17:56:10  brouard
     Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
   
     Revision 1.296  2019/05/20 13:03:18  brouard
     Summary: Projection syntax simplified
   
   
     We can now start projections, forward or backward, from the mean date
     of inteviews up to or down to a number of years of projection:
     prevforecast=1 yearsfproj=15.3 mobil_average=0
     or
     prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
     or
     prevbackcast=1 yearsbproj=12.3 mobil_average=1
     or
     prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
   
     Revision 1.295  2019/05/18 09:52:50  brouard
     Summary: doxygen tex bug
   
     Revision 1.294  2019/05/16 14:54:33  brouard
     Summary: There was some wrong lines added
   
     Revision 1.293  2019/05/09 15:17:34  brouard
     *** empty log message ***
   
     Revision 1.292  2019/05/09 14:17:20  brouard
     Summary: Some updates
   
     Revision 1.291  2019/05/09 13:44:18  brouard
     Summary: Before ncovmax
   
     Revision 1.290  2019/05/09 13:39:37  brouard
     Summary: 0.99r18 unlimited number of individuals
   
     The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
   
     Revision 1.289  2018/12/13 09:16:26  brouard
     Summary: Bug for young ages (<-30) will be in r17
   
     Revision 1.288  2018/05/02 20:58:27  brouard
     Summary: Some bugs fixed
   
     Revision 1.287  2018/05/01 17:57:25  brouard
     Summary: Bug fixed by providing frequencies only for non missing covariates
   
   Revision 1.286  2018/04/27 14:27:04  brouard    Revision 1.286  2018/04/27 14:27:04  brouard
   Summary: some minor bugs    Summary: some minor bugs
   
Line 1040  typedef struct { Line 1105  typedef struct {
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20  /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 /* #define AGESUP 130 */  /* #define AGESUP 130 */
 #define AGESUP 150  /* #define AGESUP 150 */
   #define AGESUP 200
 #define AGEINF 0  #define AGEINF 0
 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
Line 1067  typedef struct { Line 1133  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";  char copyright[]="May 2019,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020";
 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 1091  int nqfveff=0; /**< nqfveff Number of Qu Line 1157  int nqfveff=0; /**< nqfveff Number of Qu
 int ntveff=0; /**< ntveff number of effective time varying variables */  int ntveff=0; /**< ntveff number of effective time varying variables */
 int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int nobs=10;  /* Number of observations in the data lastobs-firstobs */
 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; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
 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 */
Line 1231  double **pmmij, ***probs; /* Global poin Line 1298  double **pmmij, ***probs; /* Global poin
 double ***mobaverage, ***mobaverages; /* New global variable */  double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
     double anprojd, mprojd, jprojd; /* For eventual projections */
     double anprojf, mprojf, jprojf;
   
     double anbackd, mbackd, jbackd; /* For eventual backprojections */
     double anbackf, mbackf, jbackf;
     double jintmean,mintmean,aintmean;  
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc;  double *agedc;
Line 2350  void powell(double p[], double **xi, int Line 2422  void powell(double p[], double **xi, int
     /* 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++) {        for(j=1;j<=n;j++) {
                                 if(flatdir[j] >0){          if(flatdir[j] >0){
                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);            printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);            fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                 }          }
                                 /* printf("\n"); */          /* printf("\n"); */
                                 /* fprintf(ficlog,"\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? *\/ */
     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */      if (2.0*fabs(fp-(*fret)) <= ftol) { /* 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 */
Line 2574  void powell(double p[], double **xi, int Line 2646  void powell(double p[], double **xi, int
   double **newm;    double **newm;
   double agefin, delaymax=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
     int first=0;
       
   min=vector(1,nlstate);    min=vector(1,nlstate);
   max=vector(1,nlstate);    max=vector(1,nlstate);
Line 2670  void powell(double p[], double **xi, int Line 2743  void powell(double p[], double **xi, int
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\    if(!first){
 Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);      first=1;
       printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
     }
     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
   
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
   free_vector(max,1,nlstate);    free_vector(max,1,nlstate);
Line 2739  Earliest age to start was %d-%d=%d, ncvl Line 2816  Earliest age to start was %d-%d=%d, ncvl
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */    /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
     ncvloop++;      ncvloop++;
     newm=savm; /* oldm should be kept from previous iteration or unity at start */      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
Line 2853  Earliest age to start was %d-%d=%d, ncvl Line 2931  Earliest age to start was %d-%d=%d, ncvl
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return bprlim;        return bprlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   if(first){    if(!first){
     first=1;      first=1;
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\      printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
 Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
Line 2938  double **pmij(double **ps, double *cov, Line 3016  double **pmij(double **ps, double *cov,
       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]); */
Line 2959  double **pmij(double **ps, double *cov, Line 3037  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 combination ij. In fact cov is already filled and x too.    /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
    */     */
   int i, ii, j,k;    int i, ii, j,k;
Line 2967  double **pmij(double **ps, double *cov, Line 3045  double **pmij(double **ps, double *cov,
   double **out, **pmij();    double **out, **pmij();
   double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
   double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */    double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
   double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
   double **bbmij;    double **bbmij;
       
Line 2986  double **pmij(double **ps, double *cov, Line 3064  double **pmij(double **ps, double *cov,
   /* outputs pmmij which is a stochastic matrix in row */    /* outputs pmmij which is a stochastic matrix in row */
   
   /* Diag(w_x) */    /* Diag(w_x) */
   /* Problem with prevacurrent which can be zero */    /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
   sumnew=0.;    sumnew=0.;
   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/    /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */    for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */      /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
     sumnew+=prevacurrent[(int)agefin][ii][ij];      sumnew+=prevacurrent[(int)agefin][ii][ij];
   }    }
   if(sumnew >0.01){  /* At least some value in the prevalence */    if(sumnew >0.01){  /* At least some value in the prevalence */
Line 3013  double **pmij(double **ps, double *cov, Line 3091  double **pmij(double **ps, double *cov,
   }    }
   /* End doldm, At the end doldm is diag[(w_i)] */    /* End doldm, At the end doldm is diag[(w_i)] */
       
   /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */    /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */    bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
   
   /* Diag(Sum_i w^i_x p^ij_x */    /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */    /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
   for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
     sumnew=0.;      sumnew=0.;
Line 3034  double **pmij(double **ps, double *cov, Line 3112  double **pmij(double **ps, double *cov,
     } /*End ii */      } /*End ii */
   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */    } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
   
   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
   /* end bmij */    /* end bmij */
   return ps; /*pointer is unchanged */    return ps; /*pointer is unchanged */
Line 3106  double **bpmij(double **ps, double *cov, Line 3184  double **bpmij(double **ps, double *cov,
       ps[ii][ii]=1;        ps[ii][ii]=1;
     }      }
   }    }
   /* Added for backcast */ /* Transposed matrix too */    /* Added for prevbcast */ /* Transposed matrix too */
   for(jj=1; jj<= nlstate+ndeath; jj++){    for(jj=1; jj<= nlstate+ndeath; jj++){
     s1=0.;      s1=0.;
     for(ii=1; ii<= nlstate+ndeath; ii++){      for(ii=1; ii<= nlstate+ndeath; ii++){
Line 3866  return -l; Line 3944  return -l;
   
   
 /*************** function likelione ***********/  /*************** function likelione ***********/
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
 {  {
   /* This routine should help understanding what is done with     /* This routine should help understanding what is done with 
      the selection of individuals/waves and       the selection of individuals/waves and
Line 3890  void likelione(FILE *ficres,double p[], Line 3968  void likelione(FILE *ficres,double p[],
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
   *fretone=(*funcone)(p);    *fretone=(*func)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     if (mle ==0)      if (mle ==0)
Line 4365  void pstamp(FILE *fichier) Line 4443  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
   void date2dmy(double date,double *day, double *month, double *year){
     double yp=0., yp1=0., yp2=0.;
     
     yp1=modf(date,&yp);/* extracts integral of date in yp  and
                           fractional in yp1 */
     *year=yp;
     yp2=modf((yp1*12),&yp);
     *month=yp;
     yp1=modf((yp2*30.5),&yp);
     *day=yp;
     if(*day==0) *day=1;
     if(*month==0) *month=1;
   }
   
   
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
Line 4939  Title=%s <br>Datafile=%s Firstpass=%d La Line 5031  Title=%s <br>Datafile=%s Firstpass=%d La
     }      }
   } /* end mle=-2 */    } /* end mle=-2 */
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
     date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
       
   fclose(ficresp);    fclose(ficresp);
   fclose(ficresphtm);    fclose(ficresphtm);
Line 5052  void prevalence(double ***probs, double Line 5145  void prevalence(double ***probs, double
   /*j=cptcoveff;*/    /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;    first=0;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
Line 5110  void prevalence(double ***probs, double Line 5203  void prevalence(double ***probs, double
           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){
               first=0;                first=1;
               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);  
             }else{              }else{
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
             }              }
           }            }
         }           } 
Line 5133  void prevalence(double ***probs, double Line 5225  void prevalence(double ***probs, double
   
 void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
      Death is a valid wave (if date is known).       Death is a valid wave (if date is known).
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      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. s[m][i] exists for any wave from firstpass to lastpass
   */    */
   
   int i=0, mi=0, m=0, mli=0;    int i=0, mi=0, m=0, mli=0;
Line 5175  void  concatwav(int wav[], int **dh, int Line 5267  void  concatwav(int wav[], int **dh, int
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){            if(firsthree == 0){
             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 1-p%d%d .\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, s[m][i], nlstate+ndeath);              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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
           }            }
           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 1-p%d%d .\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, s[m][i], nlstate+ndeath);            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 1-p_{%d%d} .\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, s[m][i], nlstate+ndeath);
           mw[++mi][i]=m;            mw[++mi][i]=m;
           mli=m;            mli=m;
         }          }
Line 5366  void  concatwav(int wav[], int **dh, int Line 5458  void  concatwav(int wav[], int **dh, int
        nbcode[k][j]=0; /* Valgrind */         nbcode[k][j]=0; /* Valgrind */
   
    /* Loop on covariates without age and products and no quantitative variable */     /* 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 (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */     for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
Line 5384  void  concatwav(int wav[], int **dh, int Line 5475  void  concatwav(int wav[], int **dh, int
              modmaxcovj=ij;                modmaxcovj=ij; 
            else if (ij < modmincovj)              else if (ij < modmincovj) 
              modmincovj=ij;                modmincovj=ij; 
            if ((ij < -1) && (ij > NCOVMAX)){             if (ij <0 || ij >1 ){
                printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
                fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
              }
              if ((ij < -1) || (ij > NCOVMAX)){
              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
              exit(1);               exit(1);
            }else             }else
Line 5430  void  concatwav(int wav[], int **dh, int Line 5525  void  concatwav(int wav[], int **dh, int
          /* nbcode[Tvar[j]][3]=2; */           /* nbcode[Tvar[j]][3]=2; */
          /* To be continued (not working yet). */           /* To be continued (not working yet). */
          ij=0; /* ij is similar to i but can jump over null modalities */           ij=0; /* ij is similar to i but can jump over null modalities */
          for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/  
            /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
            /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
            /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
             * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
            /*, could be restored in the future */
            for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
            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[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/             nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
            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 */
          break;           break;
Line 5451  void  concatwav(int wav[], int **dh, int Line 5552  void  concatwav(int wav[], int **dh, int
          break;           break;
        } /* end switch */         } /* end switch */
      } /* end dummy test */       } /* end dummy test */
          } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */  
      /*         /\*recode from 0 *\/ */  
      /*                                      k is a modality. If we have model=V1+V1*sex  */  
      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */  
      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */  
      /*         } */  
      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */  
      /*         if (ij > ncodemax[j]) { */  
      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */  
      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */  
      /*           break; */  
      /*         } */  
      /*   }  /\* end of loop on modality k *\/ */  
    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/    
       
    for (k=-1; k< maxncov; k++) Ndum[k]=0;      for (k=-1; k< maxncov; k++) Ndum[k]=0; 
    /* Look at fixed dummy (single or product) covariates to check empty modalities */     /* Look at fixed dummy (single or product) covariates to check empty modalities */
Line 5849  void  concatwav(int wav[], int **dh, int Line 5936  void  concatwav(int wav[], int **dh, int
    double **dnewm,**doldm;     double **dnewm,**doldm;
    double **dnewmp,**doldmp;     double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;     int i, j, nhstepm, hstepm, h, nstepm ;
      int first=0;
    int k;     int k;
    double *xp;     double *xp;
    double **gp, **gm;  /**< for var eij */     double **gp, **gm;  /**< for var eij */
Line 5973  void  concatwav(int wav[], int **dh, int Line 6061  void  concatwav(int wav[], int **dh, int
        }         }
        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and          /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
         * returns into prlim .          * returns into prlim .
         */                        */
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
   
        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */         /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
Line 5986  void  concatwav(int wav[], int **dh, int Line 6074  void  concatwav(int wav[], int **dh, int
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.         /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
         */                                */                      
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability         /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
         * at horizon h in state j including mortality.          * at horizon h in state j including mortality.
         */          */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
Line 6011  void  concatwav(int wav[], int **dh, int Line 6099  void  concatwav(int wav[], int **dh, int
                                                   
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);           xp[i] = x[i] - (i==theta ?delti[theta]:0);
                           
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
Line 6197  void  concatwav(int wav[], int **dh, int Line 6285  void  concatwav(int wav[], int **dh, int
   int theta;    int theta;
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
   fprintf(ficresvpl,"# Age ");    fprintf(ficresvpl,"# Age ");
   if(nresult >=1)    if(nresult >=1)
     fprintf(ficresvpl," Result# ");      fprintf(ficresvpl," Result# ");
Line 6226  void  concatwav(int wav[], int **dh, int Line 6314  void  concatwav(int wav[], int **dh, int
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
         mgp[theta][i] = prlim[i][i];          mgp[theta][i] = prlim[i][i];
       }        }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
         mgm[theta][i] = prlim[i][i];          mgm[theta][i] = prlim[i][i];
Line 6288  void  concatwav(int wav[], int **dh, int Line 6376  void  concatwav(int wav[], int **dh, int
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
     if(nresult >=1)      if(nresult >=1)
       fprintf(ficresvpl,"%d ",nres );        fprintf(ficresvpl,"%d ",nres );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         /* for(j=1;j<=nlstate;j++) */
         /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
       }
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
Line 6506  void varprob(char optionfilefiname[], do Line 6597  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> 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. %s</li>\n",optionfilehtmcov,optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 6776  To be simple, these graphs help to under Line 6867  To be simple, these graphs help to under
 void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, i1, cpt, k4, nres;
   
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
Line 6799  void printinghtml(char fileresu[], char Line 6890  void printinghtml(char fileresu[], char
  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
Line 6908  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6999  divided by h: <sub>h</sub>P<sub>ij</sub>
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* 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-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }       }
      /* 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 in state %d and in any other live state (total).\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   And probability to be observed in various states (up to %d) being in state %d at different ages.       \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (forward stable) 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) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(prevbcast==1){
        /* Period (stable) back prevalence in each health state */         /* Backward prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
        /* Projection of prevalence up to period (stable) prevalence in each health state */         /* Projection of prevalence up to period (forward 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 and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
        }         }
      }       }
      if(backcast==1){       if(prevbcast==1){
       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */        /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \           fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
Line 6985  See page 'Matrix of variance-covariance Line 7076  See page 'Matrix of variance-covariance
    <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 forward (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 forward (period) 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 */
Line 7049  true period expectancies (those weighted Line 7140  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[132], gplotlabel[132];
Line 7127  void printinggnuplot(char fileresu[], ch Line 7218  void printinggnuplot(char fileresu[], ch
           continue;            continue;
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcoveff; 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,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
Line 7165  void printinggnuplot(char fileresu[], ch Line 7256  void printinggnuplot(char fileresu[], ch
           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==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         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)");
Line 7203  void printinggnuplot(char fileresu[], ch Line 7294  void printinggnuplot(char fileresu[], ch
           } /* end covariate */            } /* end covariate */
         } /* end if no covariate */          } /* end if no covariate */
   
         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */          if(prevbcast==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, nres in 2 to be fixed */            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
           if(cptcoveff ==0){            if(cptcoveff ==0){
Line 7230  void printinggnuplot(char fileresu[], ch Line 7321  void printinggnuplot(char fileresu[], ch
               }                }
             } /* end covariate */              } /* end covariate */
           } /* end if no covariate */            } /* end if no covariate */
           if(backcast == 1){            if(prevbcast == 1){
             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);              fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
             /* k1-1 error should be nres-1*/              /* k1-1 error should be nres-1*/
             for (i=1; i<= nlstate ; i ++) {              for (i=1; i<= nlstate ; i ++) {
Line 7249  void printinggnuplot(char fileresu[], ch Line 7340  void printinggnuplot(char fileresu[], ch
             }               } 
             fprintf(ficgp,"\" t\"\" w l lt 4");              fprintf(ficgp,"\" t\"\" w l lt 4");
           } /* end if backprojcast */            } /* end if backprojcast */
         } /* end if backcast */          } /* end if prevbcast */
         /* fprintf(ficgp,"\nset out ;unset label;\n"); */          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
         fprintf(ficgp,"\nset out ;unset title;\n");          fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
Line 7494  set ter svg size 640, 480\nunset log y\n Line 7585  set ter svg size 640, 480\nunset log y\n
       continue;        continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
       strcpy(gplotlabel,"(");              strcpy(gplotlabel,"(");      
       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 (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; 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,cptcoveff); /* 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 */
Line 7537  set ter svg size 640, 480\nunset log y\n Line 7628  set ter svg size 640, 480\nunset log y\n
       
       
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(prevbcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV backward prevalence  for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcoveff; 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,cptcoveff); /* 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 */
Line 7589  set ter svg size 640, 480\nunset log y\n Line 7680  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if prevbcast */
       
   /* 8eme */    /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
Line 7601  set ter svg size 640, 480\nunset log y\n Line 7692  set ter svg size 640, 480\nunset log y\n
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         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 forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
Line 7705  set ter svg size 640, 480\nunset log y\n Line 7796  set ter svg size 640, 480\nunset log y\n
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
       
   if(backcast==1){    if(prevbcast==1){
     /* Back projection from cross-sectional to stable (mixed) for each covariate */      /* Back projection from cross-sectional to stable (mixed) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
Line 7818  set ter svg size 640, 480\nunset log y\n Line 7909  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* end covariate */      } /* end covariate */
   } /* End if backcast */    } /* End if prevbcast */
       
       
   /* 9eme writing MLE parameters */    /* 9eme writing MLE parameters */
Line 8035  set ter svg size 640, 480\nunset log y\n Line 8126  set ter svg size 640, 480\nunset log y\n
    int modcovmax =1;     int modcovmax =1;
    int mobilavrange, mob;     int mobilavrange, mob;
    int iage=0;     int iage=0;
      int firstA1=0, firstA2=0;
   
    double sum=0., sumr=0.;     double sum=0., sumr=0.;
    double age;     double age;
Line 8132  set ter svg size 640, 480\nunset log y\n Line 8224  set ter svg size 640, 480\nunset log y\n
      } /* age */       } /* age */
      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */       /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
      /* but they will change */       /* but they will change */
        firstA1=0;firstA2=0;
      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */       for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
        sumnewmr[cptcod]=0.;         sumnewmr[cptcod]=0.;
Line 8164  set ter svg size 640, 480\nunset log y\n Line 8257  set ter svg size 640, 480\nunset log y\n
          sumr+=probs[(int)age][i][cptcod];           sumr+=probs[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);           if(!firstA1){
              firstA1=1;
              printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         if(fabs(sumr - 1.) > 1.e-3) { /* bad */
          printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);           if(!firstA2){
              firstA2=1;
              printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
   
Line 8256  set ter svg size 640, 480\nunset log y\n Line 8357  set ter svg size 640, 480\nunset log y\n
  }/* End movingaverage */   }/* 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 ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
   /* proj1, year, month, day of starting projection   void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
     /* dateintemean, mean date of interviews
        dateprojd, year, month, day of starting projection 
        dateprojf date of end of projection;year of end of projection (same day and month as proj1).
      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
      anproj2 year of en of projection (same day and month as proj1).  
   */    */
     /* double anprojd, mprojd, jprojd; */
     /* double anprojf, mprojf, jprojf; */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
Line 8302  set ter svg size 640, 480\nunset log y\n Line 8408  set ter svg size 640, 480\nunset log y\n
   if(estepm > stepm){ /* Yes every two year */    if(estepm > stepm){ /* Yes every two year */
     stepsize=2;      stepsize=2;
   }    }
     hstepm=hstepm/stepm;
   
   hstepm=hstepm/stepm;     
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and    /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                                fractional in yp1 */    /*                              fractional in yp1 *\/ */
   anprojmean=yp;    /* aintmean=yp; */
   yp2=modf((yp1*12),&yp);    /* yp2=modf((yp1*12),&yp); */
   mprojmean=yp;    /* mintmean=yp; */
   yp1=modf((yp2*30.5),&yp);    /* yp1=modf((yp2*30.5),&yp); */
   jprojmean=yp;    /* jintmean=yp; */
   if(jprojmean==0) jprojmean=1;    /* if(jintmean==0) jintmean=1; */
   if(mprojmean==0) jprojmean=1;    /* if(mintmean==0) mintmean=1; */
   
   
     /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
     /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
     /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   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",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       
Line 8343  set ter svg size 640, 480\nunset log y\n Line 8454  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresf," p%d%d",i,j);          fprintf(ficresf," p%d%d",i,j);
       fprintf(ficresf," wp.%d",j);        fprintf(ficresf," wp.%d",j);
     }      }
     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {      for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
       fprintf(ficresf,"\n");        fprintf(ficresf,"\n");
       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);   
       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */        /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
       for (agec=fage; agec>=(bage); agec--){         for (agec=fage; agec>=(bage); agec--){ 
         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
Line 8363  set ter svg size 640, 480\nunset log y\n Line 8474  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;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 ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
                   
         for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j<=nlstate+ndeath;j++) {
           ppij=0.;            ppij=0.;
Line 8391  set ter svg size 640, 480\nunset log y\n Line 8502  set ter svg size 640, 480\nunset log y\n
 }  }
   
 /************** Back Forecasting ******************/  /************** Back Forecasting ******************/
  void prevbackforecast(char fileres[], double ***prevacurrent, 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 ***prevacurrent, 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){ */
   /* back1, year, month, day of starting backection   void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
     /* back1, year, month, day of starting backprojection
      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
      anback2 year of end of backprojection (same day and month as back1).       anback2 year of end of backprojection (same day and month as back1).
Line 8400  set ter svg size 640, 480\nunset log y\n Line 8512  set ter svg size 640, 480\nunset log y\n
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
Line 8443  set ter svg size 640, 480\nunset log y\n Line 8555  set ter svg size 640, 480\nunset log y\n
   }    }
       
   hstepm=hstepm/stepm;    hstepm=hstepm/stepm;
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and    /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                                fractional in yp1 */    /*                              fractional in yp1 *\/ */
   anprojmean=yp;    /* aintmean=yp; */
   yp2=modf((yp1*12),&yp);    /* yp2=modf((yp1*12),&yp); */
   mprojmean=yp;    /* mintmean=yp; */
   yp1=modf((yp2*30.5),&yp);    /* yp1=modf((yp2*30.5),&yp); */
   jprojmean=yp;    /* jintmean=yp; */
   if(jprojmean==0) jprojmean=1;    /* if(jintmean==0) jintmean=1; */
   if(mprojmean==0) jprojmean=1;    /* if(mintmean==0) jintmean=1; */
       
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   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",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
       
   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
       
Line 8482  set ter svg size 640, 480\nunset log y\n Line 8594  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresfb," b%d%d",i,j);          fprintf(ficresfb," b%d%d",i,j);
       fprintf(ficresfb," b.%d",j);        fprintf(ficresfb," b.%d",j);
     }      }
     for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {      for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
       fprintf(ficresfb,"\n");        fprintf(ficresfb,"\n");
       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);        fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */        /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */        /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
       for (agec=bage; agec<=fage; agec++){  /* testing */        for (agec=bage; agec<=fage; agec++){  /* testing */
Line 8508  set ter svg size 640, 480\nunset log y\n Line 8620  set ter svg size 640, 480\nunset log y\n
         fprintf(ficresfb,"\n");          fprintf(ficresfb,"\n");
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;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 ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
         for(i=1; i<=nlstate+ndeath;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
           ppij=0.;ppi=0.;            ppij=0.;ppi=0.;
           for(j=1; j<=nlstate;j++) {            for(j=1; j<=nlstate;j++) {
Line 8543  set ter svg size 640, 480\nunset log y\n Line 8655  set ter svg size 640, 480\nunset log y\n
   
 /* Variance of prevalence limit: varprlim */  /* Variance of prevalence limit: varprlim */
  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){   void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of forward period (stable) prevalence------*/   
     
    char fileresvpl[FILENAMELENGTH];       char fileresvpl[FILENAMELENGTH];  
    FILE *ficresvpl;     FILE *ficresvpl;
Line 8554  set ter svg size 640, 480\nunset log y\n Line 8666  set ter svg size 640, 480\nunset log y\n
     strcpy(fileresvpl,"VPL_");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileresu);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);      printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);      fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
           
     /*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++){*/
Line 8595  set ter svg size 640, 480\nunset log y\n Line 8707  set ter svg size 640, 480\nunset log y\n
     }      }
           
     fclose(ficresvpl);      fclose(ficresvpl);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);      printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
   
  }   }
 /* Variance of back prevalence: varbprlim */  /* Variance of back prevalence: varbprlim */
Line 8956  void prwizard(int ncovmodel, int nlstate Line 9068  void prwizard(int ncovmodel, int nlstate
 /******************* Gompertz Likelihood ******************************/  /******************* Gompertz Likelihood ******************************/
 double gompertz(double x[])  double gompertz(double x[])
 {   { 
   double A,B,L=0.0,sump=0.,num=0.;    double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
   for (i=1;i<=imx ; i++) {    for (i=1;i<=imx ; i++) {
Line 8964  double gompertz(double x[]) Line 9076  double gompertz(double x[])
     /*    sump=sump+1;*/      /*    sump=sump+1;*/
     num=num+1;      num=num+1;
   }    }
      L=0.0;
      /* agegomp=AGEGOMP; */
   /* for (i=0; i<=imx; i++)     /* for (i=0; i<=imx; i++) 
      if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
   for (i=1;i<=imx ; i++)    for (i=1;i<=imx ; i++) {
     {      /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
       if (cens[i] == 1 && wav[i]>1)         mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));       * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month) 
              *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
       if (cens[i] == 0 && wav[i]>1)       * +
        * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
        */
        if (wav[i] > 1 || agedc[i] < AGESUP) {
          if (cens[i] == 1){
            A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
          } else if (cens[i] == 0){
         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);              +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
               } else
            printf("Gompertz cens[%d] neither 1 nor 0\n",i);
       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
       if (wav[i] > 1 ) { /* ??? */         L=L+A*weight[i];
         L=L+A*weight[i];  
         /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
       }       }
     }    }
   
  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     
   return -2*L*num/sump;    return -2*L*num/sump;
 }  }
Line 8994  double gompertz(double x[]) Line 9112  double gompertz(double x[])
 /******************* Gompertz_f Likelihood ******************************/  /******************* Gompertz_f Likelihood ******************************/
 double gompertz_f(const gsl_vector *v, void *params)  double gompertz_f(const gsl_vector *v, void *params)
 {   { 
   double A,B,LL=0.0,sump=0.,num=0.;    double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
   double *x= (double *) v->data;    double *x= (double *) v->data;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
Line 9087  int readdata(char datafile[], int firsto Line 9205  int readdata(char datafile[], int firsto
   int i=0, j=0, n=0, iv=0, v;    int i=0, j=0, n=0, iv=0, v;
   int lstra;    int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
     int noffset=0; /* This is the offset if BOM data file */
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
Line 9120  int readdata(char datafile[], int firsto Line 9239  int readdata(char datafile[], int firsto
     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;      /* Is it a BOM UTF-8 Windows file? */
     /* First data line */
   linei=0;    linei=0;
     while(fgets(line, MAXLINE, fic)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
       {
         noffset=noffset+2;
         printf("# Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
         fprintf(ficlog,"# Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
         fflush(ficlog); return 1;
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
           fprintf(ficlog,"# Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
           fflush(ficlog); return 1;
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
           /* If line starts with a # it is a comment */
       if (line[noffset] == '#') {
         linei=linei+1;
         break;
       }else{
         break;
       }
     }
     fclose(fic);
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
     /* Not a Bom file */
     
     i=1;
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
     linei=linei+1;      linei=linei+1;
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
Line 9242  int readdata(char datafile[], int firsto Line 9406  int readdata(char datafile[], int firsto
         return 1;          return 1;
       }        }
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month;
         /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
         /*        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /*        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
         /* } */
       strcpy(line,stra);        strcpy(line,stra);
     } /* End loop on waves */      } /* End loop on waves */
           
Line 9281  int readdata(char datafile[], int firsto Line 9449  int readdata(char datafile[], int firsto
               
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month);
       for (j=1;j<=maxwav;j++){
         if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
           printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
           fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
         }
       }
   
     strcpy(line,stra);      strcpy(line,stra);
           
     /* Sample weight */      /* Sample weight */
Line 10166  BOOL IsWow64() Line 10341  BOOL IsWow64()
 #endif  #endif
   
 void syscompilerinfo(int logged)  void syscompilerinfo(int logged)
  {  {
    /* #include "syscompilerinfo.h"*/  #include <stdint.h>
   
     /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/     /* command line Intel compiler 32bit windows, XP compatible:*/
    /* /GS /W3 /Gy     /* /GS /W3 /Gy
       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 10202  void syscompilerinfo(int logged) Line 10379  void syscompilerinfo(int logged)
       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
       /NOLOGO /TLBID:1        /NOLOGO /TLBID:1
    */     */
   
   
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 10218  void syscompilerinfo(int logged) Line 10397  void syscompilerinfo(int logged)
    }     }
 #endif  #endif
   
 #include <stdint.h>  
   
    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
Line 10326  void syscompilerinfo(int logged) Line 10503  void syscompilerinfo(int logged)
 }  }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
   int i, j, k, i1, k4=0, nres=0 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
Line 10335  int prevalence_limit(double *p, double * Line 10512  int prevalence_limit(double *p, double *
   strcpy(filerespl,"PL_");    strcpy(filerespl,"PL_");
   strcat(filerespl,fileresu);    strcat(filerespl,fileresu);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   pstamp(ficrespl);    pstamp(ficrespl);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
   fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
Line 10416  int prevalence_limit(double *p, double * Line 10593  int prevalence_limit(double *p, double *
 }  }
   
 int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/          /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
                   
         /* Computes the back prevalence limit  for any combination      of covariate values           /* Computes the back prevalence limit  for any combination      of covariate values 
    * at any age between ageminpar and agemaxpar     * at any age between ageminpar and agemaxpar
Line 10431  int back_prevalence_limit(double *p, dou Line 10608  int back_prevalence_limit(double *p, dou
   strcpy(fileresplb,"PLB_");    strcpy(fileresplb,"PLB_");
   strcat(fileresplb,fileresu);    strcat(fileresplb,fileresu);
   if((ficresplb=fopen(fileresplb,"w"))==NULL) {    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
   }    }
   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
   pstamp(ficresplb);    pstamp(ficresplb);
   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficresplb,"#Age ");    fprintf(ficresplb,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
   fprintf(ficresplb,"\n");    fprintf(ficresplb,"\n");
Line 10626  int hPijx(double *p, int bage, int fage) Line 10803  int hPijx(double *p, int bage, int fage)
   /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
       
   /* agelim=AGESUP; */    /* agelim=AGESUP; */
   ageminl=30;    ageminl=AGEINF; /* was 30 */
   hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
       
Line 10656  int hPijx(double *p, int bage, int fage) Line 10833  int hPijx(double *p, int bage, int fage)
       /* 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) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */          /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
                   
         /*        nhstepm=nhstepm*YEARM; aff par mois*/          /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   
Line 10705  int main(int argc, char *argv[]) Line 10882  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
     /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
   int ncvyear=0; /* Number of years needed for the period prevalence to converge */    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
Line 10740  int main(int argc, char *argv[]) Line 10918  int main(int argc, char *argv[])
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
   int c,  h , cpt, c2;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 10748  int main(int argc, char *argv[]) Line 10926  int main(int argc, char *argv[])
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int backcast=0;    /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
     /* double anprojf, mprojf, jprojf; */
     /* double jintmean,mintmean,aintmean;   */
     int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
     double yrfproj= 10.0; /* Number of years of forward projections */
     double yrbproj= 10.0; /* Number of years of backward projections */
     int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 10773  int main(int argc, char *argv[]) Line 10958  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2;    double dateprev1, dateprev2;
   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;    double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;    double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
   
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 10969  int main(int argc, char *argv[]) Line 11155  int main(int argc, char *argv[])
       noffset=noffset+3;        noffset=noffset+3;
       printf("# File is an UTF8 Bom.\n"); // 0xBF        printf("# File is an UTF8 Bom.\n"); // 0xBF
     }      }
     else if( line[0] == (char)0xFE && line[1] == (char)0xFF)  /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
       else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
     {      {
       noffset=noffset+2;        noffset=noffset+2;
       printf("# File is an UTF16BE BOM file\n");        printf("# File is an UTF16BE BOM file\n");
Line 11057  int main(int argc, char *argv[]) Line 11244  int main(int argc, char *argv[])
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled != 1){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       model[0]='\0';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 11107  int main(int argc, char *argv[]) Line 11294  int main(int argc, char *argv[])
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
   if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/    if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
   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 11173  int main(int argc, char *argv[]) Line 11360  int main(int argc, char *argv[])
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;          if(jj==i) continue;
         j++;          j++;
           while((c=getc(ficpar))=='#' && c!= EOF){
             ungetc(c,ficpar);
             fgets(line, MAXLINE, ficpar);
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
           }
           ungetc(c,ficpar);
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) || (j1 != jj)){          if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
Line 11313  Please run with mle=-1 to get a correct Line 11509  Please run with mle=-1 to get a correct
       
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    nobs=lastobs-firstobs+1; /* was = lastobs;*/
   num=lvector(1,n);    /* num=lvector(1,n); */
   moisnais=vector(1,n);    /* moisnais=vector(1,n); */
   annais=vector(1,n);    /* annais=vector(1,n); */
   moisdc=vector(1,n);    /* moisdc=vector(1,n); */
   andc=vector(1,n);    /* andc=vector(1,n); */
   weight=vector(1,n);    /* weight=vector(1,n); */
   agedc=vector(1,n);    /* agedc=vector(1,n); */
   cod=ivector(1,n);    /* cod=ivector(1,n); */
   for(i=1;i<=n;i++){    /* for(i=1;i<=n;i++){ */
     num=lvector(firstobs,lastobs);
     moisnais=vector(firstobs,lastobs);
     annais=vector(firstobs,lastobs);
     moisdc=vector(firstobs,lastobs);
     andc=vector(firstobs,lastobs);
     weight=vector(firstobs,lastobs);
     agedc=vector(firstobs,lastobs);
     cod=ivector(firstobs,lastobs);
     for(i=firstobs;i<=lastobs;i++){
     num[i]=0;      num[i]=0;
     moisnais[i]=0;      moisnais[i]=0;
     annais[i]=0;      annais[i]=0;
Line 11332  Please run with mle=-1 to get a correct Line 11537  Please run with mle=-1 to get a correct
     cod[i]=0;      cod[i]=0;
     weight[i]=1.0; /* Equal weights, 1 by default */      weight[i]=1.0; /* Equal weights, 1 by default */
   }    }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,firstobs,lastobs);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,firstobs,lastobs);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
Line 11436  Please run with mle=-1 to get a correct Line 11641  Please run with mle=-1 to get a correct
   
   
   agegomp=(int)agemin;    agegomp=(int)agemin;
   free_vector(moisnais,1,n);    free_vector(moisnais,firstobs,lastobs);
   free_vector(annais,1,n);    free_vector(annais,firstobs,lastobs);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   /* free_vector(moisdc,1,n); */    /* free_vector(moisdc,1,n); */
Line 11463  Please run with mle=-1 to get a correct Line 11668  Please run with mle=-1 to get a correct
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* Concatenates waves */    /* Concatenates waves */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,firstobs,lastobs);
   free_vector(andc,1,n);    free_vector(andc,firstobs,lastobs);
   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
Line 11654  Title=%s <br>Datafile=%s Firstpass=%d La Line 11859  Title=%s <br>Datafile=%s Firstpass=%d La
   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);    fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);    fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
   ncurrv=i;    ncurrv=i;
   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);    for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \    fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
Line 11689  Interval (in months) between two waves: Line 11894  Interval (in months) between two waves:
       for(j=1;j<=NDIM;j++)        for(j=1;j<=NDIM;j++)
         ximort[i][j]=0.;          ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(firstobs,lastobs);
     ageexmed=vector(1,n);      ageexmed=vector(firstobs,lastobs);
     agecens=vector(1,n);      agecens=vector(firstobs,lastobs);
     dcwave=ivector(1,n);      dcwave=ivector(firstobs,lastobs);
                                   
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
Line 11726  Interval (in months) between two waves: Line 11931  Interval (in months) between two waves:
         ximort[i][j]=(i == j ? 1.0 : 0.0);          ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     /*p[1]=0.0268; p[NDIM]=0.083;*/      p[1]=0.0268; p[NDIM]=0.083;
     /*printf("%lf %lf", p[1], p[2]);*/      /* printf("%lf %lf", p[1], p[2]); */
           
           
 #ifdef GSL  #ifdef GSL
Line 11853  Interval (in months) between two waves: Line 12058  Interval (in months) between two waves:
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     }      }
     lsurv=vector(1,AGESUP);      lsurv=vector(agegomp,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(agegomp,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(agegomp,AGESUP);
     lsurv[agegomp]=100000;      lsurv[agegomp]=100000;
           
     for (k=agegomp;k<=AGESUP;k++) {      for (k=agegomp;k<=AGESUP;k++) {
Line 11902  Please run with mle=-1 to get a correct Line 12107  Please run with mle=-1 to get a correct
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,agegomp,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,agegomp,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,agegomp,AGESUP);
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(dcwave,firstobs,lastobs);
     free_vector(agecens,1,n);      free_vector(agecens,firstobs,lastobs);
     free_ivector(dcwave,1,n);      free_vector(ageexmed,firstobs,lastobs);
       free_ivector(cens,firstobs,lastobs);
 #ifdef GSL  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
Line 12104  Please run with mle=-1 to get a correct Line 12310  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12149  Please run with mle=-1 to get a correct Line 12356  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12174  Please run with mle=-1 to get a correct Line 12382  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else        }else
         break;          break;
Line 12207  Please run with mle=-1 to get a correct Line 12416  Please run with mle=-1 to get a correct
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
           fputs(line,ficres);
         continue;          continue;
       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))        }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
         parameterline=11;          parameterline=11;
       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))        else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
         parameterline=12;          parameterline=12;
       else if(sscanf(line,"result:%[^\n]\n",modeltemp))        else if(sscanf(line,"result:%[^\n]\n",modeltemp))
         parameterline=13;          parameterline=13;
Line 12219  Please run with mle=-1 to get a correct Line 12429  Please run with mle=-1 to get a correct
       }        }
       switch (parameterline){         switch (parameterline){ 
       case 11:        case 11:
         if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){          if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
           if (num_filled != 8) {                    fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
             goto end;  
           }  
           fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
           printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,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.*/
           dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;            dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
           dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;            dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
             prvforecast = 1;
           } 
           else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
             printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
             prvforecast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
         }          }
         break;          break;
       case 12:        case 12:
         /*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);*/          if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
         if((num_filled=sscanf(line,"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)) !=EOF){            fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
           if (num_filled != 8) {            printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);            fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);            fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             goto end;            /* day and month of back2 are not used but only year anback2.*/
           }  
           printf("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(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.*/  
           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;            dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;            dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
             prvbackcast = 1;
           } 
           else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
             printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
             prvbackcast = 2;
           }
           else {
             printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
             goto end;
         }          }
         break;          break;
       case 13:        case 13:
Line 12275  Please run with mle=-1 to get a correct Line 12497  Please run with mle=-1 to get a correct
           fprintf(ficres,"result: %s\n",resultline);            fprintf(ficres,"result: %s\n",resultline);
           fprintf(ficlog,"result: %s\n",resultline);            fprintf(ficlog,"result: %s\n",resultline);
           break;            break;
         case 14:           case 14:
           if(ncovmodel >2 && nresult==0 ){            printf("Error: Unknown command '%s'\n",line);
             fprintf(ficlog,"Error: Unknown command '%s'\n",line);
             if(ncovmodel >=2 && nresult==0 ){
             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);              printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
             goto end;              fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
           }            }
             goto end;
           break;            break;
         default:          default:
           nresult=1;            nresult=1;
Line 12301  This is probably because your parameter Line 12526  This is probably because your parameter
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else{      }else{
       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);        /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
         /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
         if(prvforecast==1){
           dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
           jprojd=jproj1;
           mprojd=mproj1;
           anprojd=anproj1;
           dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
           jprojf=jproj2;
           mprojf=mproj2;
           anprojf=anproj2;
         } else if(prvforecast == 2){
           dateprojd=dateintmean;
           date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
           dateprojf=dateintmean+yrfproj;
           date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
         }
         if(prvbackcast==1){
           datebackd=(jback1+12*mback1+365*anback1)/365;
           jbackd=jback1;
           mbackd=mback1;
           anbackd=anback1;
           datebackf=(jback2+12*mback2+365*anback2)/365;
           jbackf=jback2;
           mbackf=mback2;
           anbackf=anback2;
         } else if(prvbackcast == 2){
           datebackd=dateintmean;
           date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
           datebackf=dateintmean-yrbproj;
           date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
         }
         
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
     }      }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
                  jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);                   jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
                                   
     /*------------ free_vector  -------------*/      /*------------ free_vector  -------------*/
     /*  chdir(path); */      /*  chdir(path); */
Line 12314  Please run with mle=-1 to get a correct Line 12572  Please run with mle=-1 to get a correct
     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,firstobs,lastobs);
     free_vector(agedc,1,n);      free_vector(agedc,firstobs,lastobs);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
Line 12378  Please run with mle=-1 to get a correct Line 12636  Please run with mle=-1 to get a correct
     }/* end if moving average */      }/* end if moving average */
           
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     if(prevfcast==1){      if(prevfcast==1){ 
       /*    if(stepm ==1){*/        /*   /\*    if(stepm ==1){*\/ */
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
         /*This done previously after freqsummary.*/
         /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
         /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
         
         /* } else if (prvforecast==2){ */
         /*   /\*    if(stepm ==1){*\/ */
         /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
         /* } */
         /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
         prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
     }      }
   
     /* Backcasting */      /* Prevbcasting */
     if(backcast==1){      if(prevbcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 12399  Please run with mle=-1 to get a correct Line 12667  Please run with mle=-1 to get a correct
       hBijx(p, bage, fage, mobaverage);        hBijx(p, bage, fage, mobaverage);
       fclose(ficrespijb);        fclose(ficrespijb);
   
       prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,        /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
                        mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);        /* /\*                   mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
         /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
         /*                       mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
                          mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
   
         
       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);        varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
               
Line 12408  Please run with mle=-1 to get a correct Line 12682  Please run with mle=-1 to get a correct
       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);
     }    /* end  Backcasting */      }    /* end  Prevbcasting */
     
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
Line 12572  Please run with mle=-1 to get a correct Line 12846  Please run with mle=-1 to get a correct
         if(vpopbased==1)          if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
         else          else
           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
         printf("Computing age specific period (stable) prevalences in each health state \n");          printf("Computing age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");          fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
         for(age=bage; age <=fage ;age++){          for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {            if (vpopbased==1) {
Line 12625  Please run with mle=-1 to get a correct Line 12899  Please run with mle=-1 to get a correct
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /* variance-covariance of period prevalence*/      /* variance-covariance of forward period prevalence*/
     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);      varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
           
     free_vector(weight,1,n);      free_vector(weight,firstobs,lastobs);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,1,n);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,firstobs,lastobs);
     free_ivector(cod,1,n);      free_ivector(cod,firstobs,lastobs);
     free_ivector(tab,1,NCOVMAX);      free_ivector(tab,1,NCOVMAX);
     fclose(ficresstdeij);      fclose(ficresstdeij);
     fclose(ficrescveij);      fclose(ficrescveij);
Line 12654  Please run with mle=-1 to get a correct Line 12928  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);
   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);    if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
   if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);    if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
   free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
   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);
   /*free_vector(delti,1,npar);*/    /*free_vector(delti,1,npar);*/
Line 12777  Please run with mle=-1 to get a correct Line 13051  Please run with mle=-1 to get a correct
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     strcpy(pplotcmd,plotcmd);
       
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
     if((outcmd=system(plotcmd)) != 0)      if((outcmd=system(plotcmd)) != 0){
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
         strcpy(plotcmd,pplotcmd);
       }
   }    }
   printf(" Successful, please wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {

Removed from v.1.286  
changed lines
  Added in v.1.303


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>