Diff for /imach/src/imach.c between versions 1.274 and 1.296

version 1.274, 2017/06/29 09:47:08 version 1.296, 2019/05/20 13:03:18
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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
     Summary: some minor bugs
   
     Revision 1.285  2018/04/21 21:02:16  brouard
     Summary: Some bugs fixed, valgrind tested
   
     Revision 1.284  2018/04/20 05:22:13  brouard
     Summary: Computing mean and stdeviation of fixed quantitative variables
   
     Revision 1.283  2018/04/19 14:49:16  brouard
     Summary: Some minor bugs fixed
   
     Revision 1.282  2018/02/27 22:50:02  brouard
     *** empty log message ***
   
     Revision 1.281  2018/02/27 19:25:23  brouard
     Summary: Adding second argument for quitting
   
     Revision 1.280  2018/02/21 07:58:13  brouard
     Summary: 0.99r15
   
     New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
   
     Revision 1.279  2017/07/20 13:35:01  brouard
     Summary: temporary working
   
     Revision 1.278  2017/07/19 14:09:02  brouard
     Summary: Bug for mobil_average=0 and prevforecast fixed(?)
   
     Revision 1.277  2017/07/17 08:53:49  brouard
     Summary: BOM files can be read now
   
     Revision 1.276  2017/06/30 15:48:31  brouard
     Summary: Graphs improvements
   
     Revision 1.275  2017/06/30 13:39:33  brouard
     Summary: Saito's color
   
   Revision 1.274  2017/06/29 09:47:08  brouard    Revision 1.274  2017/06/29 09:47:08  brouard
   Summary: Version 0.99r14    Summary: Version 0.99r14
   
Line 1002  typedef struct { Line 1083  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 1029  typedef struct { Line 1111  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";  char 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 fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1053  int nqfveff=0; /**< nqfveff Number of Qu Line 1135  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;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
Line 1193  double **pmmij, ***probs; /* Global poin Line 1276  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 2504  void powell(double p[], double **xi, int Line 2592  void powell(double p[], double **xi, int
       
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
   {    {
     /* Computes the prevalence limit in each live state at age x and for covariate combination ij       /**< Computes the prevalence limit in each live state at age x and for covariate combination ij 
        (and selected quantitative values in nres)       *   (and selected quantitative values in nres)
        by left multiplying the unit       *  by left multiplying the unit
        matrix by transitions matrix until convergence is reached with precision ftolpl */       *  matrix by transitions matrix until convergence is reached with precision ftolpl 
   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */       * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
   /* Wx is row vector: population in state 1, population in state 2, population dead */       * Wx is row vector: population in state 1, population in state 2, population dead
   /* or prevalence in state 1, prevalence in state 2, 0 */       * or prevalence in state 1, prevalence in state 2, 0
   /* newm is the matrix after multiplications, its rows are identical at a factor */       * newm is the matrix after multiplications, its rows are identical at a factor.
   /* Initial matrix pimij */       * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
        * Output is prlim.
        * Initial matrix pimij 
        */
   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   /*  0,                   0                  , 1} */    /*  0,                   0                  , 1} */
Line 2533  void powell(double p[], double **xi, int Line 2624  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 2629  void powell(double p[], double **xi, int Line 2721  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 2698  Earliest age to start was %d-%d=%d, ncvl Line 2794  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 2812  Earliest age to start was %d-%d=%d, ncvl Line 2909  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 2897  double **pmij(double **ps, double *cov, Line 2994  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 2926  double **pmij(double **ps, double *cov, Line 3023  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 2945  double **pmij(double **ps, double *cov, Line 3042  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 */
Line 2972  double **pmij(double **ps, double *cov, Line 3069  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 2993  double **pmij(double **ps, double *cov, Line 3090  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 3065  double **bpmij(double **ps, double *cov, Line 3162  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 3825  return -l; Line 3922  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 3849  void likelione(FILE *ficres,double p[], Line 3946  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 4339  void  freqsummary(char fileres[], double Line 4436  void  freqsummary(char fileres[], double
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */    double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);    int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
   double *meanq;    double *meanq, *stdq, *idq;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
Line 4352  void  freqsummary(char fileres[], double Line 4449  void  freqsummary(char fileres[], double
   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
   meanqt=matrix(1,lastpass,1,nqtveff);    meanqt=matrix(1,lastpass,1,nqtveff);
   strcpy(fileresp,"P_");    strcpy(fileresp,"P_");
   strcat(fileresp,fileresu);    strcat(fileresp,fileresu);
Line 4460  Title=%s <br>Datafile=%s Firstpass=%d La Line 4559  Title=%s <br>Datafile=%s Firstpass=%d La
         posprop[i]=0;          posprop[i]=0;
         pospropt[i]=0;          pospropt[i]=0;
       }        }
       /* for (z1=1; z1<= nqfveff; z1++) {   */        for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
       /*   meanq[z1]+=0.; */          idq[z1]=0.;
           meanq[z1]=0.;
           stdq[z1]=0.;
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
       /*   for(m=1;m<=lastpass;m++){ */        /*   for(m=1;m<=lastpass;m++){ */
       /*        meanqt[m][z1]=0.; */        /*          meanqt[m][z1]=0.; */
       /*   } */        /*        } */
       /* } */        /* }       */
         
       /* dateintsum=0; */        /* dateintsum=0; */
       /* k2cpt=0; */        /* k2cpt=0; */
               
Line 4476  Title=%s <br>Datafile=%s Firstpass=%d La Line 4578  Title=%s <br>Datafile=%s Firstpass=%d La
         if(j !=0){          if(j !=0){
           if(anyvaryingduminmodel==0){ /* If All fixed covariates */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               /* for (z1=1; z1<= nqfveff; z1++) {   */  
               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */  
               /* } */  
               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                 /* if(Tvaraff[z1] ==-20){ */                  /* if(Tvaraff[z1] ==-20){ */
                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
Line 4499  Title=%s <br>Datafile=%s Firstpass=%d La Line 4598  Title=%s <br>Datafile=%s Firstpass=%d La
         }/* end j==0 */          }/* end j==0 */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
           /* for(m=firstpass; m<=lastpass; m++){ */            /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[iind];mi++){ /* For that wave */            for(mi=1; mi<wav[iind];mi++){ /* For each wave */
             m=mw[mi][iind];              m=mw[mi][iind];
             if(j!=0){              if(j!=0){
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
Line 4519  Title=%s <br>Datafile=%s Firstpass=%d La Line 4618  Title=%s <br>Datafile=%s Firstpass=%d La
               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */                }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
             } /* end j==0 */              } /* end j==0 */
             /* bool =0 we keep that guy which corresponds to the combination of dummy values */              /* bool =0 we keep that guy which corresponds to the combination of dummy values */
             if(bool==1){              if(bool==1){ /*Selected */
               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]                /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                  and mw[mi+1][iind]. dh depends on stepm. */                   and mw[mi+1][iind]. dh depends on stepm. */
               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/                agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
Line 4537  Title=%s <br>Datafile=%s Firstpass=%d La Line 4636  Title=%s <br>Datafile=%s Firstpass=%d La
                   if(s[m][iind]==-1)                    if(s[m][iind]==-1)
                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));                      printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                     for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
                       idq[z1]=idq[z1]+weight[iind];
                       meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                     }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */                    /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */                    /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
Line 4552  Title=%s <br>Datafile=%s Firstpass=%d La Line 4656  Title=%s <br>Datafile=%s Firstpass=%d La
               bool=1;                bool=1;
             }/* end bool 2 */              }/* end bool 2 */
           } /* end m */            } /* end m */
             /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
             /*   idq[z1]=idq[z1]+weight[iind]; */
             /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
             /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
             /* } */
         } /* end bool */          } /* end bool */
       } /* end iind = 1 to imx */        } /* end iind = 1 to imx */
       /* prop[s][age] is feeded for any initial and valid live state as well as        /* prop[s][age] is feeded for any initial and valid live state as well as
Line 4589  Title=%s <br>Datafile=%s Firstpass=%d La Line 4698  Title=%s <br>Datafile=%s Firstpass=%d La
         fprintf(ficresphtmfr, "**********</h3>\n");          fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "**********\n");          fprintf(ficlog, "**********\n");
       }        }
         /*
           Printing means of quantitative variables if any
         */
         for (z1=1; z1<= nqfveff; z1++) {
           fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
           fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
           if(weightopt==1){
             printf(" Weighted mean and standard deviation of");
             fprintf(ficlog," Weighted mean and standard deviation of");
             fprintf(ficresphtmfr," Weighted mean and standard deviation of");
           }
           printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
         /*        for(m=1;m<=lastpass;m++){ */
         /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
         /*   } */
         /* } */
   
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");          fprintf(ficresp, " Age");
Line 4823  Title=%s <br>Datafile=%s Firstpass=%d La Line 4953  Title=%s <br>Datafile=%s Firstpass=%d La
             fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
           }            }
         }          }
       }        } /* end of state i */
       printf("#Freqsummary\n");        printf("#Freqsummary\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       for(s1=-1; s1 <=nlstate+ndeath; s1++){        for(s1=-1; s1 <=nlstate+ndeath; s1++){
Line 4865  Title=%s <br>Datafile=%s Firstpass=%d La Line 4995  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);
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
     free_vector(idq,1,nqfveff);
   free_vector(meanq,1,nqfveff);    free_vector(meanq,1,nqfveff);
     free_vector(stdq,1,nqfveff);
   free_matrix(meanqt,1,lastpass,1,nqtveff);    free_matrix(meanqt,1,lastpass,1,nqtveff);
   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);    free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);    free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
Line 4976  void prevalence(double ***probs, double Line 5109  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 5034  void prevalence(double ***probs, double Line 5167  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 5285  void  concatwav(int wav[], int **dh, int Line 5417  void  concatwav(int wav[], int **dh, int
    /* *cptcov=0; */     /* *cptcov=0; */
     
    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      for (k=1; k <= maxncov; k++)
        for(j=1; j<=2; j++)
          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 5305  void  concatwav(int wav[], int **dh, int Line 5439  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 5351  void  concatwav(int wav[], int **dh, int Line 5489  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 5372  void  concatwav(int wav[], int **dh, int Line 5516  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 5760  void  concatwav(int wav[], int **dh, int Line 5890  void  concatwav(int wav[], int **dh, int
 /************ Variance ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
  {   {
    /* Variance of health expectancies */     /** Variance of health expectancies 
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
    /* double **newm;*/      * double **newm;
    /* 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 movingaverage(); */     /* int movingaverage(); */
    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 */
    double ***gradg, ***trgradg; /*for var eij */     double ***gradg, ***trgradg; /**< for var eij */
    double **gradgp, **trgradgp; /* for var p point j */     double **gradgp, **trgradgp; /**< for var p point j */
    double *gpp, *gmp; /* for var p point j */     double *gpp, *gmp; /**< for var p point j */
    double **varppt; /* for var p point j nlstate to nlstate+ndeath */     double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;     double ***p3mat;
    double age,agelim, hf;     double age,agelim, hf;
    /* double ***mobaverage; */     /* double ***mobaverage; */
Line 5836  void  concatwav(int wav[], int **dh, int Line 5968  void  concatwav(int wav[], int **dh, int
    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */  
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    pstamp(ficresvij);     pstamp(ficresvij);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
Line 5891  void  concatwav(int wav[], int **dh, int Line 6023  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);
        }         }
                                  /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
           * returns into prlim .
           */
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                           
          /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
            for(i=1; i<=nlstate;i++)             for(i=1; i<=nlstate;i++)
Line 5903  void  concatwav(int wav[], int **dh, int Line 6038  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.
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 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
           * at horizon h in state j including mortality.
           */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }           }
        }         }
        /* Next for computing probability of death (h=1 means         /* Next for computing shifted+ probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim.            as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gpp[j]=0.; i<= nlstate; i++)           for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];             gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }
        /* end probability of death */         
          /* Again with minus shift */
                                                   
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         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 5952  void  concatwav(int wav[], int **dh, int Line 6092  void  concatwav(int wav[], int **dh, int
          for(i=1,gmp[j]=0.; i<= nlstate; i++)           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];             gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }    
        /* end probability of death */         /* end shifting computations */
                           
          /**< Computing gradient matrix at horizon h 
           */
        for(j=1; j<= nlstate; j++) /* vareij */         for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }           }
                                  /**< Gradient of overall mortality p.3 (or p.j) 
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          */
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }         }
                                                   
      } /* End theta */       } /* End theta */
                        
        /* We got the gradient matrix for each theta and state j */                
      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                                   
      for(h=0; h<=nhstepm; h++) /* veij */       for(h=0; h<=nhstepm; h++) /* veij */
Line 5975  void  concatwav(int wav[], int **dh, int Line 6119  void  concatwav(int wav[], int **dh, int
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        for(theta=1; theta <=npar; theta++)         for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];           trgradgp[j][theta]=gradgp[theta][j];
                        /**< as well as its transposed matrix 
         */                
                                   
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)       for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)         for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;           vareij[i][j][(int)age] =0.;
                   
        /* Computing trgradg by matcov by gradg at age and summing over h
         * and k (nhstepm) formula 15 of article
         * Lievre-Brouard-Heathcote
         */
        
      for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){         for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 5992  void  concatwav(int wav[], int **dh, int Line 6142  void  concatwav(int wav[], int **dh, int
        }         }
      }       }
                                   
      /* pptj */       /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
         * p.j overall mortality formula 49 but computed directly because
         * we compute the grad (wix pijx) instead of grad (pijx),even if
         * wix is independent of theta.
         */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 6095  void  concatwav(int wav[], int **dh, int Line 6249  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 6124  void  concatwav(int wav[], int **dh, int Line 6278  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 6186  void  concatwav(int wav[], int **dh, int Line 6340  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 6404  void varprob(char optionfilefiname[], do Line 6561  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 6601  To be simple, these graphs help to under Line 6758  To be simple, these graphs help to under
                  }                   }
                                                                                                                                   
                  /* Eigen vectors */                   /* Eigen vectors */
                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                   if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                      printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                    }else
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                  /*v21=sqrt(1.-v11*v11); *//* error */                   /*v21=sqrt(1.-v11*v11); *//* error */
                  v21=(lc1-v1)/cv12*v11;                   v21=(lc1-v1)/cv12*v11;
                  v12=-v21;                   v12=-v21;
Line 6632  To be simple, these graphs help to under Line 6794  To be simple, these graphs help to under
                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \                             mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */                             mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                  }else{                   }else{
                    first=0;                     first=0;
                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
Line 6669  To be simple, these graphs help to under Line 6831  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 6692  void printinghtml(char fileresu[], char Line 6854  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 6801  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6963  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 6878  See page 'Matrix of variance-covariance Line 7040  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 6942  true period expectancies (those weighted Line 7104  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 7020  void printinggnuplot(char fileresu[], ch Line 7182  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 7049  void printinggnuplot(char fileresu[], ch Line 7211  void printinggnuplot(char fileresu[], ch
               
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
           fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */          /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
       /* k1-1 error should be nres-1*/        /* k1-1 error should be nres-1*/
Line 7057  void printinggnuplot(char fileresu[], ch Line 7220  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 7095  void printinggnuplot(char fileresu[], ch Line 7258  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 7122  void printinggnuplot(char fileresu[], ch Line 7285  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 7134  void printinggnuplot(char fileresu[], ch Line 7297  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\"95%% CI\" w l lt 5,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);               fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
             for (i=1; i<= nlstate ; i ++) {              for (i=1; i<= nlstate ; i ++) {
               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");                else fprintf(ficgp," %%*lf (%%*lf)");
             }               } 
             fprintf(ficgp,"\" t\"\" w l lt 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");
       } /* nres */        } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
Line 7385  set ter svg size 640, 480\nunset log y\n Line 7549  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 7428  set ter svg size 640, 480\nunset log y\n Line 7592  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 7480  set ter svg size 640, 480\nunset log y\n Line 7644  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 7492  set ter svg size 640, 480\nunset log y\n Line 7656  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 7596  set ter svg size 640, 480\nunset log y\n Line 7760  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 7709  set ter svg size 640, 480\nunset log y\n Line 7873  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 7756  set ter svg size 640, 480\nunset log y\n Line 7920  set ter svg size 640, 480\nunset log y\n
         continue;          continue;
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);        fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);        /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */        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 7773  set ter svg size 640, 480\nunset log y\n Line 7937  set ter svg size 640, 480\nunset log y\n
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
       fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);        fprintf(ficgp,"\nset key outside ");
         /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
         fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
       fprintf(ficgp,"\nset ter svg size 640, 480 ");        fprintf(ficgp,"\nset ter svg size 640, 480 ");
       if (ng==1){        if (ng==1){
         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
Line 7893  set ter svg size 640, 480\nunset log y\n Line 8059  set ter svg size 640, 480\nunset log y\n
             }              }
             fprintf(ficgp,")");              fprintf(ficgp,")");
             if(ng ==2)              if(ng ==2)
               fprintf(ficgp," t \"p%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             else /* ng= 3 */              else /* ng= 3 */
               fprintf(ficgp," t \"i%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
             if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }            }
           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
             fprintf(ficgp,",");              fprintf(ficgp,",");
Line 7907  set ter svg size 640, 480\nunset log y\n Line 8073  set ter svg size 640, 480\nunset log y\n
           i=i+ncovmodel;            i=i+ncovmodel;
         } /* end k */          } /* end k */
       } /* end k2 */        } /* end k2 */
       fprintf(ficgp,"\n set out; unset label;\n");        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
         fprintf(ficgp,"\n set out; unset title;set key default;\n");
     } /* end k1 */      } /* end k1 */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
Line 7923  set ter svg size 640, 480\nunset log y\n Line 8090  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 7931  set ter svg size 640, 480\nunset log y\n Line 8099  set ter svg size 640, 480\nunset log y\n
    double *agemingoodr, *agemaxgoodr;      double *agemingoodr, *agemaxgoodr; 
       
       
    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */     /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */     /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
   
    sumnewp = vector(1,ncovcombmax);     sumnewp = vector(1,ncovcombmax);
    sumnewm = vector(1,ncovcombmax);     sumnewm = vector(1,ncovcombmax);
Line 8020  set ter svg size 640, 480\nunset log y\n Line 8188  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 8052  set ter svg size 640, 480\nunset log y\n Line 8221  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 8144  set ter svg size 640, 480\nunset log y\n Line 8321  set ter svg size 640, 480\nunset log y\n
  }/* End movingaverage */   }/* End movingaverage */
     
   
    int 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;
      return;
    }
    
 /************** 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; */
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   if(estepm > stepm){ /* Yes every two year */    if(estepm > stepm){ /* Yes every two year */
     stepsize=2;      stepsize=2;
   }    }
     hstepm=hstepm/stepm;
   
     
     /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
     /*                              fractional in yp1 *\/ */
     /* aintmean=yp; */
     /* yp2=modf((yp1*12),&yp); */
     /* mintmean=yp; */
     /* yp1=modf((yp2*30.5),&yp); */
     /* jintmean=yp; */
     /* if(jintmean==0) jintmean=1; */
     /* if(mintmean==0) mintmean=1; */
   
   hstepm=hstepm/stepm;   
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and  
                                fractional in yp1 */  
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=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");
       
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         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 8251  set ter svg size 640, 480\nunset log y\n Line 8452  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.;
           for(i=1; i<=nlstate;i++) {            for(i=1; i<=nlstate;i++) {
             /* if (mobilav>=1)  */              if (mobilav>=1)
             ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];               ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
             /* else { */ /* even if mobilav==-1 we use mobaverage */              else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
             /*  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
             /* } */              }
             fprintf(ficresf," %.3f", p3mat[i][j][h]);              fprintf(ficresf," %.3f", p3mat[i][j][h]);
           } /* end i */            } /* end i */
           fprintf(ficresf," %.3f", ppij);            fprintf(ficresf," %.3f", ppij);
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 }  }
   
 /************** 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 8288  set ter svg size 640, 480\nunset log y\n Line 8490  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; */
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   }    }
       
   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");
       
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         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 */
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         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 8431  set ter svg size 640, 480\nunset log y\n Line 8633  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;
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     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++){*/
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     }      }
           
     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 9627  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9829  Dummy[k] 0=dummy (0 1), 1 quantitative (
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}    for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */    for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
       Fixed[k]= 0;        Fixed[k]= 0;
Line 9877  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10079  Dummy[k] 0=dummy (0 1), 1 quantitative (
   /* Searching for doublons in the model */    /* Searching for doublons in the model */
   for(k1=1; k1<= cptcovt;k1++){    for(k1=1; k1<= cptcovt;k1++){
     for(k2=1; k2 <k1;k2++){      for(k2=1; k2 <k1;k2++){
       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){        /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
         if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
           if(Tvar[k1]==Tvar[k2]){            if(Tvar[k1]==Tvar[k2]){
             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);              printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);              fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
             return(1);              return(1);
           }            }
         }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
Line 10053  BOOL IsWow64() Line 10256  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 10089  void syscompilerinfo(int logged) Line 10294  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 10105  void syscompilerinfo(int logged) Line 10312  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 10192  void syscompilerinfo(int logged) Line 10397  void syscompilerinfo(int logged)
 #endif  #endif
 #endif  #endif
   
    //   void main()     //   void main ()
    //   {     //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    if (IsWow64()){     if (IsWow64()){
Line 10213  void syscompilerinfo(int logged) Line 10418  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 10222  int prevalence_limit(double *p, double * Line 10427  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 10303  int prevalence_limit(double *p, double * Line 10508  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 10318  int back_prevalence_limit(double *p, dou Line 10523  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 10513  int hPijx(double *p, int bage, int fage) Line 10718  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 10592  int main(int argc, char *argv[]) Line 10797  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 10602  int main(int argc, char *argv[]) Line 10808  int main(int argc, char *argv[])
   int vpopbased=0;    int vpopbased=0;
   int nres=0;    int nres=0;
   int endishere=0;    int endishere=0;
     int noffset=0;
   int ncurrv=0; /* Temporary variable */    int ncurrv=0; /* Temporary variable */
       
   char ca[32], cb[32];    char ca[32], cb[32];
Line 10627  int main(int argc, char *argv[]) Line 10833  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 10635  int main(int argc, char *argv[]) Line 10841  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 10660  int main(int argc, char *argv[]) Line 10873  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 10739  int main(int argc, char *argv[]) Line 10953  int main(int argc, char *argv[])
       if(pathr[0] == '\0') break; /* Dirty */        if(pathr[0] == '\0') break; /* Dirty */
     }      }
   }    }
     else if (argc<=2){
       strcpy(pathtot,argv[1]);
     }
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
       strcpy(z,argv[2]);
       printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
   }    }
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
Line 10818  int main(int argc, char *argv[]) Line 11037  int main(int argc, char *argv[])
     exit(70);       exit(70); 
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileresu);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
Line 10828  int main(int argc, char *argv[]) Line 11045  int main(int argc, char *argv[])
     fflush(ficlog);      fflush(ficlog);
     goto end;      goto end;
   }    }
         /*-------- Rewriting parameter file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name */
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       fflush(ficlog);
       goto end;
     }
     fprintf(ficres,"#IMaCh %s\n",version);
   
                                         
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
     /* Is it a BOM UTF-8 Windows file? */
     /* First parameter line */    /* First parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# File is an UTF8 Bom.\n"); // 0xBF
       }
       else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
       {
         noffset=noffset+2;
         printf("# File is an UTF16BE BOM file\n");
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# File is an UTF16BE BOM file\n");
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
     
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[noffset] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
Line 10848  int main(int argc, char *argv[]) Line 11100  int main(int argc, char *argv[])
                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
     if (num_filled != 5) {      if (num_filled != 5) {
       printf("Should be 5 parameters\n");        printf("Should be 5 parameters\n");
         fprintf(ficlog,"Should be 5 parameters\n");
     }      }
     numlinepar++;      numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
   }    }
   /* Second parameter line */    /* Second parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* while(fscanf(ficpar,"%[^\n]", line)) { */
       /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
Line 10869  int main(int argc, char *argv[]) Line 11127  int main(int argc, char *argv[])
     if (num_filled != 11) {      if (num_filled != 11) {
       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       printf("but line=%s\n",line);        printf("but line=%s\n",line);
         fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         fprintf(ficlog,"but line=%s\n",line);
       }
       if( lastpass > maxwav){
         printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fflush(ficlog);
         goto end;
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);        printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
       fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
       fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
       fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 10879  int main(int argc, char *argv[]) Line 11148  int main(int argc, char *argv[])
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
   }    }
   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 == 0){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
       model[0]='\0';  
       goto end;  
     } else if (num_filled != 1){  
       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       model[0]='\0';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 10907  int main(int argc, char *argv[]) Line 11172  int main(int argc, char *argv[])
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
     printf("model=1+age+%s\n",model);fflush(stdout);      printf("model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
   }    }
   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
   /* numlinepar=numlinepar+3; /\* In general *\/ */    /* numlinepar=numlinepar+3; /\* In general *\/ */
   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);    /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);    /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \      printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \   'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \   'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
     if(mle != -1){      if(mle != -1){
       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");        printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
       exit(1);        exit(1);
     }      }
   }    }
Line 10940  int main(int argc, char *argv[]) Line 11208  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 11006  int main(int argc, char *argv[]) Line 11274  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 11142  Please run with mle=-1 to get a correct Line 11419  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
           
     /*-------- Rewriting parameter file ----------*/  
     strcpy(rfileres,"r");    /* "Rparameterfile */  
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
     strcat(rfileres,".");    /* */  
     strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;  
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;  
     }  
     fprintf(ficres,"#%s\n",version);  
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
       
   /*  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 11175  Please run with mle=-1 to get a correct Line 11451  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 11279  Please run with mle=-1 to get a correct Line 11555  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 11306  Please run with mle=-1 to get a correct Line 11582  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 11489  Title=%s <br>Datafile=%s Firstpass=%d La Line 11765  Title=%s <br>Datafile=%s Firstpass=%d La
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\    fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
           ftol, stepm);            ftol, stepm);
   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);    fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
   ncurrv=1;    ncurrv=1;
Line 11497  Title=%s <br>Datafile=%s Firstpass=%d La Line 11773  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 11532  Interval (in months) between two waves: Line 11808  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 11749  Please run with mle=-1 to get a correct Line 12025  Please run with mle=-1 to get a correct
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,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 11785  Please run with mle=-1 to get a correct Line 12062  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);      /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 12053  Please run with mle=-1 to get a correct Line 12330  Please run with mle=-1 to get a correct
         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 12062  Please run with mle=-1 to get a correct Line 12339  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(" Num_filled=%d, yearsfproj=%lf, 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(" Num_filled=%d, yearsbproj=%lf, 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;
           /* /\*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,"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){ */
           /*   if (num_filled != 8) { */
           /*     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,"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); */
           /*     goto end; */
           /*   } */
           /*   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.; */
           /*   dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.; */
           /* } */
           /* break; */
       case 13:        case 13:
         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){          if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
           if (num_filled == 0){            if (num_filled == 0){
Line 12144  This is probably because your parameter Line 12445  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 12157  Please run with mle=-1 to get a correct Line 12491  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 12221  Please run with mle=-1 to get a correct Line 12555  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 12242  Please run with mle=-1 to get a correct Line 12586  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 12251  Please run with mle=-1 to get a correct Line 12601  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 12415  Please run with mle=-1 to get a correct Line 12765  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 12468  Please run with mle=-1 to get a correct Line 12818  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 12497  Please run with mle=-1 to get a correct Line 12847  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 12583  Please run with mle=-1 to get a correct Line 12933  Please run with mle=-1 to get a correct
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
       
   
   /* Executes gnuplot */
       
   printf("Before Current directory %s!\n",pathcd);    printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
Line 12618  Please run with mle=-1 to get a correct Line 12970  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') {
Line 12651  end: Line 13006  end:
     printf("\nType  q for exiting: "); fflush(stdout);      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
     printf("End\n");
     exit(0);
 }  }

Removed from v.1.274  
changed lines
  Added in v.1.296


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