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version 1.225, 2016/07/12 08:40:03 version 1.243, 2016/09/02 06:45:35
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 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.243  2016/09/02 06:45:35  brouard
     *** empty log message ***
   
     Revision 1.242  2016/08/30 15:01:20  brouard
     Summary: Fixing a lots
   
     Revision 1.241  2016/08/29 17:17:25  brouard
     Summary: gnuplot problem in Back projection to fix
   
     Revision 1.240  2016/08/29 07:53:18  brouard
     Summary: Better
   
     Revision 1.239  2016/08/26 15:51:03  brouard
     Summary: Improvement in Powell output in order to copy and paste
   
     Author:
   
     Revision 1.238  2016/08/26 14:23:35  brouard
     Summary: Starting tests of 0.99
   
     Revision 1.237  2016/08/26 09:20:19  brouard
     Summary: to valgrind
   
     Revision 1.236  2016/08/25 10:50:18  brouard
     *** empty log message ***
   
     Revision 1.235  2016/08/25 06:59:23  brouard
     *** empty log message ***
   
     Revision 1.234  2016/08/23 16:51:20  brouard
     *** empty log message ***
   
     Revision 1.233  2016/08/23 07:40:50  brouard
     Summary: not working
   
     Revision 1.232  2016/08/22 14:20:21  brouard
     Summary: not working
   
     Revision 1.231  2016/08/22 07:17:15  brouard
     Summary: not working
   
     Revision 1.230  2016/08/22 06:55:53  brouard
     Summary: Not working
   
     Revision 1.229  2016/07/23 09:45:53  brouard
     Summary: Completing for func too
   
     Revision 1.228  2016/07/22 17:45:30  brouard
     Summary: Fixing some arrays, still debugging
   
     Revision 1.226  2016/07/12 18:42:34  brouard
     Summary: temp
   
   Revision 1.225  2016/07/12 08:40:03  brouard    Revision 1.225  2016/07/12 08:40:03  brouard
   Summary: saving but not running    Summary: saving but not running
   
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   Short summary of the programme:    Short summary of the programme:
       
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies or State-specific
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (if states aren't health statuses) Expectancies from
   first survey ("cross") where individuals from different ages are    cross-longitudinal data. Cross-longitudinal data consist in: 
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    -1- a first survey ("cross") where individuals from different ages
   second wave of interviews ("longitudinal") which measure each change    are interviewed on their health status or degree of disability (in
   (if any) in individual health status.  Health expectancies are    the case of a health survey which is our main interest)
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    -2- at least a second wave of interviews ("longitudinal") which
   Maximum Likelihood of the parameters involved in the model.  The    measure each change (if any) in individual health status.  Health
   simplest model is the multinomial logistic model where pij is the    expectancies are computed from the time spent in each health state
   probability to be observed in state j at the second wave    according to a model. More health states you consider, more time is
   conditional to be observed in state i at the first wave. Therefore    necessary to reach the Maximum Likelihood of the parameters involved
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    in the model.  The simplest model is the multinomial logistic model
   'age' is age and 'sex' is a covariate. If you want to have a more    where pij is the probability to be observed in state j at the second
   complex model than "constant and age", you should modify the program    wave conditional to be observed in state i at the first
   where the markup *Covariates have to be included here again* invites    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
   you to do it.  More covariates you add, slower the    etc , where 'age' is age and 'sex' is a covariate. If you want to
     have a more complex model than "constant and age", you should modify
     the program where the markup *Covariates have to be included here
     again* invites you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
Line 675 Line 731
   of the life expectancies. It also computes the period (stable) prevalence.    of the life expectancies. It also computes the period (stable) prevalence.
   
 Back prevalence and projections:  Back prevalence and projections:
  - 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)  
     Computes the back prevalence limit  for any combination     of covariate values k   - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,     double agemaxpar, double ftolpl, int *ncvyearp, double
    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);     dateprev1,double dateprev2, int firstpass, int lastpass, int
  - hBijx Back Probability to be in state i at age x-h being in j at x     mobilavproj)
   
       Computes the back prevalence limit for any combination of
       covariate values k at any age between ageminpar and agemaxpar and
       returns it in **bprlim. In the loops,
   
      - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
          **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
   
      - hBijx Back Probability to be in state i at age x-h being in j at x
    Computes for any combination of covariates k and any age between bage and fage      Computes for any combination of covariates k and any age between bage and fage 
    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                         oldm=oldms;savm=savms;                          oldm=oldms;savm=savms;
          - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
      Computes the transition matrix starting at age 'age' over       Computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
      nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling        nhstepm*hstepm matrices. 
      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\  
                                                                          1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   
        Returns p3mat[i][j][h] after calling
        p3mat[i][j][h]=matprod2(newm,
        bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
        dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
        oldm);
   
   Important routines
   
   - func (or funcone), computes logit (pij) distinguishing
     o fixed variables (single or product dummies or quantitative);
     o varying variables by:
      (1) wave (single, product dummies, quantitative), 
      (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
          % fixed dummy (treated) or quantitative (not done because time-consuming);
          % varying dummy (not done) or quantitative (not done);
   - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
     and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
   - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
     o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
       race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
   
   
     
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
Line 761  Back prevalence and projections: Line 848  Back prevalence and projections:
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   #include <ctype.h>
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
Line 861  int cptcovsnq=0; /**< cptcovsnq number o Line 949  int cptcovsnq=0; /**< cptcovsnq number o
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 int ncoveff=0; /* Total number of effective covariates in the model */  int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
   int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
   int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
   int nsd=0; /**< Total number of single dummy variables (output) */
   int nsq=0; /**< Total number of single quantitative variables (output) */
   int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
 int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */  int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
 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 */
Line 886  int **dh; /* dh[mi][i] is number of step Line 979  int **dh; /* dh[mi][i] is number of step
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int countcallfunc=0;  /* Count the number of calls to func */  int countcallfunc=0;  /* Count the number of calls to func */
   int selected(int kvar); /* Is covariate kvar selected for printing results */
   
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
Line 916  char fileresv[FILENAMELENGTH]; Line 1011  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
   char model[MAXLINE]; /**< The model line */
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
 char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
Line 953  double dval; Line 1049  double dval;
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
   
 #define NRANSI   #define NRANSI 
 #define ITMAX 200   #define ITMAX 200
   #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
   
 #define TOL 2.0e-4   #define TOL 2.0e-4 
   
Line 1015  double ***cotvar; /* Time varying covari Line 1112  double ***cotvar; /* Time varying covari
 double ***cotqvar; /* Time varying quantitative covariate itqv */  double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Typevar; /**< 1 for qualitative fixed, 2 for quantitative fixed, 3 for qualitive varying, 4 for quanti varying*/  /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /*k          1  2   3   4     5    6    7     8    9 */
   /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
   /* Tndvar[k]    1   2   3               4          5 */
   /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
   /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
   /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
   /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
   /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
   /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
   /* Tprod[i]=k           4               7            */
   /* Tage[i]=k                  5               8      */
   /* */
   /* Type                    */
   /* V         1  2  3  4  5 */
   /*           F  F  V  V  V */
   /*           D  Q  D  D  Q */
   /*                         */
   int *TvarsD;
   int *TvarsDind;
   int *TvarsQ;
   int *TvarsQind;
   
   #define MAXRESULTLINES 10
   int nresult=0;
   int TKresult[MAXRESULTLINES];
   int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
   double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
   
   /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
   int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   
   int *Tvarsel; /**< Selected covariates for output */
   double *Tvalsel; /**< Selected modality value of covariate for output */
   int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
   int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
   int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
 int *Tage;  int *Tage;
   int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
   int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ 
   int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;  int **Tvard;
   int *Tprod;/**< Gives the k position of the k1 product */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
   int *Tposprod; /**< Gives the k1 product from the k position */
      /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
      /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
   int cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
   #define FD 1; /* Fixed dummy covariate */
   #define FQ 2; /* Fixed quantitative covariate */
   #define FP 3; /* Fixed product covariate */
   #define FPDD 7; /* Fixed product dummy*dummy covariate */
   #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
   #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
   #define VD 10; /* Varying dummy covariate */
   #define VQ 11; /* Varying quantitative covariate */
   #define VP 12; /* Varying product covariate */
   #define VPDD 13; /* Varying product dummy*dummy covariate */
   #define VPDQ 14; /* Varying product dummy*quantitative covariate */
   #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
   #define APFD 16; /* Age product * fixed dummy covariate */
   #define APFQ 17; /* Age product * fixed quantitative covariate */
   #define APVD 18; /* Age product * varying dummy covariate */
   #define APVQ 19; /* Age product * varying quantitative covariate */
   
   #define FTYPE 1; /* Fixed covariate */
   #define VTYPE 2; /* Varying covariate (loop in wave) */
   #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
   
   struct kmodel{
           int maintype; /* main type */
           int subtype; /* subtype */
   };
   struct kmodel modell[NCOVMAX];
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 double ftolhess; /**< Tolerance for computing hessian */  double ftolhess; /**< Tolerance for computing hessian */
   
Line 1217  int nbocc(char *s, char occ) Line 1406  int nbocc(char *s, char occ)
   i=0;    i=0;
   lg=strlen(s);    lg=strlen(s);
   for(i=0; i<= lg; i++) {    for(i=0; i<= lg; i++) {
   if  (s[i] == occ ) j++;      if  (s[i] == occ ) j++;
   }    }
   return j;    return j;
 }  }
Line 1890  void powell(double p[], double **xi, int Line 2079  void powell(double p[], double **xi, int
  void linmin(double p[], double xi[], int n, double *fret,    void linmin(double p[], double xi[], int n, double *fret, 
               double (*func)(double []));                 double (*func)(double [])); 
 #else   #else 
  void linmin(double p[], double xi[], int n, double *fret,    void linmin(double p[], double xi[], int n, double *fret,
                                                  double (*func)(double []),int *flat);                double (*func)(double []),int *flat); 
 #endif  #endif
   int i,ibig,j;    int i,ibig,j,jk,k; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double directest;    double directest;
   double fp,fptt;    double fp,fptt;
Line 1925  void powell(double p[], double **xi, int Line 2114  void powell(double p[], double **xi, int
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);  
       fprintf(ficlog," %d %.12lf",i, p[i]);  
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
       fprintf(ficrespow,"\n");fflush(ficrespow);
       printf("\n#model=  1      +     age ");
       fprintf(ficlog,"\n#model=  1      +     age ");
       if(nagesqr==1){
           printf("  + age*age  ");
           fprintf(ficlog,"  + age*age  ");
       }
       for(j=1;j <=ncovmodel-2;j++){
         if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);
           fprintf(ficlog,"  +      V%d  ",Tvar[j]);
         }else if(Typevar[j]==1) {
           printf("  +    V%d*age ",Tvar[j]);
           fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
         }else if(Typevar[j]==2) {
           printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }
       }
     printf("\n");      printf("\n");
   /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
   /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      for(i=1,jk=1; i <=nlstate; i++){
     if(*iter <=3){        for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
       if(*iter <=3 && *iter >1){
       tml = *localtime(&rcurr_time);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tml));        strcpy(strcurr,asctime(&tml));
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                                 strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                                 forecast_time = *localtime(&rforecast_time);          forecast_time = *localtime(&rforecast_time);
                                 strcpy(strfor,asctime(&forecast_time));          strcpy(strfor,asctime(&forecast_time));
                                 itmp = strlen(strfor);          itmp = strlen(strfor);
                                 if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
                                         strfor[itmp-1]='\0';            strfor[itmp-1]='\0';
                                 printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
                                 fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i */
Line 2003  void powell(double p[], double **xi, int Line 2225  void powell(double p[], double **xi, int
                                 /* printf("\n"); */                                  /* printf("\n"); */
                                 /* fprintf(ficlog,"\n"); */                                  /* fprintf(ficlog,"\n"); */
                         }                          }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */      /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
       if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
Line 2049  void powell(double p[], double **xi, int Line 2272  void powell(double p[], double **xi, int
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     } /* enough precision */       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
Line 2108  void powell(double p[], double **xi, int Line 2331  void powell(double p[], double **xi, int
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
                                 printf("Before linmin in direction P%d-P0\n",n);          printf("Before linmin in direction P%d-P0\n",n);
                                 for (j=1;j<=n;j++) {          for (j=1;j<=n;j++) {
                                         printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         if(j % ncovmodel == 0){            if(j % ncovmodel == 0){
                                                 printf("\n");              printf("\n");
                                                 fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
                                         }            }
                                 }          }
 #endif  #endif
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
 #else  #else
                                 linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                                 flatdir[i]=flat; /* Function is vanishing in that direction i */          flatdir[i]=flat; /* Function is vanishing in that direction i */
 #endif  #endif
           
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
                                 for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
                                         printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         if(j % ncovmodel == 0){            if(j % ncovmodel == 0){
                                                 printf("\n");              printf("\n");
                                                 fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
                                         }            }
                                 }          }
 #endif  #endif
                                 for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
                                         xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                         xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                 }          }
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
                                 for (j=1, flatd=0;j<=n;j++) {          for (j=1, flatd=0;j<=n;j++) {
                                         if(flatdir[j]>0)            if(flatdir[j]>0)
                                                 flatd++;              flatd++;
                                 }          }
                                 if(flatd >0){          if(flatd >0){
                                         printf("%d flat directions\n",flatd);            printf("%d flat directions\n",flatd);
                                         fprintf(ficlog,"%d flat directions\n",flatd);            fprintf(ficlog,"%d flat directions\n",flatd);
                                         for (j=1;j<=n;j++) {             for (j=1;j<=n;j++) { 
                                                 if(flatdir[j]>0){              if(flatdir[j]>0){
                                                         printf("%d ",j);                printf("%d ",j);
                                                         fprintf(ficlog,"%d ",j);                fprintf(ficlog,"%d ",j);
                                                 }              }
                                         }            }
                                         printf("\n");            printf("\n");
                                         fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
                                 }          }
 #endif  #endif
                                 printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                 fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                           
 #ifdef DEBUG  #ifdef DEBUG
                                 printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                                 fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                                 for(j=1;j<=n;j++){          for(j=1;j<=n;j++){
                                         printf(" %lf",xit[j]);            printf(" %lf",xit[j]);
                                         fprintf(ficlog," %lf",xit[j]);            fprintf(ficlog," %lf",xit[j]);
                                 }          }
                                 printf("\n");          printf("\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t or directest negative */        } /* end of t or directest negative */
 #ifdef POWELLNOF3INFF1TEST  #ifdef POWELLNOF3INFF1TEST
 #else  #else
     } /* end if (fptt < fp)  */        } /* end if (fptt < fp)  */
 #endif  #endif
 #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                 } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */      } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
 #else  #else
 #endif  #endif
   } /* loop iteration */                   } /* loop iteration */ 
 }   } 
     
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
     
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)    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 ij by left multiplying the unit      /* Computes the prevalence limit in each live state at age x and for covariate combination ij 
      matrix by transitions matrix until convergence is reached with precision ftolpl */         (and selected quantitative values in nres)
          by left multiplying the unit
          matrix by transitions matrix until convergence is reached with precision ftolpl */
   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */    /* Wx= 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 */
Line 2206  double **prevalim(double **prlim, int nl Line 2431  double **prevalim(double **prlim, int nl
   /* {0.51571254859325999, 0.4842874514067399, */    /* {0.51571254859325999, 0.4842874514067399, */
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
       
   int i, ii,j,k;    int i, ii,j,k;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
Line 2236  double **prevalim(double **prlim, int nl Line 2461  double **prevalim(double **prlim, int nl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                         /* Here comes the value of the covariate 'ij' */        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */      }
     }      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];        /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
     for (k=1; k<=cptcovprod;k++) /* Useless */      }
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];        if(Dummy[Tvar[Tage[k]]]){
               cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         } else{
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
       }
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
Line 2306  Earliest age to start was %d-%d=%d, ncvl Line 2552  Earliest age to start was %d-%d=%d, ncvl
   
  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
 {  {
   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and covariate ij 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 */
Line 2365  Earliest age to start was %d-%d=%d, ncvl Line 2611  Earliest age to start was %d-%d=%d, ncvl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */        /* printf("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
       }
       /* for (k=1; k<=cptcovn;k++) { */
       /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
       /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
       /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
       /* } */
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                           /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
         /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }
       /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
       /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
       /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
       for (k=1; k<=cptcovage;k++){  /* For product with age */
         if(Dummy[Tvar[Tage[k]]]){
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         } else{
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */  
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */  
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];  
     for (k=1; k<=cptcovprod;k++) /* Useless */  
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */  
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 2398  Earliest age to start was %d-%d=%d, ncvl Line 2676  Earliest age to start was %d-%d=%d, ncvl
     }      }
     for(j=1; j<=nlstate; j++){       for(j=1; j<=nlstate; j++){ 
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */          /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                 bprlim[i][j]= newm[i][j];          bprlim[i][j]= newm[i][j];
                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */          max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                 min[i]=FMIN(min[i],bprlim[i][j]);          min[i]=FMIN(min[i],bprlim[i][j]);
       }        }
     }      }
                                   
Line 2555  double **pmij(double **ps, double *cov, Line 2833  double **pmij(double **ps, double *cov,
         /* }else */          /* }else */
         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);          doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
       }else{        }else{
         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);          ;
           /* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
       }        }
     } /*End ii */      } /*End ii */
   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
Line 2596  double **bpmij(double **ps, double *cov, Line 2875  double **bpmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 for(j=1; j<i;j++){      for(j=1; j<i;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                 }      }
         }    }
             
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 s1=0;      s1=0;
                 for(j=1; j<i; j++){      for(j=1; j<i; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                 ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
                 /* Computing other pijs */      /* Computing other pijs */
                 for(j=1; j<i; j++)      for(j=1; j<i; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 for(j=i+1; j<=nlstate+ndeath; j++)      for(j=i+1; j<=nlstate+ndeath; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         } /* end i */    } /* end i */
             
         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                 for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
                         ps[ii][jj]=0;        ps[ii][jj]=0;
                         ps[ii][ii]=1;        ps[ii][ii]=1;
                 }      }
         }    }
         /* Added for backcast */ /* Transposed matrix too */    /* Added for backcast */ /* 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++){
                         s1+=ps[ii][jj];        s1+=ps[ii][jj];
                 }      }
                 for(ii=1; ii<= nlstate; ii++){      for(ii=1; ii<= nlstate; ii++){
                         ps[ii][jj]=ps[ii][jj]/s1;        ps[ii][jj]=ps[ii][jj]/s1;
                 }      }
         }    }
         /* Transposition */    /* Transposition */
         for(jj=1; jj<= nlstate+ndeath; jj++){    for(jj=1; jj<= nlstate+ndeath; jj++){
                 for(ii=jj; ii<= nlstate+ndeath; ii++){      for(ii=jj; ii<= nlstate+ndeath; ii++){
                         s1=ps[ii][jj];        s1=ps[ii][jj];
                         ps[ii][jj]=ps[jj][ii];        ps[ii][jj]=ps[jj][ii];
                         ps[jj][ii]=s1;        ps[jj][ii]=s1;
                 }      }
         }    }
         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         /*   } */    /*   } */
         /*   printf("\n "); */    /*   printf("\n "); */
         /* } */    /* } */
         /* printf("\n ");printf("%lf ",cov[2]);*/    /* printf("\n ");printf("%lf ",cov[2]);*/
         /*    /*
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 goto end;*/      goto end;*/
         return ps;    return ps;
 }  }
   
   
Line 2696  double **matprod2(double **out, double * Line 2975  double **matprod2(double **out, double *
   
 /************* Higher Matrix Product ***************/  /************* Higher Matrix Product ***************/
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
 {  {
   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over     /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
Line 2731  double ***hpxij(double ***po, int nhstep Line 3010  double ***hpxij(double ***po, int nhstep
       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
                                 cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */          /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */        }
                                 cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
                         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        }
         for (k=1; k<=cptcovage;k++){
           if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           } else{
             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
           }
           /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovprod;k++){ /*  */
           /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
         }
         /* for (k=1; k<=cptcovn;k++)  */
         /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
         /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
         /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
         /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
         /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
         
         
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                         /* right multiplication of oldm by the current matrix */                          /* right multiplication of oldm by the current matrix */
Line 2890  double ***hbxij(double ***po, int nhstep Line 3187  double ***hbxij(double ***po, int nhstep
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
         int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
         int ioffset=0;    int ioffset=0;
         double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         double **out;    double **out;
         double sw; /* Sum of weights */    double lli; /* Individual log likelihood */
         double lli; /* Individual log likelihood */    int s1, s2;
         int s1, s2;    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
         int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */    double bbh, survp;
         double bbh, survp;    long ipmx;
         long ipmx;    double agexact;
         double agexact;    /*extern weight */
         /*extern weight */    /* We are differentiating ll according to initial status */
         /* We are differentiating ll according to initial status */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*for(i=1;i<imx;i++) 
         /*for(i=1;i<imx;i++)       printf(" %d\n",s[4][i]);
                 printf(" %d\n",s[4][i]);    */
         */  
   
         ++countcallfunc;    ++countcallfunc;
   
         cov[1]=1.;    cov[1]=1.;
   
         for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;    ioffset=0;
         if(mle==1){    if(mle==1){
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         /* Computes the values of the ncovmodel covariates of the model        /* Computes the values of the ncovmodel covariates of the model
                                  depending if the covariates are fixed or varying (age dependent) and stores them in cov[]           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
                                  Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                                  to be observed in j being in i according to the model.           to be observed in j being in i according to the model.
                         */        */
                         ioffset=2+nagesqr+cptcovage;        ioffset=2+nagesqr ;
                         /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */     /* Fixed */
                         for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */        for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
                                 cov[++ioffset]=covar[Tvar[k]][i];          cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
                         }        }
                         for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
                                 cov[++ioffset]=coqvar[iqv][i];           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
                         }           has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
                         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* We compute the contribution to Likelihood of each effective transition
                                  is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            mw[mi][i] is real wave of the mi th effectve wave */
                                  has been calculated etc */        /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
                         /* For an individual i, wav[i] gives the number of effective waves */           s2=s[mw[mi+1][i]][i];
                         /* We compute the contribution to Likelihood of each effective transition           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
                                  mw[mi][i] is real wave of the mi th effectve wave */           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
                         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
                                  s2=s[mw[mi+1][i]][i];        */
                                  And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]        for(mi=1; mi<= wav[i]-1; mi++){
                                  But if the variable is not in the model TTvar[iv] is the real variable effective in the model:          for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
                                  meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]            /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                         */            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                         for(mi=1; mi<= wav[i]-1; mi++){          }
                                 for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];            for (j=1;j<=nlstate+ndeath;j++){
                                 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                 for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         if(cotqvar[mw[mi][i]][iqtv][i] == -1){            }
                                                 printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);          for(d=0; d<dh[mi][i]; d++){
                                         }            newm=savm;
                                         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                 }            cov[2]=agexact;
                                 /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */            if(nagesqr==1)
                                 for (ii=1;ii<=nlstate+ndeath;ii++)              cov[3]= agexact*agexact;  /* Should be changed here */
                                         for (j=1;j<=nlstate+ndeath;j++){            for (kk=1; kk<=cptcovage;kk++) {
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);            if(!FixedV[Tvar[Tage[kk]]])
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
                                         }            else
                                 for(d=0; d<dh[mi][i]; d++){              cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
                                         newm=savm;            }
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                         cov[2]=agexact;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         if(nagesqr==1)            savm=oldm;
                                                 cov[3]= agexact*agexact;  /* Should be changed here */            oldm=newm;
                                         for (kk=1; kk<=cptcovage;kk++) {          } /* end mult */
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */          
                                         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          /* But now since version 0.9 we anticipate for bias at large stepm.
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                                         savm=oldm;           * (in months) between two waves is not a multiple of stepm, we rounded to 
                                         oldm=newm;           * the nearest (and in case of equal distance, to the lowest) interval but now
                                 } /* end mult */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                                            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                                         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */           * probability in order to take into account the bias as a fraction of the way
                                 /* But now since version 0.9 we anticipate for bias at large stepm.  
                                  * If stepm is larger than one month (smallest stepm) and if the exact delay   
                                  * (in months) between two waves is not a multiple of stepm, we rounded to   
                                  * the nearest (and in case of equal distance, to the lowest) interval but now  
                                  * we keep into memory the bias bh[mi][i] and also the previous matrix product  
                                  * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the  
                                  * probability in order to take into account the bias as a fraction of the way  
                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies                                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                                  * -stepm/2 to stepm/2 .                                   * -stepm/2 to stepm/2 .
                                  * For stepm=1 the results are the same as for previous versions of Imach.                                   * For stepm=1 the results are the same as for previous versions of Imach.
                                  * For stepm > 1 the results are less biased than in previous versions.                                    * For stepm > 1 the results are less biased than in previous versions. 
                                  */                                   */
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 /* bias bh is positive if real duration          /* bias bh is positive if real duration
                                  * is higher than the multiple of stepm and negative otherwise.           * is higher than the multiple of stepm and negative otherwise.
                                  */           */
                                 /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                                 if( s2 > nlstate){           if( s2 > nlstate){ 
                                         /* i.e. if s2 is a death state and if the date of death is known             /* i.e. if s2 is a death state and if the date of death is known 
                                                  then the contribution to the likelihood is the probability to                then the contribution to the likelihood is the probability to 
                                                  die between last step unit time and current  step unit time,                die between last step unit time and current  step unit time, 
                                                  which is also equal to probability to die before dh                which is also equal to probability to die before dh 
                                                  minus probability to die before dh-stepm .                minus probability to die before dh-stepm . 
                                                  In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
                                                  as if date of death was unknown. Death was treated as any other               as if date of death was unknown. Death was treated as any other
                                                  health state: the date of the interview describes the actual state               health state: the date of the interview describes the actual state
                                                  and not the date of a change in health state. The former idea was               and not the date of a change in health state. The former idea was
                                                  to consider that at each interview the state was recorded               to consider that at each interview the state was recorded
                                                  (healthy, disable or death) and IMaCh was corrected; but when we               (healthy, disable or death) and IMaCh was corrected; but when we
                                                  introduced the exact date of death then we should have modified               introduced the exact date of death then we should have modified
                                                  the contribution of an exact death to the likelihood. This new               the contribution of an exact death to the likelihood. This new
                                                  contribution is smaller and very dependent of the step unit               contribution is smaller and very dependent of the step unit
                                                  stepm. It is no more the probability to die between last interview               stepm. It is no more the probability to die between last interview
                                                  and month of death but the probability to survive from last               and month of death but the probability to survive from last
                                                  interview up to one month before death multiplied by the               interview up to one month before death multiplied by the
                                                  probability to die within a month. Thanks to Chris               probability to die within a month. Thanks to Chris
                                                  Jackson for correcting this bug.  Former versions increased               Jackson for correcting this bug.  Former versions increased
                                                  mortality artificially. The bad side is that we add another loop               mortality artificially. The bad side is that we add another loop
                                                  which slows down the processing. The difference can be up to 10%               which slows down the processing. The difference can be up to 10%
                                                  lower mortality.               lower mortality.
                                         */            */
                                         /* If, at the beginning of the maximization mostly, the            /* If, at the beginning of the maximization mostly, the
                                                  cumulative probability or probability to be dead is               cumulative probability or probability to be dead is
                                                  constant (ie = 1) over time d, the difference is equal to               constant (ie = 1) over time d, the difference is equal to
                                                  0.  out[s1][3] = savm[s1][3]: probability, being at state               0.  out[s1][3] = savm[s1][3]: probability, being at state
                                                  s1 at precedent wave, to be dead a month before current               s1 at precedent wave, to be dead a month before current
                                                  wave is equal to probability, being at state s1 at               wave is equal to probability, being at state s1 at
                                                  precedent wave, to be dead at mont of the current               precedent wave, to be dead at mont of the current
                                                  wave. Then the observed probability (that this person died)               wave. Then the observed probability (that this person died)
                                                  is null according to current estimated parameter. In fact,               is null according to current estimated parameter. In fact,
                                                  it should be very low but not zero otherwise the log go to               it should be very low but not zero otherwise the log go to
                                                  infinity.               infinity.
                                         */            */
 /* #ifdef INFINITYORIGINAL */  /* #ifdef INFINITYORIGINAL */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #else */  /* #else */
Line 3037  double func( double *x) Line 3326  double func( double *x)
 /*        else */  /*        else */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */  /* #endif */
                                         lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
                       
                                 } else if  ( s2==-1 ) { /* alive */          } else if  ( s2==-1 ) { /* alive */
                                         for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
                                         lli= log(survp);            lli= log(survp);
                                 }          }
                                 else if  (s2==-4) {           else if  (s2==-4) { 
                                         for (j=3,survp=0. ; j<=nlstate; j++)              for (j=3,survp=0. ; j<=nlstate; j++)  
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         lli= log(survp);             lli= log(survp); 
                                 }           } 
                                 else if  (s2==-5) {           else if  (s2==-5) { 
                                         for (j=1,survp=0. ; j<=2; j++)              for (j=1,survp=0. ; j<=2; j++)  
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         lli= log(survp);             lli= log(survp); 
                                 }           } 
                                 else{          else{
                                         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                                         /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                                 }           } 
                                 /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                                 /*if(lli ==000.0)*/          /*if(lli ==000.0)*/
                                 /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                                 /* if (lli < log(mytinydouble)){ */          /* if (lli < log(mytinydouble)){ */
                                 /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
                                 /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
                                 /* } */          /* } */
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }  else if(mle==2){    }  else if(mle==2){
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                         for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         }            }
                                 for(d=0; d<=dh[mi][i]; d++){          for(d=0; d<=dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            oldm=newm;
                                 } /* end mult */          } /* end mult */
               
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }  else if(mle==3){  /* exponential inter-extrapolation */    }  else if(mle==3){  /* exponential inter-extrapolation */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                         for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            oldm=newm;
                                 } /* end mult */          } /* end mult */
               
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }else if (mle==4){  /* ml=4 no inter-extrapolation */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                         for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                   
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            oldm=newm;
                                 } /* end mult */          } /* end mult */
               
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 if( s2 > nlstate){           if( s2 > nlstate){ 
                                         lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
                                 } else if  ( s2==-1 ) { /* alive */          } else if  ( s2==-1 ) { /* alive */
                                         for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
                                                 survp += out[s1][j];              survp += out[s1][j];
                                         lli= log(survp);            lli= log(survp);
                                 }else{          }else{
                                         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                                 }          }
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
                         for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                   
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            oldm=newm;
                                 } /* end mult */          } /* end mult */
               
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                                 /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         } /* End of if */    } /* End of if */
         for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         return -l;    return -l;
 }  }
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double funcone( double *x)  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as func but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
         int ioffset=0;    int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
   int s1, s2;    int s1, s2;
         int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
Line 3246  double funcone( double *x) Line 3536  double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;    ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     ioffset=2+nagesqr+cptcovage;      /* ioffset=2+nagesqr+cptcovage; */
       ioffset=2+nagesqr;
       /* Fixed */
     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
     for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
       cov[++ioffset]=covar[Tvar[k]][i];      for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
     }        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
     for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives Fixed covariates */  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
       cov[++ioffset]=coqvar[iqv][i];  /*    cov[2+6]=covar[Tvar[6]][i];  */
   /*    cov[2+6]=covar[2][i]; V2  */
   /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
   /*    cov[2+7]=covar[Tvar[7]][i];  */
   /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
   /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
   /*    cov[2+9]=covar[Tvar[9]][i];  */
   /*    cov[2+9]=covar[1][i]; V1  */
     }      }
       /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
       /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
       /* } */
       /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
       /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
       /* } */
           
     for(mi=1; mi<= wav[i]-1; mi++){  
       for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];      /* Wave varying (but not age varying) */
       }        for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
       for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */          /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];          cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
       }        }
         /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
         /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
         /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
         /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
         /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
         /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
         /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
         /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
         /* } */
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=nlstate+ndeath;j++){
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 3279  double funcone( double *x) Line 3595  double funcone( double *x)
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;            if(!FixedV[Tvar[Tage[kk]]])
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             else
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
         }          }
         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */          /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
Line 3334  double funcone( double *x) Line 3653  double funcone( double *x)
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
     } /* end of wave */          } /* end of wave */
   } /* end of individual */  } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if(globpr==0){ /* First time we count the contributions and weights */  if(globpr==0){ /* First time we count the contributions and weights */
     gipmx=ipmx;          gipmx=ipmx;
     gsw=sw;          gsw=sw;
   }  }
   return -l;  return -l;
 }  }
   
   
Line 3839  void pstamp(FILE *fichier) Line 4158  void pstamp(FILE *fichier)
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                                                                          int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],  \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                                                                          int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies */  {  /* Some frequencies */
       
          int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, k, iv;
          int iind=0, iage=0;    int iind=0, iage=0;
          int mi; /* Effective wave */    int mi; /* Effective wave */
          int first;    int first;
          double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
          double *meanq;    double *meanq;
          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;
          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];    char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
          double agebegin, ageend;    double agebegin, ageend;
       
          pp=vector(1,nlstate);  
          prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);   
          posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */   
          pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */   
          /* prop=matrix(1,nlstate,iagemin,iagemax+3); */  
          meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */  
          meanqt=matrix(1,lastpass,1,nqtveff);  
          strcpy(fileresp,"P_");  
          strcat(fileresp,fileresu);  
          /*strcat(fileresphtm,fileresu);*/  
          if((ficresp=fopen(fileresp,"w"))==NULL) {  
                  printf("Problem with prevalence resultfile: %s\n", fileresp);  
                  fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);  
                  exit(0);  
          }  
   
          strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));  
          if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {  
                  printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));  
                  fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));  
                  fflush(ficlog);  
                  exit(70);   
          }  
          else{  
                  fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \  
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\  
                                                  fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);  
          }  
          fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);  
           
          strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));    pp=vector(1,nlstate);
          if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
                  printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));    posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
                  fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
                  fflush(ficlog);    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
                  exit(70);     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
          }    meanqt=matrix(1,lastpass,1,nqtveff);
          else{    strcpy(fileresp,"P_");
                  fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    strcat(fileresp,fileresu);
 <hr size=\"2\" color=\"#EC5E5E\"> \n\    /*strcat(fileresphtm,fileresu);*/
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     }
     
     strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
     if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
       printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
                                                  fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
          }    }
          fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
   
          freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);  
          j1=0;  
       
          j=ncoveff;    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
          if (cptcovn<1) {j=1;ncodemax[1]=1;}    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
       printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
          first=1;      fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fflush(ficlog);
          /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:      exit(70); 
                         reference=low_education V1=0,V2=0    } else{
                         med_educ                V1=1 V2=0,       fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
                         high_educ               V1=0 V2=1  <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
                         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
          */              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
          for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
                  posproptt=0.;    
                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
                          scanf("%d", i);*/    j1=0;
                  for (i=-5; i<=nlstate+ndeath; i++)      
                          for (jk=-5; jk<=nlstate+ndeath; jk++)      /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
                                  for(m=iagemin; m <= iagemax+3; m++)    j=cptcoveff;  /* Only dummy covariates of the model */
                                          freq[i][jk][m]=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           
                  for (i=1; i<=nlstate; i++)  {    first=1;
                          for(m=iagemin; m <= iagemax+3; m++)    
                                  prop[i][m]=0;    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
                          posprop[i]=0;       reference=low_education V1=0,V2=0
                          pospropt[i]=0;       med_educ                V1=1 V2=0, 
                  }       high_educ               V1=0 V2=1
                  for (z1=1; z1<= nqfveff; z1++) {         Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
                          meanq[z1]+=0.;    */
                          for(m=1;m<=lastpass;m++){    
                                  meanqt[m][z1]=0.;    for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
                          }      posproptt=0.;
                  }      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
               scanf("%d", i);*/
                  dateintsum=0;      for (i=-5; i<=nlstate+ndeath; i++)  
                  k2cpt=0;        for (jk=-5; jk<=nlstate+ndeath; jk++)  
      /* For that comination of covariate j1, we count and print the frequencies */          for(m=iagemin; m <= iagemax+3; m++)
                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */            freq[i][jk][m]=0;
                          bool=1;      
                          if (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */      for (i=1; i<=nlstate; i++)  {
                                  for (z1=1; z1<= nqfveff; z1++) {          for(m=iagemin; m <= iagemax+3; m++)
                                          meanq[z1]+=coqvar[Tvar[z1]][iind];          prop[i][m]=0;
                                  }        posprop[i]=0;
                                  for (z1=1; z1<=ncoveff; z1++) {          pospropt[i]=0;
                                          /* if(Tvaraff[z1] ==-20){ */      }
                                          /*      /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */      /* for (z1=1; z1<= nqfveff; z1++) {   */
                                          /* }else  if(Tvaraff[z1] ==-10){ */      /*   meanq[z1]+=0.; */
                                          /*      /\* sumnew+=coqvar[z1][iind]; *\/ */      /*   for(m=1;m<=lastpass;m++){ */
                                          /* }else  */      /*  meanqt[m][z1]=0.; */
                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){      /*   } */
                                                  /* Tests if this individual i responded to j1 (V4=1 V3=0) */      /* } */
                                                  bool=0;      
                                                  /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",       dateintsum=0;
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),      k2cpt=0;
                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/      /* For that combination of covariate j1, we count and print the frequencies in one pass */
                                                  /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                                          }         bool=1;
                                  } /* end z1 */        if(anyvaryingduminmodel==0){ /* If All fixed covariates */
                          } /* cptcovn > 0 */          if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             /* for (z1=1; z1<= nqfveff; z1++) {   */
                          if (bool==1){ /* We selected an individual iin satisfying combination j1 */            /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
                                  /* for(m=firstpass; m<=lastpass; m++){ */            /* } */
                                  for(mi=1; mi<wav[iind];mi++){            for (z1=1; z1<=cptcoveff; z1++) {  
                                          m=mw[mi][iind];              /* if(Tvaraff[z1] ==-20){ */
                                          /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]              /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                                                         and mw[mi+1][iind]. dh depends on stepm. */              /* }else  if(Tvaraff[z1] ==-10){ */
                                          agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/              /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
                                          ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */              /* }else  */
                                          if(m >=firstpass && m <=lastpass){              if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                                                  k2=anint[m][iind]+(mint[m][iind]/12.);                /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/                bool=0;
                                                  if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                                                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                                                  if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */                   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                                                          prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                                                  if (m<lastpass) {              } /* Onlyf fixed */
                                                          /* if(s[m][iind]==4 && s[m+1][iind]==4) */            } /* end z1 */
                                                          /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */          } /* cptcovn > 0 */
                                                          if(s[m][iind]==-1)        } /* end any */
                                                                  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.));        if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
                                                          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(m=firstpass; m<=lastpass; m++){ */
                                                          /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */          for(mi=1; mi<wav[iind];mi++){ /* For that wave */
                                                          freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */            m=mw[mi][iind];
                                                  }            if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                                          }                for (z1=1; z1<=cptcoveff; z1++) {
                                          if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {                if( Fixed[Tmodelind[z1]]==1){
                                                  dateintsum=dateintsum+k2;                  iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                                                  k2cpt++;                  if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                                                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */                    bool=0;
                                          }                }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                                          /*}*/                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                                  } /* end m */                    bool=0;
                          } /* end bool */                  }
                  } /* end iind = 1 to imx */                }
        /* prop[s][age] is feeded for any initial and valid live state as well as              }
                                         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */            }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
             if(bool==1){
                  /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/              /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                  pstamp(ficresp);                 and mw[mi+1][iind]. dh depends on stepm. */
                  if  (ncoveff>0) {              agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                          fprintf(ficresp, "\n#********** Variable ");               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");               if(m >=firstpass && m <=lastpass){
                          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");                 k2=anint[m][iind]+(mint[m][iind]/12.);
                          for (z1=1; z1<=ncoveff; z1++){                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                                  fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                                  fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                                  fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                          }                  prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                          fprintf(ficresp, "**********\n#");                if (m<lastpass) {
                          fprintf(ficresphtm, "**********</h3>\n");                  /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                          fprintf(ficresphtmfr, "**********</h3>\n");                  /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                          fprintf(ficlog, "\n#********** Variable ");                   if(s[m][iind]==-1)
                          for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                    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.));
                          fprintf(ficlog, "**********\n");                  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)((agebegin+ageend)/2.)] += weight[iind]; */
                  fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");                  freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                  for(i=1; i<=nlstate;i++) {                }
                          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              } /* end if between passes */  
                          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);              if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
                  }                dateintsum=dateintsum+k2;
                  fprintf(ficresp, "\n");                k2cpt++;
                  fprintf(ficresphtm, "\n");                /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                     }
                  /* Header of frequency table by age */            } /* end bool 2 */
                  fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");          } /* end m */
                  fprintf(ficresphtmfr,"<th>Age</th> ");        } /* end bool */
                  for(jk=-1; jk <=nlstate+ndeath; jk++){      } /* end iind = 1 to imx */
                          for(m=-1; m <=nlstate+ndeath; m++){      /* prop[s][age] is feeded for any initial and valid live state as well as
                                  if(jk!=0 && m!=0)         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
                                          fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);      
                          }      
                  }      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                  fprintf(ficresphtmfr, "\n");      pstamp(ficresp);
       if  (cptcoveff>0){
         fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++){
           if(DummyV[z1]){
             fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           }else{
             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           }
         }
         fprintf(ficresp, "**********\n#");
         fprintf(ficresphtm, "**********</h3>\n");
         fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "**********\n");
       }
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       for(i=1; i<=nlstate;i++) {
         fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }
       fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");
       
       /* Header of frequency table by age */
       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       fprintf(ficresphtmfr,"<th>Age</th> ");
       for(jk=-1; jk <=nlstate+ndeath; jk++){
         for(m=-1; m <=nlstate+ndeath; m++){
           if(jk!=0 && m!=0)
             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
         }
       }
       fprintf(ficresphtmfr, "\n");
       
       /* For each age */
       for(iage=iagemin; iage <= iagemax+3; iage++){
         fprintf(ficresphtm,"<tr>");
         if(iage==iagemax+1){
           fprintf(ficlog,"1");
           fprintf(ficresphtmfr,"<tr><th>0</th> ");
         }else if(iage==iagemax+2){
           fprintf(ficlog,"0");
           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
         }else if(iage==iagemax+3){
           fprintf(ficlog,"Total");
           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
         }else{
           if(first==1){
             first=0;
             printf("See log file for details...\n");
           }
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", iage);
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][iage]; 
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][iage];
           if(pp[jk]>=1.e-10){
             if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }else{
             if(first==1)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           }
         }
               
                  /* For each age */        for(jk=1; jk <=nlstate ; jk++){ 
                  for(iage=iagemin; iage <= iagemax+3; iage++){          /* posprop[jk]=0; */
                          fprintf(ficresphtm,"<tr>");          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
                          if(iage==iagemax+1){            pp[jk] += freq[jk][m][iage];
                                  fprintf(ficlog,"1");        } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
                                  fprintf(ficresphtmfr,"<tr><th>0</th> ");        
                          }else if(iage==iagemax+2){        for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
                                  fprintf(ficlog,"0");          pos += pp[jk]; /* pos is the total number of transitions until this age */
                                  fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");          posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                          }else if(iage==iagemax+3){                                            from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                                  fprintf(ficlog,"Total");          pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
                                  fprintf(ficresphtmfr,"<tr><th>Total</th> ");                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                          }else{        }
                                  if(first==1){        for(jk=1; jk <=nlstate ; jk++){
                                          first=0;          if(pos>=1.e-5){
                                          printf("See log file for details...\n");            if(first==1)
                                  }              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                                  fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                                  fprintf(ficlog,"Age %d", iage);          }else{
                          }            if(first==1)
                          for(jk=1; jk <=nlstate ; jk++){              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                                  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                                          pp[jk] += freq[jk][m][iage];           }
                          }          if( iage <= iagemax){
                          for(jk=1; jk <=nlstate ; jk++){            if(pos>=1.e-5){
                                  for(m=-1, pos=0; m <=0 ; m++)              fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                                          pos += freq[jk][m][iage];              fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                                  if(pp[jk]>=1.e-10){              /*probs[iage][jk][j1]= pp[jk]/pos;*/
                                          if(first==1){              /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
                                                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
                                          }            else{
                                          fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
                                  }else{              fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
                                          if(first==1)            }
                                                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }
                                          fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          pospropt[jk] +=posprop[jk];
                                  }        } /* end loop jk */
                          }        /* pospropt=0.; */
         for(jk=-1; jk <=nlstate+ndeath; jk++){
                          for(jk=1; jk <=nlstate ; jk++){           for(m=-1; m <=nlstate+ndeath; m++){
                                  /* posprop[jk]=0; */            if(freq[jk][m][iage] !=0 ) { /* minimizing output */
                                  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */              if(first==1){
                                          pp[jk] += freq[jk][m][iage];                printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                          }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */              }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
                          for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){            }
                                  pos += pp[jk]; /* pos is the total number of transitions until this age */            if(jk!=0 && m!=0)
                                  posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state              fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */          }
                                  pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state        } /* end loop jk */
                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */        posproptt=0.; 
                          }        for(jk=1; jk <=nlstate; jk++){
                          for(jk=1; jk <=nlstate ; jk++){          posproptt += pospropt[jk];
                                  if(pos>=1.e-5){        }
                                          if(first==1)        fprintf(ficresphtmfr,"</tr>\n ");
                                                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        if(iage <= iagemax){
                                          fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          fprintf(ficresp,"\n");
                                  }else{          fprintf(ficresphtm,"</tr>\n");
                                          if(first==1)        }
                                                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        if(first==1)
                                          fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          printf("Others in log...\n");
                                  }        fprintf(ficlog,"\n");
                                  if( iage <= iagemax){      } /* end loop age iage */
                                          if(pos>=1.e-5){      fprintf(ficresphtm,"<tr><th>Tot</th>");
                                                  fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);      for(jk=1; jk <=nlstate ; jk++){
                                                  fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);        if(posproptt < 1.e-5){
                                                  /*probs[iage][jk][j1]= pp[jk]/pos;*/          fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);   
                                                  /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/        }else{
                                          }          fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);    
                                          else{        }
                                                  fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);      }
                                                  fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);      fprintf(ficresphtm,"</tr>\n");
                                          }      fprintf(ficresphtm,"</table>\n");
                                  }      fprintf(ficresphtmfr,"</table>\n");
                                  pospropt[jk] +=posprop[jk];      if(posproptt < 1.e-5){
                          } /* end loop jk */        fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                          /* pospropt=0.; */        fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                          for(jk=-1; jk <=nlstate+ndeath; jk++){        fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
                                  for(m=-1; m <=nlstate+ndeath; m++){        invalidvarcomb[j1]=1;
                                          if(freq[jk][m][iage] !=0 ) { /* minimizing output */      }else{
                                                  if(first==1){        fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
                                                          printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);        invalidvarcomb[j1]=0;
                                                  }      }
                                                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);      fprintf(ficresphtmfr,"</table>\n");
                                          }    } /* end selected combination of covariate j1 */
                                          if(jk!=0 && m!=0)    dateintmean=dateintsum/k2cpt; 
                                                  fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);    
                                  }    fclose(ficresp);
                          } /* end loop jk */    fclose(ficresphtm);
                          posproptt=0.;     fclose(ficresphtmfr);
                          for(jk=1; jk <=nlstate; jk++){    free_vector(meanq,1,nqfveff);
                                  posproptt += pospropt[jk];    free_matrix(meanqt,1,lastpass,1,nqtveff);
                          }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
                          fprintf(ficresphtmfr,"</tr>\n ");    free_vector(pospropt,1,nlstate);
                          if(iage <= iagemax){    free_vector(posprop,1,nlstate);
                                  fprintf(ficresp,"\n");    free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
                                  fprintf(ficresphtm,"</tr>\n");    free_vector(pp,1,nlstate);
                          }    /* End of freqsummary */
                          if(first==1)  }
                                  printf("Others in log...\n");  
                          fprintf(ficlog,"\n");  
                  } /* end loop age iage */  
                  fprintf(ficresphtm,"<tr><th>Tot</th>");  
                  for(jk=1; jk <=nlstate ; jk++){  
                          if(posproptt < 1.e-5){  
                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);    
                          }else{  
                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);     
                          }  
                  }  
                  fprintf(ficresphtm,"</tr>\n");  
                  fprintf(ficresphtm,"</table>\n");  
                  fprintf(ficresphtmfr,"</table>\n");  
                  if(posproptt < 1.e-5){  
                          fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);  
                          fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);  
                          fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);  
                          invalidvarcomb[j1]=1;  
                  }else{  
                          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);  
                          invalidvarcomb[j1]=0;  
                  }  
                  fprintf(ficresphtmfr,"</table>\n");  
          } /* end selected combination of covariate j1 */  
          dateintmean=dateintsum/k2cpt;   
                    
          fclose(ficresp);  
          fclose(ficresphtm);  
          fclose(ficresphtmfr);  
          free_vector(meanq,1,nqfveff);  
          free_matrix(meanqt,1,lastpass,1,nqtveff);  
          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);  
          free_vector(pospropt,1,nlstate);  
          free_vector(posprop,1,nlstate);  
          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);  
          free_vector(pp,1,nlstate);  
          /* End of freqsummary */  
  }  
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  {    {  
    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       in each health status at the date of interview (if between dateprev1 and dateprev2).       in each health status at the date of interview (if between dateprev1 and dateprev2).
       We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
    */    */
     
    int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, iv;
    int mi; /* Effective wave */    int mi; /* Effective wave */
    int iage;    int iage;
    double agebegin, ageend;    double agebegin, ageend;
   
    double **prop;    double **prop;
    double posprop;     double posprop; 
    double  y2; /* in fractional years */    double  y2; /* in fractional years */
    int iagemin, iagemax;    int iagemin, iagemax;
    int first; /** to stop verbosity which is redirected to log file */    int first; /** to stop verbosity which is redirected to log file */
   
    iagemin= (int) agemin;    iagemin= (int) agemin;
    iagemax= (int) agemax;    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;    j1=0;
       
    /*j=cptcoveff;*/    /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
    first=1;    first=1;
    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,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+3+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
          prop[i][iage]=0.0;          prop[i][iage]=0.0;
           printf("Prevalence combination of varying and fixed dummies %d\n",j1);
      for (i=1; i<=imx; i++) { /* Each individual */      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
        bool=1;      fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
        if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */      
          for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/      for (i=1; i<=imx; i++) { /* Each individual */
            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])         bool=1;
              bool=0;        /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
        }         for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
        if (bool==1) { /* For this combination of covariates values, this individual fits */          m=mw[mi][i];
          /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */          /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
          for(mi=1; mi<wav[i];mi++){          /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
            m=mw[mi][i];          for (z1=1; z1<=cptcoveff; z1++){
            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/            if( Fixed[Tmodelind[z1]]==1){
            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */              iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
            if(m >=firstpass && m <=lastpass){              if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */                bool=0;
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                if(agev[m][i]==1) agev[m][i]=iagemax+2;                bool=0;
                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){              }
                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);           }
                  exit(1);          if(bool==1){ /* Otherwise we skip that wave/person */
                }            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                if (s[m][i]>0 && s[m][i]<=nlstate) {             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/            if(m >=firstpass && m <=lastpass){
                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  prop[s[m][i]][iagemax+3] += weight[i];               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                } /* end valid statuses */                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
              } /* end selection of dates */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
            } /* end selection of waves */                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
          } /* end effective waves */                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
        } /* end bool */                  exit(1);
      }                }
      for(i=iagemin; i <= iagemax+3; i++){                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
        for(jk=1,posprop=0; jk <=nlstate ; jk++) {                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
          posprop += prop[jk][i];                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
        }                   prop[s[m][i]][iagemax+3] += weight[i]; 
                       } /* end valid statuses */ 
        for(jk=1; jk <=nlstate ; jk++){                    } /* end selection of dates */
          if( i <=  iagemax){             } /* end selection of waves */
            if(posprop>=1.e-5){           } /* end bool */
              probs[i][jk][j1]= prop[jk][i]/posprop;        } /* end wave */
            } else{      } /* end individual */
              if(first==1){      for(i=iagemin; i <= iagemax+3; i++){  
                first=0;        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);          posprop += prop[jk][i]; 
              }        } 
            }        
          }         for(jk=1; jk <=nlstate ; jk++){       
        }/* end jk */           if( i <=  iagemax){ 
      }/* end i */             if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;
             } else{
               if(first==1){
                 first=0;
                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
               }
             }
           } 
         }/* end jk */ 
       }/* end i */ 
      /*} *//* end i1 */       /*} *//* end i1 */
    } /* end j1 */    } /* end j1 */
       
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
  }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
Line 4281  void  concatwav(int wav[], int **dh, int Line 4633  void  concatwav(int wav[], int **dh, int
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */    */
   
   int i=0, mi=0, m=0, mli=0;    int i=0, mi=0, m=0, mli=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
Line 4300  void  concatwav(int wav[], int **dh, int Line 4652  void  concatwav(int wav[], int **dh, int
 /* Treating live states */  /* Treating live states */
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */      mi=0;  /* First valid wave */
                 mli=0; /* Last valid wave */      mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state */
                         if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
                                 mli=m-1;/* mw[++mi][i]=m-1; */          mli=m-1;/* mw[++mi][i]=m-1; */
                         }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
                                 mw[++mi][i]=m;          mw[++mi][i]=m;
                                 mli=m;          mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */        if(m < lastpass){ /* m < lastpass, standard case */
                                 m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
                         else{ /* m >= lastpass, eventual special issue with warning */        else{ /* m >= lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
                                 break;          break;
 #else  #else
                                 if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
                                         if(firsthree == 0){            if(firsthree == 0){
                                                 printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);              printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
                                                 firsthree=1;              firsthree=1;
                                         }            }
                                         fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);            fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
                                         mw[++mi][i]=m;            mw[++mi][i]=m;
                                         mli=m;            mli=m;
                                 }          }
                                 if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
                                         nbwarn++;            nbwarn++;
                                         if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
                                                 printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                                 fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                         }            }
                                         break;            break;
                                 }          }
                                 break;          break;
 #endif  #endif
                         }/* End m >= lastpass */        }/* End m >= lastpass */
     }/* end while */      }/* end while */
   
         /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */      /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
     /* After last pass */      /* After last pass */
 /* Treating death states */  /* Treating death states */
     if (s[m][i] > nlstate){  /* In a death state */      if (s[m][i] > nlstate){  /* In a death state */
                         /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */        /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                         /* } */        /* } */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
                         /* Only death is a correct wave */        /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }      }
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
                 else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */      else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
       /* m++; */        /* m++; */
       /* mi++; */        /* mi++; */
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
       /* mw[mi][i]=m; */        /* mw[mi][i]=m; */
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
                                 if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
                                         nbwarn++;            nbwarn++;
                                         if(firstfiv==0){            if(firstfiv==0){
                                                 printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                                 firstfiv=1;              firstfiv=1;
                                         }else{            }else{
                                                 fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                         }            }
                                 }else{ /* Death occured afer last wave potential bias */          }else{ /* Death occured afer last wave potential bias */
                                         nberr++;            nberr++;
                                         if(firstwo==0){            if(firstwo==0){
                                                 printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );              printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                                 firstwo=1;              firstwo=1;
                                         }            }
                                         fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                 }          }
       }else{ /* end date of interview is known */        }else{ /* end date of interview is known */
                                 /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
                                 if(firstfour==0){          if(firstfour==0){
                                         printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
                                         firstfour=1;            firstfour=1;
                                 }          }
                                 fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );          fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }        }
     } /* end if date of death is known */      } /* end if date of death is known */
 #endif  #endif
Line 4387  void  concatwav(int wav[], int **dh, int Line 4739  void  concatwav(int wav[], int **dh, int
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
                                 printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                                 first=1;          first=1;
       }        }
       if(first==1){        if(first==1){
                                 fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
Line 4401  void  concatwav(int wav[], int **dh, int Line 4753  void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
                                 dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
                                 if (s[mw[mi+1][i]][i] > nlstate) { /* A death */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                                         if (agedc[i] < 2*AGESUP) {            if (agedc[i] < 2*AGESUP) {
                                                 j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                                                 if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
                                                 else if(j<0){              else if(j<0){
                                                         nberr++;                nberr++;
                                                         printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                         j=1; /* Temporary Dangerous patch */                j=1; /* Temporary Dangerous patch */
                                                         printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                                                         fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                         fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                                                 }              }
                                                 k=k+1;              k=k+1;
                                                 if (j >= jmax){              if (j >= jmax){
                                                         jmax=j;                jmax=j;
                                                         ijmax=i;                ijmax=i;
                                                 }              }
                                                 if (j <= jmin){              if (j <= jmin){
                                                         jmin=j;                jmin=j;
                                                         ijmin=i;                ijmin=i;
                                                 }              }
                                                 sum=sum+j;              sum=sum+j;
                                                 /*if (j<0) printf("j=%d num=%d \n",j,i);*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                                                 /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                                         }            }
                                 }          }
                                 else{          else{
                                         j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                                                                   
                                         k=k+1;            k=k+1;
                                         if (j >= jmax) {            if (j >= jmax) {
                                                 jmax=j;              jmax=j;
                                                 ijmax=i;              ijmax=i;
                                         }            }
                                         else if (j <= jmin){            else if (j <= jmin){
                                                 jmin=j;              jmin=j;
                                                 ijmin=i;              ijmin=i;
                                         }            }
                                         /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                                         /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                                         if(j<0){            if(j<0){
                                                 nberr++;              nberr++;
                                                 printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                 fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                         }            }
                                         sum=sum+j;            sum=sum+j;
                                 }          }
                                 jk= j/stepm;          jk= j/stepm;
                                 jl= j -jk*stepm;          jl= j -jk*stepm;
                                 ju= j -(jk+1)*stepm;          ju= j -(jk+1)*stepm;
                                 if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                                         if(jl==0){            if(jl==0){
                                                 dh[mi][i]=jk;              dh[mi][i]=jk;
                                                 bh[mi][i]=0;              bh[mi][i]=0;
                                         }else{ /* We want a negative bias in order to only have interpolation ie            }else{ /* We want a negative bias in order to only have interpolation ie
                                                                         * to avoid the price of an extra matrix product in likelihood */                    * to avoid the price of an extra matrix product in likelihood */
                                                 dh[mi][i]=jk+1;              dh[mi][i]=jk+1;
                                                 bh[mi][i]=ju;              bh[mi][i]=ju;
                                         }            }
                                 }else{          }else{
                                         if(jl <= -ju){            if(jl <= -ju){
                                                 dh[mi][i]=jk;              dh[mi][i]=jk;
                                                 bh[mi][i]=jl;   /* bias is positive if real duration              bh[mi][i]=jl;       /* bias is positive if real duration
                                                                                                          * is higher than the multiple of stepm and negative otherwise.                                   * is higher than the multiple of stepm and negative otherwise.
                                                                                                          */                                   */
                                         }            }
                                         else{            else{
                                                 dh[mi][i]=jk+1;              dh[mi][i]=jk+1;
                                                 bh[mi][i]=ju;              bh[mi][i]=ju;
                                         }            }
                                         if(dh[mi][i]==0){            if(dh[mi][i]==0){
                                                 dh[mi][i]=1; /* At least one step */              dh[mi][i]=1; /* At least one step */
                                                 bh[mi][i]=ju; /* At least one step */              bh[mi][i]=ju; /* At least one step */
                                                 /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                                         }            }
                                 } /* end if mle */          } /* end if mle */
       }        }
     } /* end wave */      } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }  }
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
 {   {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1      /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    * Boring subroutine which should only output nbcode[Tvar[j]][k]      * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable      * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);      * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
   */      */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   int modmaxcovj=0; /* Modality max of covariates j */     int modmaxcovj=0; /* Modality max of covariates j */
   int cptcode=0; /* Modality max of covariates j */     int cptcode=0; /* Modality max of covariates j */
   int modmincovj=0; /* Modality min of covariates j */     int modmincovj=0; /* Modality min of covariates j */
   
   
   /* cptcoveff=0;  */     /* cptcoveff=0;  */
         /* *cptcov=0; */     /* *cptcov=0; */
     
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products 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 (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
   for (j=1; j<=cptcovsnq; 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 < maxncov; k++) Ndum[k]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                                 modality of this covariate Vj*/         switch(Fixed[k]) {
       switch(Typevar[j]) {         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
       case 1: /* A real fixed dummy covariate */           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             ij=(int)(covar[Tvar[k]][i]);
                                       * If product of Vn*Vm, still boolean *:             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables              * If product of Vn*Vm, still boolean *:
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */              * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the              * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
            modality of the nth covariate of individual i. */             /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
         if (ij > modmaxcovj)                modality of the nth covariate of individual i. */
           modmaxcovj=ij;              if (ij > modmaxcovj)
         else if (ij < modmincovj)                modmaxcovj=ij; 
           modmincovj=ij;              else if (ij < modmincovj) 
         if ((ij < -1) && (ij > NCOVMAX)){               modmincovj=ij; 
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );             if ((ij < -1) && (ij > NCOVMAX)){
           exit(1);               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         }else               exit(1);
           Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/             }else
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */               Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/             /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /* getting the maximum value of the modality of the covariate             /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and             /* getting the maximum value of the modality of the covariate
            female ies 1, then modmaxcovj=1.*/                (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         break;                female ies 1, then modmaxcovj=1.
       case 2:             */
         break;           } /* end for loop on individuals i */
            printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
       }           fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
     } /* end for loop on individuals i */           cptcode=modmaxcovj;
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);           /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);           /*for (i=0; i<=cptcode; i++) {*/
     cptcode=modmaxcovj;           for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */             printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
     /*for (i=0; i<=cptcode; i++) {*/             fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);               if( j != -1){
       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);                 ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */                                    covariate for which somebody answered excluding 
         if( k != -1){                                    undefined. Usually 2: 0 and 1. */
           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th               }
                              covariate for which somebody answered excluding                ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                              undefined. Usually 2: 0 and 1. */                                       covariate for which somebody answered including 
         }                                       undefined. Usually 3: -1, 0 and 1. */
         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th             }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
                                 covariate for which somebody answered including                    * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                                 undefined. Usually 3: -1, 0 and 1. */           } /* Ndum[-1] number of undefined modalities */
       }                          
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for           /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
        * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */           /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
     } /* Ndum[-1] number of undefined modalities */           /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
                /* modmincovj=3; modmaxcovj = 7; */
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */           /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.            /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;           /*              defining two dummy variables: variables V1_1 and V1_2.*/
        modmincovj=3; modmaxcovj = 7;           /* nbcode[Tvar[j]][ij]=k; */
        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;           /* nbcode[Tvar[j]][1]=0; */
        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;           /* nbcode[Tvar[j]][2]=1; */
        defining two dummy variables: variables V1_1 and V1_2.           /* nbcode[Tvar[j]][3]=2; */
        nbcode[Tvar[j]][ij]=k;           /* To be continued (not working yet). */
        nbcode[Tvar[j]][1]=0;           ij=0; /* ij is similar to i but can jump over null modalities */
        nbcode[Tvar[j]][2]=1;           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*/
        nbcode[Tvar[j]][3]=2;             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
        To be continued (not working yet).               break;
     */             }
     ij=0; /* ij is similar to i but can jump over null modalities */             ij++;
     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*/             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*/
       if (Ndum[i] == 0) { /* If nobody responded to this modality k */             cptcode = ij; /* New max modality for covar j */
         break;           } /* end of loop on modality i=-1 to 1 or more */
       }           break;
       ij++;         case 1: /* Testing on varying covariate, could be simple and
       nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/                  * should look at waves or product of fixed *
       cptcode = ij; /* New max modality for covar j */                  * varying. No time to test -1, assuming 0 and 1 only */
     } /* end of loop on modality i=-1 to 1 or more */           ij=0;
                for(i=0; i<=1;i++){
     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */             nbcode[Tvar[k]][++ij]=i;
     /*  /\*recode from 0 *\/ */           }
     /*                               k is a modality. If we have model=V1+V1*sex  */           break;
     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */         default:
     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */           break;
     /*  } */         } /* end switch */
     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */       } /* end dummy test */
     /*  if (ij > ncodemax[j]) { */      
     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */       /*         /\*recode from 0 *\/ */
     /*    break; */       /*                                      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; */
     /*   }  /\* end of loop on modality k *\/ */       /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/         /*         } */
          /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
   for (k=-1; k< maxncov; k++) Ndum[k]=0;        /*         if (ij > ncodemax[j]) { */
          /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */        /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/        /*           break; */
     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */        /*         } */
     Ndum[ij]++; /* Might be supersed V1 + V1*age */       /*   }  /\* end of loop on modality k *\/ */
   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       
   ij=0;     for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */     /* Look at fixed dummy (single or product) covariates to check empty modalities */
     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
     if((Ndum[i]!=0) && (i<=ncovcol)){       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/       ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
       Tvaraff[++ij]=i; /*For printing (unclear) */       Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){       /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
       Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */     } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){    
       Tvaraff[++ij]=i; /*For printing (unclear) */     ij=0;
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){     /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
       Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */     for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     }       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */       /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
   /* ij--; */       if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
   /* cptcoveff=ij; /\*Number of total covariates*\/ */         /* If product not in single variable we don't print results */
   *cptcov=ij; /*Number of total real effective covariates: effective         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
                * because they can be excluded from the model and real         ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
                * if in the model but excluded because missing values*/         Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
 }         Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
          TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
          if(Fixed[k]!=0)
            anyvaryingduminmodel=1;
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
          /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
          /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
          /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
          /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
        } 
      } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
      /* ij--; */
      /* cptcoveff=ij; /\*Number of total covariates*\/ */
      *cptcov=ij; /*Number of total real effective covariates: effective
                   * because they can be excluded from the model and real
                   * if in the model but excluded because missing values, but how to get k from ij?*/
      for(j=ij+1; j<= cptcovt; j++){
        Tvaraff[j]=0;
        Tmodelind[j]=0;
      }
      for(j=ntveff+1; j<= cptcovt; j++){
        TmodelInvind[j]=0;
      }
      /* To be sorted */
      ;
    }
   
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
Line 4645  void evsij(double ***eij, double x[], in Line 5023  void evsij(double ***eij, double x[], in
   double ***p3mat;    double ***p3mat;
   double eip;    double eip;
   
   pstamp(ficreseij);    /* pstamp(ficreseij); */
   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++){    for(i=1; i<=nlstate;i++){
Line 4708  void evsij(double ***eij, double x[], in Line 5086  void evsij(double ***eij, double x[], in
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           
     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           
Line 4743  void evsij(double ***eij, double x[], in Line 5121  void evsij(double ***eij, double x[], in
       
 }  }
   
 void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
Line 4856  void cvevsij(double ***eij, double x[], Line 5234  void cvevsij(double ***eij, double x[],
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         xm[i] = x[i] - (i==theta ?delti[theta]:0);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
                                                   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
Line 4898  void cvevsij(double ***eij, double x[], Line 5276  void cvevsij(double ***eij, double x[],
     }      }
                                   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
Line 4953  void cvevsij(double ***eij, double x[], Line 5331  void cvevsij(double ***eij, double x[],
 }  }
     
 /************ Variance ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *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);*/
Line 5010  void cvevsij(double ***eij, double x[], Line 5388  void cvevsij(double ***eij, double x[],
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    pstamp(ficresprobmorprev);     pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
      for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
        fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
      }
      for(j=1;j<=cptcoveff;j++) 
        fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
      fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      fprintf(ficresprobmorprev," p.%-d SE",j);       fprintf(ficresprobmorprev," p.%-d SE",j);
Line 5079  void cvevsij(double ***eij, double x[], Line 5465  void cvevsij(double ***eij, double x[],
          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);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
Line 5091  void cvevsij(double ***eij, double x[], Line 5477  void cvevsij(double ***eij, double x[],
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* 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=1 to nhstepm */
        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++)
Line 5111  void cvevsij(double ***eij, double x[], Line 5497  void cvevsij(double ***eij, double x[],
        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);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
Line 5123  void cvevsij(double ***eij, double x[], Line 5509  void cvevsij(double ***eij, double x[],
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);           hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
                                                   
        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
Line 5188  void cvevsij(double ***eij, double x[], Line 5574  void cvevsij(double ***eij, double x[],
      /* end ppptj */       /* end ppptj */
      /*  x centered again */       /*  x centered again */
                                   
      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                                   
      if (popbased==1) {       if (popbased==1) {
        if(mobilav ==0){         if(mobilav ==0){
Line 5204  void cvevsij(double ***eij, double x[], Line 5590  void cvevsij(double ***eij, double x[],
         computed over hstepm (estepm) matrices product = hstepm*stepm months)           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         as a weighted average of prlim.          as a weighted average of prlim.
      */       */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);         hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
      for(j=nlstate+1;j<=nlstate+ndeath;j++){       for(j=nlstate+1;j<=nlstate+ndeath;j++){
        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]; 
Line 5267  void cvevsij(double ***eij, double x[], Line 5653  void cvevsij(double ***eij, double x[],
  }  /* end varevsij */   }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
Line 5283  void cvevsij(double ***eij, double x[], Line 5669  void cvevsij(double ***eij, double x[],
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvpl," Result# ");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
   fprintf(ficresvpl,"\n");    fprintf(ficresvpl,"\n");
Line 5310  void cvevsij(double ***eij, double x[], Line 5698  void cvevsij(double ***eij, double x[],
         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);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       else        else
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);          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];
Line 5320  void cvevsij(double ***eij, double x[], Line 5708  void cvevsij(double ***eij, double x[],
       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);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       else        else
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);          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 5369  void cvevsij(double ***eij, double x[], Line 5757  void cvevsij(double ***eij, double x[],
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
       if(nresult >=1)
         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]));
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
Line 5730  void printinghtml(char fileresu[], char Line 6120  void printinghtml(char fileresu[], char
                   int popforecast, int prevfcast, int backcast, int estepm , \                    int popforecast, int prevfcast, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2){
   int jj1, k1, i1, cpt;    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 \
    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
      fprintf(fichtm,"<ul><li> model=1+age+%s\n \
   </ul>", model);
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 5769  void printinghtml(char fileresu[], char Line 6161  void printinghtml(char fileresu[], char
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;     jj1=0;
    for(k1=1; k1<=m;k1++){  
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(TKresult[nres]!= k1)
          continue;
   
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
            /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
        }         }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
         }
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
Line 5787  void printinghtml(char fileresu[], char Line 6191  void printinghtml(char fileresu[], char
        }         }
      }       }
      /* aij, bij */       /* aij, bij */
      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \       fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
 <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
 <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);       <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
 divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
 <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);   <img src=\"%s_%d-3-%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.svg\">%s%d_%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);  <img src=\"%s_%d-%d-%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 from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);   <a href=\"%s_%d-%d-%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 (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 to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(backcast==1){
        /* Period (stable) back prevalence in each health state */         /* Period (stable) back prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);  <img src=\"%s_%d-%d-%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 (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
        }         }
      }       }
                     
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
 <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);  <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
Line 5889  See page 'Matrix of variance-covariance Line 6293  See page 'Matrix of variance-covariance
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;     jj1=0;
   
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
        if(TKresult[nres]!= k1)
          continue;
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */         for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
   
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
Line 5905  See page 'Matrix of variance-covariance Line 6318  See page 'Matrix of variance-covariance
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
 <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);    <img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
 <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);  <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
     }/* End nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
    fflush(fichtm);     fflush(fichtm);
 }  }
Line 5925  void printinggnuplot(char fileresu[], ch Line 6339  void printinggnuplot(char fileresu[], ch
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132];    char gplotcondition[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
   int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
     int nres=0; /* Index of resultline */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 5973  void printinggnuplot(char fileresu[], ch Line 6388  void printinggnuplot(char fileresu[], ch
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          if(TKresult[nres]!= k1)
         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            continue;
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* We are interested in selected combination by the resultline */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
       }            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       fprintf(ficgp,"\n#\n");            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
       if(invalidvarcomb[k1]){            vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
         continue;            printf(" V%d=%d ",Tvaraff[k],vlv);
       }            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);            printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       fprintf(ficgp,"set xlabel \"Age\" \n\            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 set ylabel \"Probability\" \n   \          }       
 set ter svg size 640, 480\n     \          printf("\n#\n");
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);          fprintf(ficgp,"\n#\n");
                                   if(invalidvarcomb[k1]){
       for (i=1; i<= nlstate ; i ++) {            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            continue;
         else        fprintf(ficgp," %%*lf (%%*lf)");          }
       }        
       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
       for (i=1; i<= nlstate ; i ++) {          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          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);
         else fprintf(ficgp," %%*lf (%%*lf)");        
       }           for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
       for (i=1; i<= nlstate ; i ++) {            else        fprintf(ficgp," %%*lf (%%*lf)");
         if (i==cpt) 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*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
       }            for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */            else fprintf(ficgp," %%*lf (%%*lf)");
         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */          } 
         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */          fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); 
         if(cptcoveff ==0){          for (i=1; i<= nlstate ; i ++) {
           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
         }else{            else fprintf(ficgp," %%*lf (%%*lf)");
           kl=0;          }  
           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */          fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            if(cptcoveff ==0){
             vlv= nbcode[Tvaraff[k]][lv];              fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",        2+(cpt-1),  cpt );
             kl++;            }else{
             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              kl=0;
             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */               for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             if(k==cptcoveff){                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                       6+(cpt-1),  cpt );                vlv= nbcode[Tvaraff[k]][lv];
             }else{  
               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);  
               kl++;                kl++;
             }                /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
           } /* end covariate */                /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
         } /* end if no covariate */                /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
       } /* end if backcast */                /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
       fprintf(ficgp,"\nset out \n");                if(k==cptcoveff){
                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                           2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                 }else{
                   fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   kl++;
                 }
               } /* end covariate */
             } /* end if no covariate */
           } /* end if backcast */
           fprintf(ficgp,"\nset out \n");
         } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   /*2 eme*/  
   for (k1=1; k1<= m ; k1 ++) {   
   
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");    
     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */    /*2 eme*/
       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */    for (k1=1; k1<= m ; k1 ++){  
       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        if(TKresult[nres]!= k1)
       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          continue;
       vlv= nbcode[Tvaraff[k]][lv];        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);  
     }  
     fprintf(ficgp,"\n#\n");  
     if(invalidvarcomb[k1]){  
       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
       continue;  
     }  
                           
     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);  
     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/  
       if(vpopbased==0)  
         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);  
       else  
         fprintf(ficgp,"\nreplot ");  
       for (i=1; i<= nlstate+1 ; i ++) {  
         k=2*i;  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);  
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         fprintf(ficgp,"\" t\"\" w l lt 0,");  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");  
         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");  
       } /* state */  
     } /* vpopbased */  
     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */  
   } /* k1 */  
           
           
   /*3eme*/  
   for (k1=1; k1<= m ; k1 ++) {   
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);  
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=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 6110  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6485  plot [%.f:%.f] \"%s\" every :::%d::%d u
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
         /* for(k=1; k <= ncovds; k++){ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         continue;          continue;
       }        }
                                                   
       /*       k=2+nlstate*(2*cpt-2); */        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
       k=2+(nlstate+1)*(cpt-1);        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);          if(vpopbased==0)
       fprintf(ficgp,"set ter svg size 640, 480\n\            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
           else
             fprintf(ficgp,"\nreplot ");
           for (i=1; i<= nlstate+1 ; i ++) {
             k=2*i;
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
             else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             fprintf(ficgp,"\" t\"\" w l lt 0,");
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
             else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
           } /* state */
         } /* vpopbased */
         fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
       } /* end nres */
     } /* k1 end 2 eme*/
           
           
     /*3eme*/
     for (k1=1; k1<= m ; k1 ++){
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= k1)
           continue;
   
         for (cpt=1; cpt<= nlstate ; cpt ++) {
           fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
           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 */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
                           
           /*       k=2+nlstate*(2*cpt-2); */
           k=2+(nlstate+1)*(cpt-1);
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
           fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                                                   
       */          */
       for (i=1; i< nlstate ; i ++) {          for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);            fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/            /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                                                   
       }           } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }        }
   }      } /* end nres */
     } /* end kl 3eme */
       
   /* 4eme */    /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
           fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           for (i=1; i<= nlstate ; i ++){
             if(i==1){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
             }else{
               fprintf(ficgp,", '' ");
             }
             l=(nlstate+ndeath)*(i-1)+1;
             fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
             for (j=2; j<= nlstate+ndeath ; j ++)
               fprintf(ficgp,"+$%d",k+l+j-1);
             fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end nres */
     } /* end covariate k1 */  
   
   /* 5eme */
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
           fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
           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 */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
             if(j==1)
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
             else
               fprintf(ficgp,", '' ");
             l=(nlstate+ndeath)*(cpt-1) +j;
             fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
             /* for (i=2; i<= nlstate+ndeath ; i ++) */
             /*   fprintf(ficgp,"+$%d",k+l+i-1); */
             fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
           } /* nlstate */
           fprintf(ficgp,", '' ");
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
           for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
             l=(nlstate+ndeath)*(cpt-1) +j;
             if(j < nlstate)
               fprintf(ficgp,"$%d +",k+l);
             else
               fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
           }
           fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* end nres */
     
   /* 6eme */
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)
         continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);        
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=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 6152  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6696  plot [%.f:%.f] \"%s\" every :::%d::%d u
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         } 
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         continue;          continue;
       }        }
                                 
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n                                                                                                                                                                                     \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n                                                                                                                                                                                                                                           \        k=3; /* Offset */
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3;  
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1){          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         }else{          else
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
         }  
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1;
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=2; j<= nlstate+ndeath ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
             
 /* 5eme */    
   /* Survival functions (period) from state i in state j by final state j */  
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */  
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */  
                           
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);  
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */  
                                 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */  
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */  
                                 vlv= nbcode[Tvaraff[k]][lv];  
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);  
       }  
       fprintf(ficgp,"\n#\n");  
       if(invalidvarcomb[k1]){  
                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
                                 continue;  
       }  
                           
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\  
 set ter svg size 640, 480\n                                                                                                                                                                                     \  
 unset log y\n                                                                                                                                                                                                                                           \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3;  
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */  
                                 if(j==1)  
                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));  
                                 else  
                                         fprintf(ficgp,", '' ");  
                                 l=(nlstate+ndeath)*(cpt-1) +j;  
                                 fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);  
                                 /* for (i=2; i<= nlstate+ndeath ; i ++) */  
                                 /*   fprintf(ficgp,"+$%d",k+l+i-1); */  
                                 fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);  
       } /* nlstate */  
       fprintf(ficgp,", '' ");  
       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);  
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */  
                                 l=(nlstate+ndeath)*(cpt-1) +j;  
                                 if(j < nlstate)  
                                         fprintf(ficgp,"$%d +",k+l);  
                                 else  
                                         fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);  
       }  
       fprintf(ficgp,"\nset out\n");  
     } /* end cpt state*/   
   } /* end covariate */    
           
 /* 6eme */  
   /* CV preval stable (period) for each covariate */  
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */  
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */  
                           
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);  
       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 */  
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */  
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */  
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */  
                                 vlv= nbcode[Tvaraff[k]][lv];  
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);  
       }  
       fprintf(ficgp,"\n#\n");  
       if(invalidvarcomb[k1]){  
                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
                                 continue;  
       }  
                           
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\  
 set ter svg size 640, 480\n                                                                                                                                                                              \  
 unset log y\n                                                                                                                                                                                                                                    \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3; /* Offset */  
       for (i=1; i<= nlstate ; i ++){  
                                 if(i==1)  
                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));  
                                 else  
                                         fprintf(ficgp,", '' ");  
                                 l=(nlstate+ndeath)*(i-1)+1;  
                                 fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);  
                                 for (j=2; j<= nlstate ; j ++)  
                                         fprintf(ficgp,"+$%d",k+l+j-1);  
                                 fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);  
       } /* nlstate */  
       fprintf(ficgp,"\nset out\n");  
     } /* end cpt state*/   
   } /* end covariate */    
           
           
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(backcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= k1)
           continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=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 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }          }
                                 fprintf(ficgp,"\n#\n");          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                                 if(invalidvarcomb[k1]){            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           }       
                                         continue;          fprintf(ficgp,"\n#\n");
                                 }          if(invalidvarcomb[k1]){
                                             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);            continue;
                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          }
 set ter svg size 640, 480\n                                                                                                                                                                                     \          
 unset log y\n                                                                                                                                                                                                                                           \          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
 plot [%.f:%.f]  ", ageminpar, agemaxpar);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
                                 k=3; /* Offset */  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                                 for (i=1; i<= nlstate ; i ++){          k=3; /* Offset */
                                         if(i==1)          for (i=1; i<= nlstate ; i ++){
                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));            if(i==1)
                                         else              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
                                                 fprintf(ficgp,", '' ");            else
                                         /* l=(nlstate+ndeath)*(i-1)+1; */              fprintf(ficgp,", '' ");
                                         l=(nlstate+ndeath)*(cpt-1)+1;            /* l=(nlstate+ndeath)*(i-1)+1; */
                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */            l=(nlstate+ndeath)*(cpt-1)+1;
                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
                                         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
                                         /* for (j=2; j<= nlstate ; j ++) */            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
                                         /*      fprintf(ficgp,"+$%d",k+l+j-1); */            /* for (j=2; j<= nlstate ; j ++) */
                                         /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
                                         fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
                                 } /* nlstate */            fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
                                 fprintf(ficgp,"\nset out\n");          } /* nlstate */
           fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
Line 6322  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6779  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to stable (period) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= k1)
           continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                 for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=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 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }          }
                                 fprintf(ficgp,"\n#\n");          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                                 if(invalidvarcomb[k1]){            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           }       
                                         continue;          fprintf(ficgp,"\n#\n");
                                 }          if(invalidvarcomb[k1]){
                                             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");            continue;
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);          }
                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\          
 set ter svg size 640, 480\n                                                                                                                                                                                     \          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
 unset log y\n                                                                                                                                                                                                                                           \          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
 plot [%.f:%.f]  ", ageminpar, agemaxpar);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/          for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                         /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                         /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */               /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                         if(i==1){            /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));            if(i==1){
                                         }else{              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                                                 fprintf(ficgp,",\\\n '' ");            }else{
                                         }              fprintf(ficgp,",\\\n '' ");
                                         if(cptcoveff ==0){ /* No covariate */            }
                                                 ioffset=2; /* Age is in 2 */            if(cptcoveff ==0){ /* No covariate */
                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              ioffset=2; /* Age is in 2 */
                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                 /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                 /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                 fprintf(ficgp," u %d:(", ioffset);               /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                 if(i==nlstate+1)              fprintf(ficgp," u %d:(", ioffset); 
                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \              if(i==nlstate+1)
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
                                                 else                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \              else
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                                         }else{ /* more than 2 covariates */                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                 if(cptcoveff ==1){            }else{ /* more than 2 covariates */
                                                         ioffset=4; /* Age is in 4 */              if(cptcoveff ==1){
                                                 }else{                ioffset=4; /* Age is in 4 */
                                                         ioffset=6; /* Age is in 6 */              }else{
                                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/                ioffset=6; /* Age is in 6 */
                                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */                /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                 }                   /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                 fprintf(ficgp," u %d:(",ioffset);               }   
                                                 kl=0;              fprintf(ficgp," u %d:(",ioffset); 
                                                 strcpy(gplotcondition,"(");              kl=0;
                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              strcpy(gplotcondition,"(");
                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */              for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                         vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                                         kl++;                vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                kl++;
                                                         kl++;                sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                         if(k <cptcoveff && cptcoveff>1)                kl++;
                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                if(k <cptcoveff && cptcoveff>1)
                                                 }                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                 strcpy(gplotcondition+strlen(gplotcondition),")");              }
                                                 /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              strcpy(gplotcondition+strlen(gplotcondition),")");
                                                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                                 /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                 /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                                 if(i==nlstate+1){              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \              if(i==nlstate+1){
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                                                 }else{                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \              }else{
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                                                 }                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                         } /* end if covariate */              }
                                 } /* nlstate */            } /* end if covariate */
                                 fprintf(ficgp,"\nset out\n");          } /* nlstate */
           fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
             
             
   /* proba elementaires */    /* 9eme writing MLE parameters */
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficgp,"# initial state %d\n",i);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
                                 fprintf(ficgp,"#   current state %d\n",k);          fprintf(ficgp,"#   current state %d\n",k);
                                 for(j=1; j <=ncovmodel; j++){          for(j=1; j <=ncovmodel; j++){
                                         fprintf(ficgp,"p%d=%f; ",jk,p[jk]);            fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
                                         jk++;             jk++; 
                                 }          }
                                 fprintf(ficgp,"\n");          fprintf(ficgp,"\n");
       }        }
     }      }
   }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
             
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");    /* 10eme Graphics of probabilities or incidences using written MLE parameters */
     fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
Line 6444  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6906  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
     fprintf(ficgp,"# ng=%d\n",ng);      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);      fprintf(ficgp,"#model=%s \n",model);
     for(jk=1; jk <=m; jk++) {      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
       fprintf(ficgp,"#    jk=%d\n",jk);      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);      for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(TKresult[nres]!= jk)
           continue;
         fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         } 
         fprintf(ficgp,"\n#\n");
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
       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 6488  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6959  plot [%.f:%.f]  ", ageminpar, agemaxpar)
               break;                break;
             }              }
             ij=1;/* To be checked else nbcode[0][0] wrong */              ij=1;/* To be checked else nbcode[0][0] wrong */
             for(j=3; j <=ncovmodel-nagesqr; j++) {              ijp=1; /* product no age */
               /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(ij <=cptcovage) { /* Bug valgrind */                if(j==Tage[ij]) { /* Product by age */
                 if((j-2)==Tage[ij]) { /* Bug valgrind */                  if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                    if(DummyV[j]==0){
                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                      fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                     }else{ /* quantitative */
                       fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                     }
                   ij++;                    ij++;
                 }                  }
               }                }else if(j==Tprod[ijp]) { /* */ 
               else                  /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                                         fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */                  if(ijp <=cptcovprod) { /* Product */
             }                    if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                       if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                         /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
                         fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                       }else{ /* Vn is dummy and Vm is quanti */
                         /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                       }
                     }else{ /* Vn*Vm Vn is quanti */
                       if(DummyV[Tvard[ijp][2]]==0){
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                       }else{ /* Both quanti */
                         fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                       }
                     }
                     ijp++;
                   }
                 } else{  /* simple covariate */
                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
                   if(Dummy[j]==0){
                     fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   }else{ /* quantitative */
                     fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                   }
                 } /* end simple */
               } /* end j */
           }else{            }else{
             i=i-ncovmodel;              i=i-ncovmodel;
             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
               fprintf(ficgp," (1.");                fprintf(ficgp," (1.");
           }            }
                        
           if(ng != 1){            if(ng != 1){
             fprintf(ficgp,")/(1");              fprintf(ficgp,")/(1");
                            
             for(k1=1; k1 <=nlstate; k1++){               for(k1=1; k1 <=nlstate; k1++){ 
               if(nagesqr==0)                if(nagesqr==0)
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
Line 6517  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7020  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 
               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                 if(ij <=cptcovage) { /* Bug valgrind */                  if((j-2)==Tage[ij]) { /* Bug valgrind */
                   if((j-2)==Tage[ij]) { /* Bug valgrind */                    if(ij <=cptcovage) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                     ij++;                      ij++;
Line 6670  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7173  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      } /* end bad */       } /* end bad */
                                   
      for (age=bage; age<=fage; age++){       for (age=bage; age<=fage; age++){
        printf("%d %d ", cptcod, (int)age);         /* printf("%d %d ", cptcod, (int)age); */
        sumnewp[cptcod]=0.;         sumnewp[cptcod]=0.;
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
Line 6709  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7212  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;     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,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
Line 6737  void prevforecast(char fileres[], double Line 7240  void prevforecast(char fileres[], double
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   }    }
   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);    printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);    fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
Line 6761  void prevforecast(char fileres[], double Line 7264  void prevforecast(char fileres[], double
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
   
   i1=cptcoveff;    i1=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",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
     
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(k=1; k<=i1;k++){
       k=k+1;      if(TKresult[nres]!= k)
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");        continue;
       for(j=1;j<=cptcoveff;j++) {      if(invalidvarcomb[k]){
                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf("\nCombination (%d) projection ignored because no cases \n",k); 
       }        continue;
       fprintf(ficresf," yearproj age");      }
       for(j=1; j<=nlstate+ndeath;j++){       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
                                 for(i=1; i<=nlstate;i++)                    for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," p%d%d",i,j);        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                 fprintf(ficresf," wp.%d",j);      }
       }      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                 fprintf(ficresf,"\n");      }
                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);         fprintf(ficresf," yearproj age");
                                 for (agec=fage; agec>=(ageminpar-1); agec--){       for(j=1; j<=nlstate+ndeath;j++){ 
                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);         for(i=1; i<=nlstate;i++)        
                                         nhstepm = nhstepm/hstepm;           fprintf(ficresf," p%d%d",i,j);
                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresf," wp.%d",j);
                                         oldm=oldms;savm=savms;      }
                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);      for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
                                                 fprintf(ficresf,"\n");
                                         for (h=0; h<=nhstepm; h++){        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                                                 if (h*hstepm/YEARM*stepm ==yearp) {        for (agec=fage; agec>=(ageminpar-1); agec--){ 
               fprintf(ficresf,"\n");          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
               for(j=1;j<=cptcoveff;j++)           nhstepm = nhstepm/hstepm; 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);          oldm=oldms;savm=savms;
                                                 }           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
                                                 for(j=1; j<=nlstate+ndeath;j++) {          
                                                         ppij=0.;          for (h=0; h<=nhstepm; h++){
                                                         for(i=1; i<=nlstate;i++) {            if (h*hstepm/YEARM*stepm ==yearp) {
                                                                 if (mobilav==1)               fprintf(ficresf,"\n");
                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];              for(j=1;j<=cptcoveff;j++) 
                                                                 else {                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                                                                 }            } 
                                                                 if (h*hstepm/YEARM*stepm== yearp) {            for(j=1; j<=nlstate+ndeath;j++) {
                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);              ppij=0.;
                                                                 }              for(i=1; i<=nlstate;i++) {
                                                         } /* end i */                if (mobilav==1) 
                                                         if (h*hstepm/YEARM*stepm==yearp) {                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
                                                                 fprintf(ficresf," %.3f", ppij);                else {
                                                         }                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
                                                 }/* end j */                }
                                         } /* end h */                if (h*hstepm/YEARM*stepm== yearp) {
                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
                                 } /* end agec */                }
       } /* end yearp */              } /* end i */
     } /* end cptcod */              if (h*hstepm/YEARM*stepm==yearp) {
   } /* end  cptcov */                fprintf(ficresf," %.3f", ppij);
               }
             }/* end j */
           } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end  k */
                   
   fclose(ficresf);    fclose(ficresf);
   printf("End of Computing forecasting \n");    printf("End of Computing forecasting \n");
Line 6959  void prevforecast(char fileres[], double Line 7469  void prevforecast(char fileres[], double
 /* } */  /* } */
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
   int *popage;  /*   int *popage; */
   double calagedatem, agelim, kk1, kk2;  /*   double calagedatem, agelim, kk1, kk2; */
   double *popeffectif,*popcount;  /*   double *popeffectif,*popcount; */
   double ***p3mat,***tabpop,***tabpopprev;  /*   double ***p3mat,***tabpop,***tabpopprev; */
   /* double ***mobaverage; */  /*   /\* double ***mobaverage; *\/ */
   char filerespop[FILENAMELENGTH];  /*   char filerespop[FILENAMELENGTH]; */
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   agelim=AGESUP;  /*   agelim=AGESUP; */
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
       
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
       
       
   strcpy(filerespop,"POP_");   /*   strcpy(filerespop,"POP_");  */
   strcat(filerespop,fileresu);  /*   strcat(filerespop,fileresu); */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
     printf("Problem with forecast resultfile: %s\n", filerespop);  /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
   }  /*   } */
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
   
   /* if (mobilav!=0) { */  /*   /\* if (mobilav!=0) { *\/ */
   /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */  /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */  /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
   /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */  /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */  /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   } */  /*   /\*   } *\/ */
   /* } */  /*   /\* } *\/ */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   if (stepm<=12) stepsize=1;  /*   if (stepm<=12) stepsize=1; */
       
   agelim=AGESUP;  /*   agelim=AGESUP; */
       
   hstepm=1;  /*   hstepm=1; */
   hstepm=hstepm/stepm;   /*   hstepm=hstepm/stepm;  */
                   
   if (popforecast==1) {  /*   if (popforecast==1) { */
     if((ficpop=fopen(popfile,"r"))==NULL) {  /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
       printf("Problem with population file : %s\n",popfile);exit(0);  /*       printf("Problem with population file : %s\n",popfile);exit(0); */
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
     }   /*     }  */
     popage=ivector(0,AGESUP);  /*     popage=ivector(0,AGESUP); */
     popeffectif=vector(0,AGESUP);  /*     popeffectif=vector(0,AGESUP); */
     popcount=vector(0,AGESUP);  /*     popcount=vector(0,AGESUP); */
           
     i=1;     /*     i=1;    */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
           
     imx=i;  /*     imx=i; */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
   }  /*   } */
       
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){  /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
       k=k+1;  /*       k=k+1; */
       fprintf(ficrespop,"\n#******");  /*       fprintf(ficrespop,"\n#******"); */
       for(j=1;j<=cptcoveff;j++) {  /*       for(j=1;j<=cptcoveff;j++) { */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
       }  /*       } */
       fprintf(ficrespop,"******\n");  /*       fprintf(ficrespop,"******\n"); */
       fprintf(ficrespop,"# Age");  /*       fprintf(ficrespop,"# Age"); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
               
       for (cpt=0; cpt<=0;cpt++) {   /*       for (cpt=0; cpt<=0;cpt++) {  */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
                   
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
           nhstepm = nhstepm/hstepm;   /*        nhstepm = nhstepm/hstepm;  */
                       
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
           oldm=oldms;savm=savms;  /*        oldm=oldms;savm=savms; */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                       
           for (h=0; h<=nhstepm; h++){  /*        for (h=0; h<=nhstepm; h++){ */
             if (h==(int) (calagedatem+YEARM*cpt)) {  /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 if (mobilav==1)   /*              if (mobilav==1)  */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
                 else {  /*              else { */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
                 }  /*              } */
               }  /*            } */
               if (h==(int)(calagedatem+12*cpt)){  /*            if (h==(int)(calagedatem+12*cpt)){ */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
                 /*fprintf(ficrespop," %.3f", kk1);  /*              /\*fprintf(ficrespop," %.3f", kk1); */
                   if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
               }  /*            } */
             }  /*          } */
             for(i=1; i<=nlstate;i++){  /*          for(i=1; i<=nlstate;i++){ */
               kk1=0.;  /*            kk1=0.; */
               for(j=1; j<=nlstate;j++){  /*            for(j=1; j<=nlstate;j++){ */
                 kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
               }  /*            } */
               tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];  /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
             }  /*          } */
                           
             if (h==(int)(calagedatem+12*cpt))  /*          if (h==(int)(calagedatem+12*cpt)) */
               for(j=1; j<=nlstate;j++)   /*            for(j=1; j<=nlstate;j++)  */
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
           }  /*        } */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
         }  /*      } */
       }  /*       } */
               
       /******/  /*       /\******\/ */
               
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {   /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
           nhstepm = nhstepm/hstepm;   /*        nhstepm = nhstepm/hstepm;  */
                       
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
           oldm=oldms;savm=savms;  /*        oldm=oldms;savm=savms; */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
           for (h=0; h<=nhstepm; h++){  /*        for (h=0; h<=nhstepm; h++){ */
             if (h==(int) (calagedatem+YEARM*cpt)) {  /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
               }  /*            } */
               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);          /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
             }  /*          } */
           }  /*        } */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
         }  /*      } */
       }  /*       } */
     }   /*     }  */
   }  /*   } */
       
   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */  /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
       
   if (popforecast==1) {  /*   if (popforecast==1) { */
     free_ivector(popage,0,AGESUP);  /*     free_ivector(popage,0,AGESUP); */
     free_vector(popeffectif,0,AGESUP);  /*     free_vector(popeffectif,0,AGESUP); */
     free_vector(popcount,0,AGESUP);  /*     free_vector(popcount,0,AGESUP); */
   }  /*   } */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fclose(ficrespop);  /*   fclose(ficrespop); */
 } /* End of popforecast */  /* } /\* End of popforecast *\/ */
     
 int fileappend(FILE *fichier, char *optionfich)  int fileappend(FILE *fichier, char *optionfich)
 {  {
Line 7384  int readdata(char datafile[], int firsto Line 7894  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0, iv=0;    int i=0, j=0, n=0, iv=0, v;
   int lstra;    int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   
     DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
   
     for(v=1; v <=ncovcol;v++){
       DummyV[v]=0;
       FixedV[v]=0;
     }
     for(v=ncovcol+1; v <=ncovcol+nqv;v++){
       DummyV[v]=1;
       FixedV[v]=0;
     }
     for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
       DummyV[v]=0;
       FixedV[v]=1;
     }
     for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
       DummyV[v]=1;
       FixedV[v]=1;
     }
     for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
     }
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
Line 7425  int readdata(char datafile[], int firsto Line 7957  int readdata(char datafile[], int firsto
         if(strb[0]=='.') { /* Missing value */          if(strb[0]=='.') { /* Missing value */
           lval=-1;            lval=-1;
           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */            cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
             cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
           if(isalpha(strb[1])) { /* .m or .d Really Missing value */            if(isalpha(strb[1])) { /* .m or .d Really Missing value */
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);              printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);              fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
Line 7444  int readdata(char datafile[], int firsto Line 7977  int readdata(char datafile[], int firsto
             return 1;              return 1;
           }            }
           cotqvar[j][iv][i]=dval;             cotqvar[j][iv][i]=dval; 
             cotvar[j][ntv+iv][i]=dval; 
         }          }
         strcpy(line,stra);          strcpy(line,stra);
       }/* end loop ntqv */        }/* end loop ntqv */
Line 7590  int readdata(char datafile[], int firsto Line 8124  int readdata(char datafile[], int firsto
           return 1;            return 1;
         }          }
         coqvar[iv][i]=dval;           coqvar[iv][i]=dval; 
           covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
       }        }
       strcpy(line,stra);        strcpy(line,stra);
     }/* end loop nqv */      }/* end loop nqv */
Line 7656  int readdata(char datafile[], int firsto Line 8191  int readdata(char datafile[], int firsto
   return (1);    return (1);
 }  }
   
 void removespace(char *str) {  void removefirstspace(char **stri){/*, char stro[]) {*/
   char *p1 = str, *p2 = str;    char *p1 = *stri, *p2 = *stri;
   do    while (*p2 == ' ')
     while (*p2 == ' ')      p2++; 
       p2++;    /* while ((*p1++ = *p2++) !=0) */
   while (*p1++ == *p2++);    /*   ; */
     /* do */
     /*   while (*p2 == ' ') */
     /*     p2++; */
     /* while (*p1++ == *p2++); */
     *stri=p2; 
   }
   
   int decoderesult ( char resultline[], int nres)
   /**< This routine decode one result line and returns the combination # of dummy covariates only **/
   {
     int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
     char resultsav[MAXLINE];
     int resultmodel[MAXLINE];
     int modelresult[MAXLINE];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     removefirstspace(&resultline);
     printf("decoderesult:%s\n",resultline);
   
     if (strstr(resultline,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
       fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
       return 1;
     }
     trimbb(resultsav, resultline);
     if (strlen(resultsav) >1){
       j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
     }
     if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
       printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
       fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     }
     for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
       if(nbocc(resultsav,'=') >1){
          cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                                         resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
          cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
       }else
         cutl(strc,strd,resultsav,'=');
       Tvalsel[k]=atof(strc); /* 1 */
       
       cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
       Tvarsel[k]=atoi(strc);
       /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
       /* cptcovsel++;     */
       if (nbocc(stra,'=') >0)
         strcpy(resultsav,stra); /* and analyzes it */
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single covariate in model */
         match=0;
         for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
             modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
             match=1;
             break;
           }
         }
         if(match == 0){
           printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         }
       }
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
       match=0;
       for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         if(Typevar[k1]==0){ /* Single */
           if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
             resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             ++match;
           }
         }
       }
       if(match == 0){
         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
       }else if(match > 1){
         printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
       }
     }
         
     /* We need to deduce which combination number is chosen and save quantitative values */
     /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
     /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
     /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
     /*    1 0 0 0 */
     /*    2 1 0 0 */
     /*    3 0 1 0 */ 
     /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
     /*    5 0 0 1 */
     /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
     /*    7 0 1 1 */
     /*    8 1 1 1 */
     /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
     /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
     /* V5*age V5 known which value for nres?  */
     /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
     for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
       if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
         k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
         k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
         Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
         Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
         printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
         k4++;;
       }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
         k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
         Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
         k4q++;;
       }
     }
     
     TKresult[nres]=++k; /* Combination for the nresult and the model */
     return (0);
 }  }
   
 int decodemodel ( char model[], int lastobs)  int decodemodel( char model[], int lastobs)
  /**< This routine decode the model and returns:   /**< This routine decodes the model and returns:
         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
         * - nagesqr = 1 if age*age in the model, otherwise 0.          * - nagesqr = 1 if age*age in the model, otherwise 0.
         * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
Line 7680  int decodemodel ( char model[], int last Line 8338  int decodemodel ( char model[], int last
         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
         */          */
 {  {
   int i, j, k, ks;    int i, j, k, ks, v;
   int  j1, k1, k2;    int  j1, k1, k2, k3, k4;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   char *strpt;    char *strpt;
Line 7782  int decodemodel ( char model[], int last Line 8440  int decodemodel ( char model[], int last
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
       /*        /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */         * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates not including constant and age, neither age*age*/        for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
         Tvar[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
         }
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
Line 7798  int decodemodel ( char model[], int last Line 8457  int decodemodel ( char model[], int last
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */              cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */              Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             Typevar[k]=1;  /* 2 for age product */              Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
Line 7815  int decodemodel ( char model[], int last Line 8474  int decodemodel ( char model[], int last
             cptcovprodnoage++;k1++;              cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                    because this model-covariate is a construction we invent a new column                                                  because this model-covariate is a construction we invent a new column
                                    which is after existing variables ncovcol+nqv+ntv+nqtv + k1                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
Line 7840  int decodemodel ( char model[], int last Line 8500  int decodemodel ( char model[], int last
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates*/            ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
           Tvar[k]=atoi(strd);            Tvar[k]=atoi(strd);
           Typevar[k]=0;  /* 0 for simple covariates */            Typevar[k]=0;  /* 0 for simple covariates */
Line 7861  int decodemodel ( char model[], int last Line 8521  int decodemodel ( char model[], int last
      scanf("%d ",i);*/       scanf("%d ",i);*/
   
   
 /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind  /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
    of variable (dummy vs quantitative, fixed vs time varying) is behind */     of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
 /* ncovcol= 1, nqv=1, ntv=2, nqtv= 1  = 5 possible variables data  /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
    model=  V2 + V4 +V3 + V4*V3 + V5*age + V5 , V1 is not used saving its place     model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
    k =      1    2   3     4       5       6     k =           1    2   3     4       5       6      7      8        9
    Tvar[k]= 2    4   3 1+1+2+1+1=6 5       5     Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
    Typevar[k]=0  0   0     2       1       0     Typevar[k]=   0    0   0     2       1       0      2      1        1
      Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
      Dummy[k]      1    0   0     0       3       1      1      2        3
             Tmodelind[combination of covar]=k;
 */    */  
 /* Dispatching between quantitative and time varying covariates */  /* Dispatching between quantitative and time varying covariates */
     /* If Tvar[k] >ncovcol it is a product */
   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
   for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
     if (Tvar[k] <=ncovcol){ /* Simple fixed dummy covariatee */    printf("Model=%s\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\
   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);
     fprintf(ficlog,"Model=%s\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\
   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, 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 */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         nsd++;
         modell[k].maintype= FTYPE;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
       ncoveff++;        ncoveff++;
     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/        ncovf++;
       nqfveff++;  /* Only simple fixed quantitative variable */        modell[k].maintype= FTYPE;
     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){        TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
         Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;
         modell[k].maintype= FTYPE;
         modell[k].subtype= FQ;
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         ncovf++;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
         Fixed[k]= 1;
         Dummy[k]= 0;
       ntveff++; /* Only simple time varying dummy variable */        ntveff++; /* Only simple time varying dummy variable */
     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){        modell[k].maintype= VTYPE;
       nqtveff++;/* Only simple time varying quantitative variable */        modell[k].subtype= VD;
         nsd++;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         ncovv++; /* Only simple time varying variables */
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
         printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
         printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
         Fixed[k]= 1;
         Dummy[k]= 1;
         nqtveff++;
         modell[k].maintype= VTYPE;
         modell[k].subtype= VQ;
         ncovv++; /* Only simple time varying variables */
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
         TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
         TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
         /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
         printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
         printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
       }else if (Typevar[k] == 1) {  /* product with age */
         ncova++;
         TvarA[ncova]=Tvar[k];
         TvarAind[ncova]=k;
         if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
           Fixed[k]= 2;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFD;
           /* ncoveff++; */
         }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
           Fixed[k]= 2;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
           /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           Fixed[k]= 3;
           Dummy[k]= 2;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVD;                /*      Product age * varying dummy */
           /* ntveff++; /\* Only simple time varying dummy variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 3;
           Dummy[k]= 3;
           modell[k].maintype= ATYPE;
           modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }
       }else if (Typevar[k] == 2) {  /* product without age */
         k1=Tposprod[k];
         if(Tvard[k1][1] <=ncovcol){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
             ncovf++; /* Varying variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
             modell[k].maintype= FTYPE;
             modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
             ncovf++; /* Fixed variables without age */
             TvarF[ncovf]=Tvar[k];
             TvarFind[ncovf]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
         }else{
           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         } /*end k1*/
     }else{      }else{
       printf("Other types in effective covariates \n");        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
         fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       }
       printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
       printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
     }
     /* Searching for doublons in the model */
     for(k1=1; k1<= cptcovt;k1++){
       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] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
             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]]);
               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);
               return(1);
             }
           }else if (Typevar[k1] ==2){
             k3=Tposprod[k1];
             k4=Tposprod[k2];
             if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
               printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }
         }
     }      }
   }    }
     
   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
     fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
   printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
Line 8201  void syscompilerinfo(int logged) Line 9131  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  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    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;
   double tot;    double tot;
Line 8212  int prevalence_limit(double *p, double * Line 9142  int prevalence_limit(double *p, double *
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing 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,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
Line 8225  int prevalence_limit(double *p, double * Line 9155  int prevalence_limit(double *p, double *
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   
   i1=pow(2,ncoveff);    /* i1=pow(2,ncoveff); */
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */        if(TKresult[nres]!= k)
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          continue;
     /* k=k+1; */  
     /* to clean */  
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));  
     fprintf(ficrespl,"#******");  
     printf("#******");  
     fprintf(ficlog,"#******");  
     for(j=1;j<=nqfveff;j++) {  
       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
     }  
     fprintf(ficrespl,"******\n");  
     printf("******\n");  
     fprintf(ficlog,"******\n");  
                 if(invalidvarcomb[k]){  
                                                 printf("\nCombination (%d) ignored because no cases \n",k);   
                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);   
                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);   
                                                 continue;  
                 }  
   
     fprintf(ficrespl,"#Age ");        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     for(j=1;j<=nqfveff;j++) {        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
     }        /* k=k+1; */
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);        /* to clean */
     fprintf(ficrespl,"Total Years_to_converge\n");        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
                 fprintf(ficrespl,"#******");
     for (age=agebase; age<=agelim; age++){        printf("#******");
       /* for (age=agebase; age<=agebase; age++){ */        fprintf(ficlog,"#******");
       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
       fprintf(ficrespl,"%.0f ",age );          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
       for(j=1;j<=nqfveff;j++)          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                                         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       tot=0.;        }
       for(i=1; i<=nlstate;i++){        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
                                                         tot +=  prlim[i][i];          printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                                         fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }          fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);        }
     } /* Age */        fprintf(ficrespl,"******\n");
     /* was end of cptcod */        printf("******\n");
   } /* cptcov */        fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no case \n",k); 
           fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
           continue;
         }
   
         fprintf(ficrespl,"#Age ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
         fprintf(ficrespl,"Total Years_to_converge\n");
       
         for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           tot=0.;
           for(i=1; i<=nlstate;i++){
             tot +=  prlim[i][i];
             fprintf(ficrespl," %.5f", prlim[i][i]);
           }
           fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
         } /* Age */
         /* was end of cptcod */
       } /* cptcov */
     } /* nres */
   return 0;    return 0;
 }  }
   
Line 8284  int back_prevalence_limit(double *p, dou Line 9225  int back_prevalence_limit(double *p, dou
         /* 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
          */           */
   int i, j, k, i1 ;    int i, j, k, i1, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
   double tot;    double tot;
Line 8312  int back_prevalence_limit(double *p, dou Line 9253  int back_prevalence_limit(double *p, dou
   agelim=agemaxpar;    agelim=agemaxpar;
       
       
   i1=pow(2,nqfveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
     
         for(k=1; k<=i1;k++){     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */        if(TKresult[nres]!= k)
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          continue;
     /* k=k+1; */        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
     /* to clean */        fprintf(ficresplb,"#******");
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        printf("#******");
     fprintf(ficresplb,"#******");        fprintf(ficlog,"#******");
     printf("#******");        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
     fprintf(ficlog,"#******");          fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     for(j=1;j<=nqfveff;j++) {          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        }
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
     }          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
     fprintf(ficresplb,"******\n");          fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
     printf("******\n");          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
     fprintf(ficlog,"******\n");        }
                 if(invalidvarcomb[k]){        fprintf(ficresplb,"******\n");
                                                 printf("\nCombination (%d) ignored because no cases \n",k);         printf("******\n");
                                                 fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);         fprintf(ficlog,"******\n");
                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);         if(invalidvarcomb[k]){
                                                 continue;          printf("\nCombination (%d) ignored because no cases \n",k); 
                 }          fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
           continue;
         }
           
     fprintf(ficresplb,"#Age ");        fprintf(ficresplb,"#Age ");
     for(j=1;j<=nqfveff;j++) {        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     }  
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);  
     fprintf(ficresplb,"Total Years_to_converge\n");  
       
       
     for (age=agebase; age<=agelim; age++){  
       /* for (age=agebase; age<=agebase; age++){ */  
       if(mobilavproj > 0){  
         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */  
         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */  
                                 bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);  
       }else if (mobilavproj == 0){  
                                 printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);  
                                 fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);  
                                 exit(1);  
       }else{  
                                 /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */  
                                 bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);  
       }        }
       fprintf(ficresplb,"%.0f ",age );        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
       for(j=1;j<=nqfveff;j++)        fprintf(ficresplb,"Total Years_to_converge\n");
                                 fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      
       tot=0.;      
       for(i=1; i<=nlstate;i++){        for (age=agebase; age<=agelim; age++){
                                 tot +=  bprlim[i][i];          /* for (age=agebase; age<=agebase; age++){ */
                                 fprintf(ficresplb," %.5f", bprlim[i][i]);          if(mobilavproj > 0){
       }            /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);            /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
     } /* Age */            bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
     /* was end of cptcod */          }else if (mobilavproj == 0){
   } /* cptcov */            printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
               fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
             exit(1);
           }else{
             /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
             bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
           }
           fprintf(ficresplb,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           tot=0.;
           for(i=1; i<=nlstate;i++){
             tot +=  bprlim[i][i];
             fprintf(ficresplb," %.5f", bprlim[i][i]);
           }
           fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
         } /* Age */
         /* was end of cptcod */
       } /* end of any combination */
     } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
   /* fclose(ficrespijb); */    /* fclose(ficrespijb); */
       
Line 8388  int hPijx(double *p, int bage, int fage) Line 9332  int hPijx(double *p, int bage, int fage)
   int agelim;    int agelim;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, k4, nres=0;
   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 8411  int hPijx(double *p, int bage, int fage) Line 9355  int hPijx(double *p, int bage, int fage)
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,nqfveff);      i1= pow(2,cptcoveff);
                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,nqfveff); k++){      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(TKresult[nres]!= k)
           continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=nqfveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 8429  int hPijx(double *p, int bage, int fage) Line 9380  int hPijx(double *p, int bage, int fage)
                   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
Line 8459  int hPijx(double *p, int bage, int fage) Line 9410  int hPijx(double *p, int bage, int fage)
         int ageminl;          int ageminl;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, nres;
                   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 8483  int hPijx(double *p, int bage, int fage) Line 9434  int hPijx(double *p, int bage, int fage)
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   pstamp(ficrespijb);    pstamp(ficrespijb);
   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");    fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
   i1= pow(2,nqfveff);    i1= pow(2,cptcoveff);
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for (k=1; k <= (int) pow(2,nqfveff); k++){    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     fprintf(ficrespijb,"\n#****** ");      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     for(j=1;j<=nqfveff;j++)        if(TKresult[nres]!= k)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          continue;
     fprintf(ficrespijb,"******\n");        fprintf(ficrespijb,"\n#****** ");
     if(invalidvarcomb[k]){        for(j=1;j<=cptcoveff;j++)
       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);           fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       continue;        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
     }          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
             }
     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        fprintf(ficrespijb,"******\n");
     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        if(invalidvarcomb[k]){
       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */          fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          continue;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */        }
               
       /*          nhstepm=nhstepm*YEARM; aff par mois*/        /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
               for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
       /* oldm=oldms;savm=savms; */          nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);          
       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /*        nhstepm=nhstepm*YEARM; aff par mois*/
       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");          
       for(i=1; i<=nlstate;i++)          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1; j<=nlstate+ndeath;j++)          /* oldm=oldms;savm=savms; */
           fprintf(ficrespijb," %1d-%1d",i,j);          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
       fprintf(ficrespijb,"\n");          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
       for (h=0; h<=nhstepm; h++){          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/          fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );  
         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */  
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);              fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       }          for (h=0; h<=nhstepm; h++){
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
       fprintf(ficrespijb,"\n");            fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
     }            /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
     /*}*/            for(i=1; i<=nlstate;i++)
   }              for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
             fprintf(ficrespijb,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespijb,"\n");
         } /* end age deb */
       } /* end combination */
     } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
   
Line 8555  int main(int argc, char *argv[]) Line 9512  int main(int argc, char *argv[])
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
     int nres=0;
   
   char ca[32], cb[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
Line 8573  int main(int argc, char *argv[]) Line 9531  int main(int argc, char *argv[])
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char model[MAXLINE], modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
     char resultline[MAXLINE];
     
   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;
Line 8885  int main(int argc, char *argv[]) Line 9845  int main(int argc, char *argv[])
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */    cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */    cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
   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
Line 8938  int main(int argc, char *argv[]) Line 9898  int main(int argc, char *argv[])
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
                         j=0;        j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
                                 if(jj==i) continue;          if(jj==i) continue;
                                 j++;          j++;
                                 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 \
 It might be a problem of design; if ncovcol and the model are correct\n \  It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
                                         exit(1);            exit(1);
                                 }          }
                                 fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
                                 if(mle==1)          if(mle==1)
                                         printf("%1d%1d",i,jj);            printf("%1d%1d",i,jj);
                                 fprintf(ficlog,"%1d%1d",i,jj);          fprintf(ficlog,"%1d%1d",i,jj);
                                 for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
                                         fscanf(ficpar," %lf",&param[i][j][k]);            fscanf(ficpar," %lf",&param[i][j][k]);
                                         if(mle==1){            if(mle==1){
                                                 printf(" %lf",param[i][j][k]);              printf(" %lf",param[i][j][k]);
                                                 fprintf(ficlog," %lf",param[i][j][k]);              fprintf(ficlog," %lf",param[i][j][k]);
                                         }            }
                                         else            else
                                                 fprintf(ficlog," %lf",param[i][j][k]);              fprintf(ficlog," %lf",param[i][j][k]);
                                         fprintf(ficparo," %lf",param[i][j][k]);            fprintf(ficparo," %lf",param[i][j][k]);
                                 }          }
                                 fscanf(ficpar,"\n");          fscanf(ficpar,"\n");
                                 numlinepar++;          numlinepar++;
                                 if(mle==1)          if(mle==1)
                                         printf("\n");            printf("\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
                                 fprintf(ficparo,"\n");          fprintf(ficparo,"\n");
       }        }
     }        }  
     fflush(ficlog);      fflush(ficlog);
       
     /* Reads scales values */      /* Reads scales values */
     p=param[1][1];      p=param[1][1];
           
Line 8989  run imach with mle=-1 to get a correct t Line 9949  run imach with mle=-1 to get a correct t
   
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
                                 fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
                                 if ( (i1-i) * (j1-j) != 0){          if ( (i1-i) * (j1-j) != 0){
                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                                         exit(1);            exit(1);
                                 }          }
                                 printf("%1d%1d",i,j);          printf("%1d%1d",i,j);
                                 fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
                                 fprintf(ficlog,"%1d%1d",i1,j1);          fprintf(ficlog,"%1d%1d",i1,j1);
                                 for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
                                         fscanf(ficpar,"%le",&delti3[i][j][k]);            fscanf(ficpar,"%le",&delti3[i][j][k]);
                                         printf(" %le",delti3[i][j][k]);            printf(" %le",delti3[i][j][k]);
                                         fprintf(ficparo," %le",delti3[i][j][k]);            fprintf(ficparo," %le",delti3[i][j][k]);
                                         fprintf(ficlog," %le",delti3[i][j][k]);            fprintf(ficlog," %le",delti3[i][j][k]);
                                 }          }
                                 fscanf(ficpar,"\n");          fscanf(ficpar,"\n");
                                 numlinepar++;          numlinepar++;
                                 printf("\n");          printf("\n");
                                 fprintf(ficparo,"\n");          fprintf(ficparo,"\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       }        }
     }      }
     fflush(ficlog);      fflush(ficlog);
                       
     /* Reads covariance matrix */      /* Reads covariance matrix */
     delti=delti3[1][1];      delti=delti3[1][1];
                                   
Line 9036  run imach with mle=-1 to get a correct t Line 9996  run imach with mle=-1 to get a correct t
                                   
     /* Scans npar lines */      /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);        count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
       if(count != 3){        if(count != 3){
                                 printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
                                 fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\          fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
                                 exit(1);          exit(1);
       }else{        }else{
                                 if(mle==1)          if(mle==1)
                                         printf("%1d%1d%1d",i1,j1,jk);            printf("%1d%1d%d",i1,j1,jk);
                         }        }
       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);        fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);        fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
                                 fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
                                 if(mle==1){          if(mle==1){
                                         printf(" %.5le",matcov[i][j]);            printf(" %.5le",matcov[i][j]);
                                 }          }
                                 fprintf(ficlog," %.5le",matcov[i][j]);          fprintf(ficlog," %.5le",matcov[i][j]);
                                 fprintf(ficparo," %.5le",matcov[i][j]);          fprintf(ficparo," %.5le",matcov[i][j]);
       }        }
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
       numlinepar++;        numlinepar++;
Line 9069  Please run with mle=-1 to get a correct Line 10029  Please run with mle=-1 to get a correct
     /* End of read covariance matrix npar lines */      /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
                                 matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
           
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
Line 9101  Please run with mle=-1 to get a correct Line 10061  Please run with mle=-1 to get a correct
   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[i]=0;      num[i]=0;
                 moisnais[i]=0;      moisnais[i]=0;
                 annais[i]=0;      annais[i]=0;
                 moisdc[i]=0;      moisdc[i]=0;
                 andc[i]=0;      andc[i]=0;
                 agedc[i]=0;      agedc[i]=0;
                 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,1,n);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
Line 9122  Please run with mle=-1 to get a correct Line 10082  Please run with mle=-1 to get a correct
     goto end;      goto end;
   
   /* Calculation of the number of parameters from char model */    /* Calculation of the number of parameters from char model */
     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
         k=3 V4 Tvar[k=3]= 4 (from V4)          k=3 V4 Tvar[k=3]= 4 (from V4)
         k=2 V1 Tvar[k=2]= 1 (from V1)          k=2 V1 Tvar[k=2]= 1 (from V1)
         k=1 Tvar[1]=2 (from V2)          k=1 Tvar[1]=2 (from V2)
     */    */
     
   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
   Typevar=ivector(1,NCOVMAX); /* -1 to 4 */    TvarsDind=ivector(1,NCOVMAX); /*  */
     TvarsD=ivector(1,NCOVMAX); /*  */
     TvarsQind=ivector(1,NCOVMAX); /*  */
     TvarsQ=ivector(1,NCOVMAX); /*  */
     TvarF=ivector(1,NCOVMAX); /*  */
     TvarFind=ivector(1,NCOVMAX); /*  */
     TvarV=ivector(1,NCOVMAX); /*  */
     TvarVind=ivector(1,NCOVMAX); /*  */
     TvarA=ivector(1,NCOVMAX); /*  */
     TvarAind=ivector(1,NCOVMAX); /*  */
     TvarFD=ivector(1,NCOVMAX); /*  */
     TvarFDind=ivector(1,NCOVMAX); /*  */
     TvarFQ=ivector(1,NCOVMAX); /*  */
     TvarFQind=ivector(1,NCOVMAX); /*  */
     TvarVD=ivector(1,NCOVMAX); /*  */
     TvarVDind=ivector(1,NCOVMAX); /*  */
     TvarVQ=ivector(1,NCOVMAX); /*  */
     TvarVQind=ivector(1,NCOVMAX); /*  */
   
     Tvalsel=vector(1,NCOVMAX); /*  */
     Tvarsel=ivector(1,NCOVMAX); /*  */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 9139  Please run with mle=-1 to get a correct Line 10123  Please run with mle=-1 to get a correct
     ncovcol + k1      ncovcol + k1
     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
     Tvar[3=V1*V4]=4+1 etc */      Tvar[3=V1*V4]=4+1 etc */
   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */    Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
     Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)       if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
        Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
   */    */
   Tvaraff=ivector(1,NCOVMAX); /* Unclear */    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
Line 9151  Please run with mle=-1 to get a correct Line 10137  Please run with mle=-1 to get a correct
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
     Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                                   * V1 df, V2 qf, V3 & V4 dv, V5 qv
                                   * Tmodelind[1]@9={9,0,3,2,}*/
     TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
     TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual quantitative, fixed or varying:
                                   * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 /* Main decodemodel */  /* Main decodemodel */
   
   
Line 9213  Please run with mle=-1 to get a correct Line 10211  Please run with mle=-1 to get a correct
   cptcoveff=0;    cptcoveff=0;
   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
         }    }
             
         ncovcombmax=pow(2,cptcoveff);    ncovcombmax=pow(2,cptcoveff);
         invalidvarcomb=ivector(1, ncovcombmax);     invalidvarcomb=ivector(1, ncovcombmax); 
         for(i=1;i<ncovcombmax;i++)    for(i=1;i<ncovcombmax;i++)
                 invalidvarcomb[i]=0;      invalidvarcomb[i]=0;
     
   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
     
   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
Line 9382  Title=%s <br>Datafile=%s Firstpass=%d La Line 10380  Title=%s <br>Datafile=%s Firstpass=%d La
   /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age 
                  and for any valid combination of covariates                   and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                                                         firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 9416  Interval (in months) between two waves: Line 10414  Interval (in months) between two waves:
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
                                 if (s[m][i]>nlstate) {          if (s[m][i]>nlstate) {
                                         dcwave[i]=m;            dcwave[i]=m;
                                         /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                                         break;            break;
                                 }          }
     }      }
                       
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       if (wav[i]>0){        if (wav[i]>0){
                                 ageexmed[i]=agev[mw[1][i]][i];          ageexmed[i]=agev[mw[1][i]][i];
                                 j=wav[i];          j=wav[i];
                                 agecens[i]=1.;           agecens[i]=1.; 
                                           
                                 if (ageexmed[i]> 1 && wav[i] > 0){          if (ageexmed[i]> 1 && wav[i] > 0){
                                         agecens[i]=agev[mw[j][i]][i];            agecens[i]=agev[mw[j][i]][i];
                                         cens[i]= 1;            cens[i]= 1;
                                 }else if (ageexmed[i]< 1)           }else if (ageexmed[i]< 1) 
                                         cens[i]= -1;            cens[i]= -1;
                                 if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)          if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                                         cens[i]=0 ;            cens[i]=0 ;
       }        }
       else cens[i]=-1;        else cens[i]=-1;
     }      }
           
     for (i=1;i<=NDIM;i++) {      for (i=1;i<=NDIM;i++) {
       for (j=1;j<=NDIM;j++)        for (j=1;j<=NDIM;j++)
                                 ximort[i][j]=(i == j ? 1.0 : 0.0);          ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     /*p[1]=0.0268; p[NDIM]=0.083;*/      /*p[1]=0.0268; p[NDIM]=0.083;*/
Line 9892  Please run with mle=-1 to get a correct Line 10890  Please run with mle=-1 to get a correct
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       fputs(line,stdout);        fputs(line,stdout);
         fputs(line,ficres);
       fputs(line,ficparo);        fputs(line,ficparo);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 9908  Please run with mle=-1 to get a correct Line 10907  Please run with mle=-1 to get a correct
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
Line 9917  Please run with mle=-1 to get a correct Line 10917  Please run with mle=-1 to get a correct
     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
       /* Results */
       nresult=0;
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           fputs(line,ficres);
           continue;
         }else
           break;
       }
       if (!feof(ficpar))
       while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
         if (num_filled == 0){
           resultline[0]='\0';
         break;
         } else if (num_filled != 1){
           printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
         }
         nresult++; /* Sum of resultlines */
         printf("Result %d: result=%s\n",nresult, resultline);
         if(nresult > MAXRESULTLINES){
           printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
           fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
           goto end;
         }
         decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
         fprintf(ficparo,"result: %s\n",resultline);
         fprintf(ficres,"result: %s\n",resultline);
         fprintf(ficlog,"result: %s\n",resultline);
         while(fgets(line, MAXLINE, ficpar)) {
           /* If line starts with a # it is a comment */
           if (line[0] == '#') {
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficres);
             fputs(line,ficlog);
             continue;
           }else
             break;
         }
         if (feof(ficpar))
           break;
         else{ /* Processess output results for this combination of covariate values */
         }                            
       } /* end while */
   
   
           
                 /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
                         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\        printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
                         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\        fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else{      }else{
Line 9964  Please run with mle=-1 to get a correct Line 11016  Please run with mle=-1 to get a correct
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
       
     /* ncovcombmax=  pow(2,cptcoveff); */      /* ncovcombmax=  pow(2,cptcoveff); */
     /*-------------- Variance of one-step probabilities---*/      /*-------------- Variance of one-step probabilities---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
       
     /* Prevalence for each covariates in probs[age][status][cov] */      /* Prevalence for each covariates in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
Line 9979  Please run with mle=-1 to get a correct Line 11031  Please run with mle=-1 to get a correct
     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     if (mobilav!=0 ||mobilavproj !=0 ) {      if (mobilav!=0 ||mobilavproj !=0 ) {
       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);        mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                         for(i=1;i<=AGESUP;i++)        for(i=1;i<=AGESUP;i++)
                                 for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate;j++)
                                         for(k=1;k<=ncovcombmax;k++)            for(k=1;k<=ncovcombmax;k++)
                                                 mobaverages[i][j][k]=0.;              mobaverages[i][j][k]=0.;
       mobaverage=mobaverages;        mobaverage=mobaverages;
       if (mobilav!=0) {        if (mobilav!=0) {
                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){          printf("Movingaveraging observed prevalence\n");
                                         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
                                         printf(" Error in movingaverage mobilav=%d\n",mobilav);            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                                 }            printf(" Error in movingaverage mobilav=%d\n",mobilav);
           }
       }        }
       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */        /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */        /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
       else if (mobilavproj !=0) {        else if (mobilavproj !=0) {
                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){          printf("Movingaveraging projected observed prevalence\n");
                                         fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
                                         printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                 }            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
           }
       }        }
     }/* end if moving average */      }/* end if moving average */
                       
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
Line 10047  Please run with mle=-1 to get a correct Line 11101  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
   
       pstamp(ficreseij);
                                   
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       if (cptcovn < 1){i1=1;}
       
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(TKresult[nres]!= k)
           continue;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
         printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
                                 fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
         printf("******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
               
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     }      }
Line 10065  Please run with mle=-1 to get a correct Line 11134  Please run with mle=-1 to get a correct
     printf("done evsij\n");fflush(stdout);      printf("done evsij\n");fflush(stdout);
     fprintf(ficlog,"done evsij\n");fflush(ficlog);      fprintf(ficlog,"done evsij\n");fflush(ficlog);
                                   
     /*---------- Health expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                                   
                                   
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
Line 10081  Please run with mle=-1 to get a correct Line 11150  Please run with mle=-1 to get a correct
     strcpy(fileresstde,"STDE_");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileresu);      strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
     }      }
     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"CVE_");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileresu);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"V_");      strcpy(fileresv,"V_");
     strcat(fileresv,fileresu);      strcat(fileresv,fileresu);
Line 10102  Please run with mle=-1 to get a correct Line 11171  Please run with mle=-1 to get a correct
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }      }
     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);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++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       fprintf(ficrest,"\n#****** ");      if (cptcovn < 1){i1=1;}
       for(j=1;j<=cptcoveff;j++)       
                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(TKresult[nres]!= k)
           continue;
         printf("\n#****** Result for:");
         fprintf(ficrest,"\n#****** Result for:");
         fprintf(ficlog,"\n#****** Result for:");
         for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
         fprintf(ficlog,"******\n");
         printf("******\n");
               
       fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
       fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
                                 fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                 fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
               
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         /* pstamp(ficresvij); */
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
                                 fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       printf(" cvevsij %d, ",k);        printf(" cvevsij ");
       fprintf(ficlog, " cvevsij %d, ",k);        fprintf(ficlog, " cvevsij ");
       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
       printf(" end cvevsij \n ");        printf(" end cvevsij \n ");
       fprintf(ficlog, " end cvevsij \n ");        fprintf(ficlog, " end cvevsij \n ");
               
Line 10145  Please run with mle=-1 to get a correct Line 11240  Please run with mle=-1 to get a correct
               
               
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
                                 oldm=oldms;savm=savms; /* ZZ Segmentation fault */          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
                                 cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
                                 printf("varevsij %d \n",vpopbased);          printf("varevsij vpopbased=%d \n",vpopbased);
                                 fprintf(ficlog, "varevsij %d \n",vpopbased);          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
                                 varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
                                 fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
                                 if(vpopbased==1)          if(vpopbased==1)
                                         fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
                                 else          else
                                         fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
                                 fprintf(ficrest,"# Age 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"); */
                                 epj=vector(1,nlstate+1);          epj=vector(1,nlstate+1);
                                 printf("Computing age specific period (stable) prevalences in each health state \n");          printf("Computing age specific 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 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); /*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) {
                                                 if(mobilav ==0){              if(mobilav ==0){
                                                         for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
                                                                 prlim[i][i]=probs[(int)age][i][k];                  prlim[i][i]=probs[(int)age][i][k];
                                                 }else{ /* mobilav */               }else{ /* mobilav */ 
                                                         for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
                                                                 prlim[i][i]=mobaverage[(int)age][i][k];                  prlim[i][i]=mobaverage[(int)age][i][k];
                                                 }              }
                                         }            }
                       
                                         fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);            fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
                                         /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */            /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                                         /* printf(" age %4.0f ",age); */            /* printf(" age %4.0f ",age); */
                                         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                                                 for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(i=1, epj[j]=0.;i <=nlstate;i++) {
                                                         epj[j] += prlim[i][i]*eij[i][j][(int)age];                epj[j] += prlim[i][i]*eij[i][j][(int)age];
                                                         /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                                                         /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */                /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
                                                 }              }
                                                 epj[nlstate+1] +=epj[j];              epj[nlstate+1] +=epj[j];
                                         }            }
                                         /* printf(" age %4.0f \n",age); */            /* printf(" age %4.0f \n",age); */
                       
                                         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1, vepp=0.;i <=nlstate;i++)
                                                 for(j=1;j <=nlstate;j++)              for(j=1;j <=nlstate;j++)
                                                         vepp += vareij[i][j][(int)age];                vepp += vareij[i][j][(int)age];
                                         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                                         for(j=1;j <=nlstate;j++){            for(j=1;j <=nlstate;j++){
                                                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                                         }            }
                                         fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
                                 }          }
       } /* End vpopbased */        } /* End vpopbased */
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_vector(epj,1,nlstate+1);        free_vector(epj,1,nlstate+1);
       printf("done \n");fflush(stdout);        printf("done selection\n");fflush(stdout);
       fprintf(ficlog,"done\n");fflush(ficlog);        fprintf(ficlog,"done selection\n");fflush(ficlog);
               
       /*}*/        /*}*/
     } /* End k */      } /* End k selection */
     free_vector(weight,1,n);  
     free_imatrix(Tvard,1,NCOVMAX,1,2);  
     free_imatrix(s,1,maxwav+1,1,n);  
     free_matrix(anint,1,maxwav,1,n);   
     free_matrix(mint,1,maxwav,1,n);  
     free_ivector(cod,1,n);  
     free_ivector(tab,1,NCOVMAX);  
     fclose(ficresstdeij);  
     fclose(ficrescveij);  
     fclose(ficresvij);  
     fclose(ficrest);  
     printf("done Health expectancies\n");fflush(stdout);  
     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);  
     fclose(ficpar);  
     
     /*------- Variance of period (stable) prevalence------*/     
   
       printf("done State-specific expectancies\n");fflush(stdout);
       fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
       /*------- Variance of period (stable) prevalence------*/   
       
     strcpy(fileresvpl,"VPL_");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileresu);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
Line 10230  Please run with mle=-1 to get a correct Line 11314  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);      printf("Computing Variance-covariance of 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 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++){*/
                 
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      i1=pow(2,cptcoveff);
         fprintf(ficresvpl,"\n#****** ");      if (cptcovn < 1){i1=1;}
                         for(j=1;j<=cptcoveff;j++)   
                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      for(nres=1; nres <= nresult; nres++) /* For each resultline */
                         fprintf(ficresvpl,"******\n");      for(k=1; k<=i1;k++){
               if(TKresult[nres]!= k)
                         varpl=matrix(1,nlstate,(int) bage, (int) fage);          continue;
                         oldm=oldms;savm=savms;        fprintf(ficresvpl,"\n#****** ");
                         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);        printf("\n#****** ");
                         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
                       
     fclose(ficresvpl);      fclose(ficresvpl);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);      printf("done variance-covariance of period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
       
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
       
       
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0 ||mobilavproj !=0)      if (mobilav!=0 ||mobilavproj !=0)
       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
Line 10258  Please run with mle=-1 to get a correct Line 11374  Please run with mle=-1 to get a correct
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
  /* endfree:*/    /* endfree:*/
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);    free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
     free_ma3x(cotvar,1,maxwav,1,ntv,1,n);    free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
     free_matrix(coqvar,1,maxwav,1,n);    free_matrix(coqvar,1,maxwav,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);    free_matrix(matcov,1,npar,1,npar);
     free_matrix(hess,1,npar,1,npar);    free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/    /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);    free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     
     free_ivector(ncodemax,1,NCOVMAX);    free_ivector(ncodemax,1,NCOVMAX);
     free_ivector(ncodemaxwundef,1,NCOVMAX);    free_ivector(ncodemaxwundef,1,NCOVMAX);
     free_ivector(Typevar,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);    free_ivector(DummyV,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(FixedV,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tage,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
     free_ivector(TvarsQ,1,NCOVMAX);
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_ivector(TvarsQind,1,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */    free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TvarsDind,1,NCOVMAX);
     free_ivector(TvarFD,1,NCOVMAX);
     free_ivector(TvarFDind,1,NCOVMAX);
     free_ivector(TvarF,1,NCOVMAX);
     free_ivector(TvarFind,1,NCOVMAX);
     free_ivector(TvarV,1,NCOVMAX);
     free_ivector(TvarVind,1,NCOVMAX);
     free_ivector(TvarA,1,NCOVMAX);
     free_ivector(TvarAind,1,NCOVMAX);
     free_ivector(TvarFQ,1,NCOVMAX);
     free_ivector(TvarFQind,1,NCOVMAX);
     free_ivector(TvarVD,1,NCOVMAX);
     free_ivector(TvarVDind,1,NCOVMAX);
     free_ivector(TvarVQ,1,NCOVMAX);
     free_ivector(TvarVQind,1,NCOVMAX);
     free_ivector(Tvarsel,1,NCOVMAX);
     free_vector(Tvalsel,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     free_ivector(TmodelInvind,1,NCOVMAX);
     free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
     
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);      printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
Line 10305  Please run with mle=-1 to get a correct Line 11449  Please run with mle=-1 to get a correct
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     
   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
Line 10318  Please run with mle=-1 to get a correct Line 11462  Please run with mle=-1 to get a correct
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
     
     
    printf("Before Current directory %s!\n",pathcd);    printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
    if (_chdir(pathcd) != 0)    if (_chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n",path);      printf("Can't move to directory %s!\n",path);
    if(_getcwd(pathcd,MAXLINE) > 0)    if(_getcwd(pathcd,MAXLINE) > 0)
 #else  #else
    if(chdir(pathcd) != 0)      if(chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n", path);        printf("Can't move to directory %s!\n", path);
    if (getcwd(pathcd, MAXLINE) > 0)    if (getcwd(pathcd, MAXLINE) > 0)
 #endif   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
Line 10354  Please run with mle=-1 to get a correct Line 11498  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);
     
   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("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");
Line 10382  Please run with mle=-1 to get a correct Line 11526  Please run with mle=-1 to get a correct
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   end:  end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: "); fflush(stdout);      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
Removed from v.1.225  
changed lines
  Added in v.1.243

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