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Diff for /imach/src/imach.c between versions 1.332 and 1.338

version 1.332, 2022/08/21 09:06:25 version 1.338, 2022/09/04 17:40:33
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.338  2022/09/04 17:40:33  brouard
     Summary: 0.99r36
   
     * imach.c (Module): Now the easy runs i.e. without result or
     model=1+age only did not work. The defautl combination should be 1
     and not 0 because everything hasn't been tranformed yet.
   
     Revision 1.337  2022/09/02 14:26:02  brouard
     Summary: version 0.99r35
   
     * src/imach.c: Version 0.99r35 because it outputs same results with
     1+age+V1+V1*age for females and 1+age for females only
     (education=1 noweight)
   
     Revision 1.336  2022/08/31 09:52:36  brouard
     *** empty log message ***
   
     Revision 1.335  2022/08/31 08:23:16  brouard
     Summary: improvements...
   
     Revision 1.334  2022/08/25 09:08:41  brouard
     Summary: In progress for quantitative
   
     Revision 1.333  2022/08/21 09:10:30  brouard
     * src/imach.c (Module): Version 0.99r33 A lot of changes in
     reassigning covariates: my first idea was that people will always
     use the first covariate V1 into the model but in fact they are
     producing data with many covariates and can use an equation model
     with some of the covariate; it means that in a model V2+V3 instead
     of codtabm(k,Tvaraff[j]) which calculates for combination k, for
     three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
     the equation model is restricted to two variables only (V2, V3)
     and the combination for V2 should be codtabm(k,1) instead of
     (codtabm(k,2), and the code should be
     codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
     made. All of these should be simplified once a day like we did in
     hpxij() for example by using precov[nres] which is computed in
     decoderesult for each nres of each resultline. Loop should be done
     on the equation model globally by distinguishing only product with
     age (which are changing with age) and no more on type of
     covariates, single dummies, single covariates.
   
   Revision 1.332  2022/08/21 09:06:25  brouard    Revision 1.332  2022/08/21 09:06:25  brouard
   Summary: Version 0.99r33    Summary: Version 0.99r33
   
Line 1263  typedef struct { Line 1305  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="August 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";  char copyright[]="September 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1271  int erreur=0, nberr=0, nbwarn=0; /* Erro Line 1313  int erreur=0, nberr=0, nbwarn=0; /* Erro
 int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
 /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */  /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
 /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */  /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age */  int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
 int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */  int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
 int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 (dummy or quantit or time varying) */  int cptcovs=0; /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
 int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */  int cptcovsnq=0; /**< cptcovsnq number of SIMPLE covariates in the model but non quantitative V2+V1 =2 */
 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 (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */  int cptcoveff=0; /* Total number of single dummy covariates (fixed or time varying) to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */
 int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) 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 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 ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
Line 1288  int nqfveff=0; /**< nqfveff Number of Qu Line 1330  int nqfveff=0; /**< nqfveff Number of Qu
 int ntveff=0; /**< ntveff number of effective time varying variables */  int ntveff=0; /**< ntveff number of effective time varying variables */
 int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs+1 declared globally ;*/
 int nobs=10;  /* Number of observations in the data lastobs-firstobs */  int nobs=10;  /* Number of observations in the data lastobs-firstobs */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */  int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
Line 1479  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1522  int **nbcode, *Tvar; /**< model=V2 => Tv
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
 /*TnsdVar[Tvar]   1   2                              3 */   /*TnsdVar[Tvar]   1   2                              3 */ 
   /*Tvaraff[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  /*TvarsDind[nsd]  2   3                              9 */ /* position K of single dummy cova */
 /*    nsq      1                     2                 */ /* Counting single quantit tv */  /*    nsq      1                     2                 */ /* Counting single quantit tv */
 /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */  /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
 /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */  /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
Line 1505  int *TvarsQind; Line 1549  int *TvarsQind;
 #define MAXRESULTLINESPONE 10+1  #define MAXRESULTLINESPONE 10+1
 int nresult=0;  int nresult=0;
 int parameterline=0; /* # of the parameter (type) line */  int parameterline=0; /* # of the parameter (type) line */
 int TKresult[MAXRESULTLINESPONE];  int TKresult[MAXRESULTLINESPONE]; /* TKresult[nres]=k for each resultline nres give the corresponding combination of dummies */
 int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */  int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
 int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */  int modelresult[MAXRESULTLINESPONE][NCOVMAX];/* modelresult[k3]=k1: k1th position in the model corresponds to the k3 position in the resultline */
   int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
 int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */  int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
 double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */  double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
 int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */  int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
 double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */  double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
 double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
 int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */  int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
Line 2472  void powell(double p[], double **xi, int Line 2517  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
   rcurr_time = time(NULL);      rcurr_time = time(NULL);
     fp=(*fret); /* Initialisation */
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
Line 2480  void powell(double p[], double **xi, int Line 2526  void powell(double p[], double **xi, int
     /* (void) gettimeofday(&curr_time,&tzp); */      /* (void) gettimeofday(&curr_time,&tzp); */
     rcurr_time = time(NULL);        rcurr_time = time(NULL);  
     curr_time = *localtime(&rcurr_time);      curr_time = *localtime(&rcurr_time);
     printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      /* printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); */
       printf("\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*fret,fp-*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); */
     fp=(*fret); /* From former iteration or initial value */      fp=(*fret); /* From former iteration or initial value */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
Line 2784  void powell(double p[], double **xi, int Line 2832  void powell(double p[], double **xi, int
       
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
   {    {
     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij       /**< Computes the prevalence limit in each live state at age x and for covariate combination ij . Nicely done
      *   (and selected quantitative values in nres)       *   (and selected quantitative values in nres)
      *  by left multiplying the unit       *  by left multiplying the unit
      *  matrix by transitions matrix until convergence is reached with precision ftolpl        *  matrix by transitions matrix until convergence is reached with precision ftolpl 
Line 3481  double **matprod2(double **out, double * Line 3529  double **matprod2(double **out, double *
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )  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 dummies values in each resultline (loop on ij to find the corresponding combination) to over     /* Already optimized with precov.
        Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to 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.        nhstepm*hstepm matrices. 
Line 3812  double ***hbxij(double ***po, int nhstep Line 3861  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, kf=0;
   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 */
   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, quantitative time varying covariate */
   
   double bbh, survp;    double bbh, survp;
   long ipmx;  
   double agexact;    double agexact;
     double agebegin, ageend;
   /*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]);*/
Line 3844  double func( double *x) Line 3894  double func( double *x)
       */        */
       ioffset=2+nagesqr ;        ioffset=2+nagesqr ;
    /* Fixed */     /* Fixed */
       for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */        for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummu or quant or prod */
         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */          /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */          /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */          /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */          /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
         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 (TvarFind[1]=6)*/          cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */          /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
       }        }
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
Line 3864  double func( double *x) Line 3914  double func( double *x)
          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
       */        */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         /* Wave varying (but not age varying) */
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/          for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */            /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
Line 3874  double func( double *x) Line 3925  double func( double *x)
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
   
           agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
           ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){          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;
Line 3964  double func( double *x) Line 4018  double func( double *x)
           /*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 */
Line 4148  double func( double *x) Line 4202  double func( double *x)
 double funcone( double *x)  double funcone( double *x)
 {  {
   /* Same as func 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, kf=0;
   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;
Line 4171  double funcone( double *x) Line 4225  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++){
       /* Computes the values of the ncovmodel covariates of the model
          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
          to be observed in j being in i according to the model.
       */
     /* ioffset=2+nagesqr+cptcovage; */      /* ioffset=2+nagesqr+cptcovage; */
     ioffset=2+nagesqr;      ioffset=2+nagesqr;
     /* Fixed */      /* 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 fixed Dummy covariates without age* products *\/ */      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */      for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
       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)*/        cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
 /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
 /*    cov[2+6]=covar[Tvar[6]][i];  */  /*    cov[2+6]=covar[Tvar[6]][i];  */
 /*    cov[2+6]=covar[2][i]; V2  */  /*    cov[2+6]=covar[2][i]; V2  */
Line 4188  double funcone( double *x) Line 4247  double funcone( double *x)
 /*    cov[2+9]=covar[Tvar[9]][i];  */  /*    cov[2+9]=covar[Tvar[9]][i];  */
 /*    cov[2+9]=covar[1][i]; V1  */  /*    cov[2+9]=covar[1][i]; V1  */
     }      }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 
            has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
         /* We compute the contribution to Likelihood of each effective transition
            mw[mi][i] is real wave of the mi th effectve wave */
         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
            s2=s[mw[mi+1][i]][i];
            And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
            But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
            meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
         */
       /* This part may be useless now because everythin should be in covar */
     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */      /* 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?)*\/ */      /*   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?)*\/ */
     /* } */      /* } */
Line 4245  double funcone( double *x) Line 4317  double funcone( double *x)
         savm=oldm;          savm=oldm;
         oldm=newm;          oldm=newm;
       } /* end mult */        } /* end mult */
                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* 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
                                    * -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 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];
       /* if(s2==-1){ */        /* if(s2==-1){ */
Line 4277  double funcone( double *x) Line 4361  double funcone( double *x)
       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("Funcone 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],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));                  2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
    /*     printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
    /* %11.6f %11.6f %11.6f ", \ */
    /*             num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, */
    /*             2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
             /* printf(" %10.6f",-ll[k]*gipmx/gsw); */
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f\n", -llt);
           /* printf(" %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 4956  Title=%s <br>Datafile=%s Firstpass=%d La Line 5046  Title=%s <br>Datafile=%s Firstpass=%d La
   j1=0;    j1=0;
       
   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
   j=cptcoveff;  /* Only dummy covariates of the model */    j=cptcoveff;  /* Only simple dummy covariates used in the model */
   /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */    /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
Line 4977  Title=%s <br>Datafile=%s Firstpass=%d La Line 5067  Title=%s <br>Datafile=%s Firstpass=%d La
   
   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */    /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
   /* Loop on nj=1 or 2 if dummy covariates j!=0    /* Loop on nj=1 or 2 if dummy covariates j!=0
    *   Loop on j1(1 to 2**cptcovn) covariate combination     *   Loop on j1(1 to 2**cptcoveff) covariate combination
    *     freq[s1][s2][iage] =0.     *     freq[s1][s2][iage] =0.
    *     Loop on iind     *     Loop on iind
    *       ++freq[s1][s2][iage] weighted     *       ++freq[s1][s2][iage] weighted
Line 5002  Title=%s <br>Datafile=%s Firstpass=%d La Line 5092  Title=%s <br>Datafile=%s Firstpass=%d La
     if(nj==1)      if(nj==1)
       j=0;  /* First pass for the constant */        j=0;  /* First pass for the constant */
     else{      else{
       j=cptcovs; /* Other passes for the covariate values */        j=cptcoveff; /* Other passes for the covariate values number of simple covariates in the model V2+V1 =2 (simple dummy fixed or time varying) */
     }      }
     first=1;      first=1;
     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
Line 5038  Title=%s <br>Datafile=%s Firstpass=%d La Line 5128  Title=%s <br>Datafile=%s Firstpass=%d La
         bool=1;          bool=1;
         if(j !=0){          if(j !=0){
           if(anyvaryingduminmodel==0){ /* If All fixed covariates */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                 /* if(Tvaraff[z1] ==-20){ */                  /* if(Tvaraff[z1] ==-20){ */
                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                 /* }else  if(Tvaraff[z1] ==-10){ */                  /* }else  if(Tvaraff[z1] ==-10){ */
                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                 /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/                  /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
                   /* if( iind >=imx-3) printf("Searching error iind=%d Tvaraff[z1]=%d covar[Tvaraff[z1]][iind]=%.f TnsdVar[Tvaraff[z1]]=%d, cptcoveff=%d, cptcovs=%d \n",iind, Tvaraff[z1], covar[Tvaraff[z1]][iind],TnsdVar[Tvaraff[z1]],cptcoveff, cptcovs); */
                   if(Tvaraff[z1]<1 || Tvaraff[z1]>=NCOVMAX)
                     printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=1+age+%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */                    /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */                    bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
Line 5054  Title=%s <br>Datafile=%s Firstpass=%d La Line 5147  Title=%s <br>Datafile=%s Firstpass=%d La
                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                    /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                 } /* Onlyf fixed */                  } /* Onlyf fixed */
               } /* end z1 */                } /* end z1 */
             } /* cptcovn > 0 */              } /* cptcoveff > 0 */
           } /* end any */            } /* end any */
         }/* end j==0 */          }/* end j==0 */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
Line 5063  Title=%s <br>Datafile=%s Firstpass=%d La Line 5156  Title=%s <br>Datafile=%s Firstpass=%d La
             m=mw[mi][iind];              m=mw[mi][iind];
             if(j!=0){              if(j!=0){
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                 for (z1=1; z1<=cptcovn; z1++) {                  for (z1=1; z1<=cptcoveff; z1++) {
                   if( Fixed[Tmodelind[z1]]==1){                    if( Fixed[Tmodelind[z1]]==1){
                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;                      iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's                       if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's 
Line 5071  Title=%s <br>Datafile=%s Firstpass=%d La Line 5164  Title=%s <br>Datafile=%s Firstpass=%d La
                                                                                       constant and age model which counts them. */                                                                                        constant and age model which counts them. */
                       bool=0; /* not selected */                        bool=0; /* not selected */
                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */                    }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {                      /* i1=Tvaraff[z1]; */
                       /* i2=TnsdVar[i1]; */
                       /* i3=nbcode[i1][i2]; */
                       /* i4=covar[i1][iind]; */
                       /* if(i4 != i3){ */
                       if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) { /* Bug valgrind */
                       bool=0;                        bool=0;
                     }                      }
                   }                    }
Line 5132  Title=%s <br>Datafile=%s Firstpass=%d La Line 5230  Title=%s <br>Datafile=%s Firstpass=%d La
               
               
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       if(cptcovn==0 && nj==1) /* no covariate and first pass */        if(cptcoveff==0 && nj==1) /* no covariate and first pass */
         pstamp(ficresp);          pstamp(ficresp);
       if  (cptcovn>0 && j!=0){        if  (cptcoveff>0 && j!=0){
         pstamp(ficresp);          pstamp(ficresp);
         printf( "\n#********** Variable ");           printf( "\n#********** Variable "); 
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
Line 5187  Title=%s <br>Datafile=%s Firstpass=%d La Line 5285  Title=%s <br>Datafile=%s Firstpass=%d La
       /* } */        /* } */
   
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       if((cptcovn==0 && nj==1)|| nj==2 ) /* no covariate and first pass */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");          fprintf(ficresp, " Age");
       if(nj==2) for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);        if(nj==2) for (z1=1; z1<=cptcoveff; z1++) {
             printf(" V%d=%d, z1=%d, Tvaraff[z1]=%d, j1=%d, TnsdVar[Tvaraff[%d]]=%d |",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])], z1, Tvaraff[z1], j1,z1,TnsdVar[Tvaraff[z1]]);
             fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }
       for(i=1; i<=nlstate;i++) {        for(i=1; i<=nlstate;i++) {
         if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);          if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," 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(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }        }
       if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");        fprintf(ficresphtm, "\n");
               
       /* Header of frequency table by age */        /* Header of frequency table by age */
Line 5262  Title=%s <br>Datafile=%s Firstpass=%d La Line 5363  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
                   
         /* Writing ficresp */          /* Writing ficresp */
         if(cptcovn==0 && nj==1){ /* no covariate and first pass */          if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
           }            }
         }else if( nj==2){          }else if( nj==2){
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
             for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }            }
         }          }
         for(s1=1; s1 <=nlstate ; s1++){          for(s1=1; s1 <=nlstate ; s1++){
Line 5284  Title=%s <br>Datafile=%s Firstpass=%d La Line 5385  Title=%s <br>Datafile=%s Firstpass=%d La
           }            }
           if( iage <= iagemax){            if( iage <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               if(cptcovn==0 && nj==1){ /* no covariate and first pass */                if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               }else if( nj==2){                }else if( nj==2){
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
Line 5293  Title=%s <br>Datafile=%s Firstpass=%d La Line 5394  Title=%s <br>Datafile=%s Firstpass=%d La
               /*probs[iage][s1][j1]= pp[s1]/pos;*/                /*probs[iage][s1][j1]= pp[s1]/pos;*/
               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/                /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
             } else{              } else{
               if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);                if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);                fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
             }              }
           }            }
Line 5319  Title=%s <br>Datafile=%s Firstpass=%d La Line 5420  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
         fprintf(ficresphtmfr,"</tr>\n ");          fprintf(ficresphtmfr,"</tr>\n ");
         fprintf(ficresphtm,"</tr>\n");          fprintf(ficresphtm,"</tr>\n");
         if((cptcovn==0 && nj==1)|| nj==2 ) {          if((cptcoveff==0 && nj==1)|| nj==2 ) {
           if(iage <= iagemax)            if(iage <= iagemax)
             fprintf(ficresp,"\n");              fprintf(ficresp,"\n");
         }          }
Line 5346  Title=%s <br>Datafile=%s Firstpass=%d La Line 5447  Title=%s <br>Datafile=%s Firstpass=%d La
         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);          printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
         invalidvarcomb[j1]=1;          invalidvarcomb[j1]=1;
       }else{        }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced (or no resultline).</p>",j1);
         invalidvarcomb[j1]=0;          invalidvarcomb[j1]=0;
       }        }
       fprintf(ficresphtmfr,"</table>\n");        fprintf(ficresphtmfr,"</table>\n");
Line 5577  void prevalence(double ***probs, double Line 5678  void prevalence(double ***probs, double
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=0;    first=0;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of simple dummy covariates */
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
         prop[i][iage]=0.0;          prop[i][iage]=0.0;
Line 5901  void  concatwav(int wav[], int **dh, int Line 6002  void  concatwav(int wav[], int **dh, int
        nbcode[k][j]=0; /* Valgrind */         nbcode[k][j]=0; /* Valgrind */
   
    /* Loop on covariates without age and products and no quantitative variable */     /* Loop on covariates without age and products and no quantitative variable */
    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */     for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
        switch(Fixed[k]) {         switch(Fixed[k]) {
Line 5999  void  concatwav(int wav[], int **dh, int Line 6100  void  concatwav(int wav[], int **dh, int
          break;           break;
        } /* end switch */         } /* end switch */
      } /* end dummy test */       } /* end dummy test */
      if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */        if(Dummy[k]==1 && Typevar[k] !=1){ /* Quantitative covariate and not age product */ 
        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*/         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*/
            if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){
              printf("Error k=%d \n",k);
              exit(1);
            }
          if(isnan(covar[Tvar[k]][i])){           if(isnan(covar[Tvar[k]][i])){
            printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);             printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
            fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);             fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
Line 6008  void  concatwav(int wav[], int **dh, int Line 6113  void  concatwav(int wav[], int **dh, int
            exit(1);             exit(1);
          }           }
        }         }
      }       } /* end Quanti */
    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/       } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
       
    for (k=-1; k< maxncov; k++) Ndum[k]=0;      for (k=-1; k< maxncov; k++) Ndum[k]=0; 
Line 6022  void  concatwav(int wav[], int **dh, int Line 6127  void  concatwav(int wav[], int **dh, int
       
    ij=0;     ij=0;
    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */     /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */     for (k=1; k<=  cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
        /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */       /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */       if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy simple and non empty in the model */
          /* Typevar[k] =0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
          /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product*/
        /* If product not in single variable we don't print results */         /* If product not in single variable we don't print results */
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */         ++ij;/*    V5 + V4 + V3 + V4*V3 + V5*age + V2 +  V1*V2 + V1*age + V1, *//* V5 quanti, V2 quanti, V4, V3, V1 dummies */
          /* k=       1    2   3     4       5       6      7       8        9  */
          /* Tvar[k]= 5    4    3    6       5       2      7       1        1  */
          /* ij            1    2                                            3  */  
          /* Tvaraff[ij]=  4    3                                            1  */
          /* Tmodelind[ij]=2    3                                            9  */
          /* TmodelInvind[ij]=2 1                                            1  */
        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*/         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, ?, ?,} */         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 */         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 */
Line 6044  void  concatwav(int wav[], int **dh, int Line 6158  void  concatwav(int wav[], int **dh, int
    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
    /* ij--; */     /* ij--; */
    /* cptcoveff=ij; /\*Number of total covariates*\/ */     /* cptcoveff=ij; /\*Number of total covariates*\/ */
    *cptcov=ij; /* cptcov= Number of total real effective covariates: effective (used as cptcoveff in other functions)     *cptcov=ij; /* cptcov= Number of total real effective simple dummies (fixed or time  arying) effective (used as cptcoveff in other functions)
                 * because they can be excluded from the model and real                  * 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?*/                  * if in the model but excluded because missing values, but how to get k from ij?*/
    for(j=ij+1; j<= cptcovt; j++){     for(j=ij+1; j<= cptcovt; j++){
Line 6177  void  concatwav(int wav[], int **dh, int Line 6291  void  concatwav(int wav[], int **dh, int
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .       to initial status i, ei. .
   */    */
     /* Very time consuming function, but already optimized with precov */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
Line 6445  void  concatwav(int wav[], int **dh, int Line 6560  void  concatwav(int wav[], int **dh, int
    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");     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][resultmodel[nres][j]]);     /* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
      /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ /\* To be done*\/ */
      /*   fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
      /* } */
      for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */ /* To be done*/
        fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
    }     }
    for(j=1;j<=cptcoveff;j++)      /* for(j=1;j<=cptcoveff;j++)  */
      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]);     /*   fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]); */
    fprintf(ficresprobmorprev,"\n");     fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
Line 7080  To be simple, these graphs help to under Line 7200  To be simple, these graphs help to under
   
    for(nres=1;nres <=nresult; nres++){ /* For each resultline */     for(nres=1;nres <=nresult; nres++){ /* For each resultline */
    for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */     for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
      printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d \n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj);       printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs);
      if(tj != 1 && TKresult[nres]!= j1)       if(tj != 1 && TKresult[nres]!= j1)
        continue;         continue;
   
Line 7088  To be simple, these graphs help to under Line 7208  To be simple, these graphs help to under
      /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */       /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */
      /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */       /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */
      if  (cptcovn>0) {       if  (cptcovn>0) {
        fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "\n#********** Variable ");
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);  
        fprintf(ficresprob, "**********\n#\n");  
        fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "\n#********** Variable "); 
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);         fprintf(ficgp, "\n#********** Variable ");
          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
          fprintf(ficresprobcor, "\n#********** Variable ");    
   
          /* Including quantitative variables of the resultline to be done */
          for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */
            printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
            fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
            /* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
            if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline  */
              if(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */
                fprintf(ficresprob,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprobcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficgp,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(fichtmcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprobcor,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprob,"fixed ");
                fprintf(ficresprobcov,"fixed ");
                fprintf(ficgp,"fixed ");
                fprintf(fichtmcov,"fixed ");
                fprintf(ficresprobcor,"fixed ");
              }else{
                fprintf(ficresprob,"varyi ");
                fprintf(ficresprobcov,"varyi ");
                fprintf(ficgp,"varyi ");
                fprintf(fichtmcov,"varyi ");
                fprintf(ficresprobcor,"varyi ");
              }
            }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
              /* For each selected (single) quantitative value */
              fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
              if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
                fprintf(ficresprob,"fixed ");
                fprintf(ficresprobcov,"fixed ");
                fprintf(ficgp,"fixed ");
                fprintf(fichtmcov,"fixed ");
                fprintf(ficresprobcor,"fixed ");
              }else{
                fprintf(ficresprob,"varyi ");
                fprintf(ficresprobcov,"varyi ");
                fprintf(ficgp,"varyi ");
                fprintf(fichtmcov,"varyi ");
                fprintf(ficresprobcor,"varyi ");
              }
            }else{
              printf("Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
              fprintf(ficlog,"Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
              exit(1);
            }
          } /* End loop on variable of this resultline */
          /* for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); */
          fprintf(ficresprob, "**********\n#\n");
        fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficresprobcov, "**********\n#\n");
                           
        fprintf(ficgp, "\n#********** Variable ");   
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);  
        fprintf(ficgp, "**********\n#\n");         fprintf(ficgp, "**********\n#\n");
                           
                           
        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");   
        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */  
        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);  
        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                           
        fprintf(ficresprobcor, "\n#********** Variable ");      
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);  
        fprintf(ficresprobcor, "**********\n#");             fprintf(ficresprobcor, "**********\n#");    
        if(invalidvarcomb[j1]){         if(invalidvarcomb[j1]){
          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
Line 7118  To be simple, these graphs help to under Line 7276  To be simple, these graphs help to under
      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      gp=vector(1,(nlstate)*(nlstate+ndeath));       gp=vector(1,(nlstate)*(nlstate+ndeath));
      gm=vector(1,(nlstate)*(nlstate+ndeath));       gm=vector(1,(nlstate)*(nlstate+ndeath));
      for (age=bage; age<=fage; age ++){        for (age=bage; age<=fage; age ++){ /* Fo each age we feed the model equation with covariates, using precov as in hpxij() ? */
        cov[2]=age;         cov[2]=age;
        if(nagesqr==1)         if(nagesqr==1)
          cov[3]= age*age;           cov[3]= age*age;
        /* for (k=1; k<=cptcovn;k++) { */         /* New code end of combination but for each resultline */
        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */         for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */           if(Typevar[k1]==1){ /* A product with age */
          /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */             cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])];  
          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4  
                                                                     * 1  1 1 1 1  
                                                                     * 2  2 1 1 1  
                                                                     * 3  1 2 1 1  
                                                                     */  
          /* nbcode[1][1]=0 nbcode[1][2]=1;*/  
        }  
        /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */  
        /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */  
        /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */  
        for (k=1; k<=cptcovage;k++){  /* For product with age */  
          if(Dummy[Tage[k]]==2){ /* dummy with age */  
            cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2];  
            /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */  
          } else if(Dummy[Tage[k]]==3){ /* quantitative with age */  
            printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);  
            /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */  
            /* exit(1); */  
            /* cov[++k1]=Tqresult[nres][k];  */  
          }  
          /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */  
        }  
        for (k=1; k<=cptcovprod;k++){/* For product without age */  
          if(Dummy[Tvard[k][1]]==0){  
            if(Dummy[Tvard[k][2]]==0){  
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])];  
              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
            }else{ /* Should we use the mean of the quantitative variables? */  
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]];  
              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */  
            }  
          }else{           }else{
            if(Dummy[Tvard[k][2]]==0){             cov[2+nagesqr+k1]=precov[nres][k1];
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]];  
              /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */  
            }else{  
              cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]];  
              /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */  
            }  
          }           }
          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */         }/* End of loop on model equation */
        }                          /* Old code */
          /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
          /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; *\/ */
          /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
          /*        /\* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates *\/ */
          /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])]; */
          /*        /\*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*\//\* j1 1 2 3 4 */
          /*                                                                   * 1  1 1 1 1 */
          /*                                                                   * 2  2 1 1 1 */
          /*                                                                   * 3  1 2 1 1 */
          /*                                                                   *\/ */
          /*        /\* nbcode[1][1]=0 nbcode[1][2]=1;*\/ */
          /* } */
          /* /\* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
          /* /\* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] *\/ */
          /* /\*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; *\/ */
          /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
          /*        if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
          /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2]; */
          /*          /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
          /*        } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
          /*          printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); */
          /*          /\* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\\* Using the mean of quantitative variable Tvar[Tage[k]] /\\* Tqresult[nres][k]; *\\/ *\/ */
          /*          /\* exit(1); *\/ */
          /*          /\* cov[++k1]=Tqresult[nres][k];  *\/ */
          /*        } */
          /*        /\* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
          /* } */
          /* for (k=1; k<=cptcovprod;k++){/\* For product without age *\/ */
          /*        if(Dummy[Tvard[k][1]]==0){ */
          /*          if(Dummy[Tvard[k][2]]==0){ */
          /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])]; */
          /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
          /*          }else{ /\* Should we use the mean of the quantitative variables? *\/ */
          /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]]; */
          /*            /\* cov[++k1]=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(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]]; */
          /*            /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
          /*          }else{ */
          /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]]; */
          /*            /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
          /*          } */
          /*        } */
          /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
          /* } */                  
 /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/                       /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/                     
        for(theta=1; theta <=npar; theta++){         for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
Line 7420  void printinghtml(char fileresu[], char Line 7587  void printinghtml(char fileresu[], char
    jj1=0;     jj1=0;
   
    fprintf(fichtm," \n<ul>");     fprintf(fichtm," \n<ul>");
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0)k1=1; /* To be checked for no result */
      /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
      /*   if(m != 1 && TKresult[nres]!= k1) */
      /*     continue; */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");         fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
          /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
          /*        fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][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,"\">");         fprintf(fichtm,"\">");
                 
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm,"************ Results for covariates");         fprintf(fichtm,"************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][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,"************ Results for covariates"); */
          /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
          /*        fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
          /* } */
          /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
          /*        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
          /* } */
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
          continue;           continue;
Line 7454  void printinghtml(char fileresu[], char Line 7631  void printinghtml(char fileresu[], char
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
      /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
      /*   if(m != 1 && 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,"\n<p><a name=\"rescov");         fprintf(fichtm,"\n<p><a name=\"rescov");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
          /* 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,"\"</a>");         fprintf(fichtm,"\"</a>");
     
        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<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);           printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */           /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
        }         }
        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 */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);         fprintf(fichtm," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
          printf("\nCombination (%d) ignored because no cases \n",k1);            printf("\nCombination (%d) ignored because no cases \n",k1); 
Line 7520  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7695  divided by h: <sub>h</sub>P<sub>ij</sub>
      /* Period (forward stable) prevalence in each health state */       /* Period (forward stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
       fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(prevbcast==1){       if(prevbcast==1){
        /* Backward prevalence in each health state */         /* Backward prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJB_"),subdirf2(optionfilefiname,"PIJB_"));
            fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
Line 7557  with weights corresponding to observed p Line 7733  with weights corresponding to observed p
        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );         fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1=nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
    fprintf(fichtm,"\     fprintf(fichtm,"\
Line 7604  See page 'Matrix of variance-covariance Line 7780  See page 'Matrix of variance-covariance
 /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=1+age+%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);     fflush(fichtm);
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
Line 7615  See page 'Matrix of variance-covariance Line 7791  See page 'Matrix of variance-covariance
   jj1=0;    jj1=0;
   
    fprintf(fichtm," \n<ul>");     fprintf(fichtm," \n<ul>");
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
        /* if(m != 1 && TKresult[nres]!= k1) */
        /*   continue; */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");         fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][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,"\">");         fprintf(fichtm,"\">");
                 
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm,"************ Results for covariates");         fprintf(fichtm,"************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
Line 7644  See page 'Matrix of variance-covariance Line 7816  See page 'Matrix of variance-covariance
        }         }
        fprintf(fichtm,"</a></li>");         fprintf(fichtm,"</a></li>");
      } /* cptcovn >0 */       } /* cptcovn >0 */
    }     } /* End nres */
    fprintf(fichtm," \n</ul>");     fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
        /* for(k1=1; k1<=m;k1++){ */
        /* if(m != 1 && 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,"\n<p><a name=\"rescovsecond");         fprintf(fichtm,"\n<p><a name=\"rescovsecond");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][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,"\"</a>");         fprintf(fichtm,"\"</a>");
                 
        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<=cptcovs;cpt++){  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);           printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
        }         }
        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," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);         fprintf(fichtm," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
   
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
          continue;           continue;
        }         }
      }       } /* If cptcovn >0 */
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
Line 7696  true period expectancies (those weighted Line 7865  true period expectancies (those weighted
      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));       fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);       fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */  
   }/* End nres */    }/* End nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
    fflush(fichtm);     fflush(fichtm);
Line 7774  void printinggnuplot(char fileresu[], ch Line 7942  void printinggnuplot(char fileresu[], ch
   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 *\/ */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
           k1=TKresult[nres];
           if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         if(m != 1 && TKresult[nres]!= k1)          /* if(m != 1 && TKresult[nres]!= k1) */
           continue;          /*   continue; */
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the value of the covariate corresponding to k1 combination *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* 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 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           /* printf(" V%d=%d ",Tvaraff[k],vlv); */          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 *\/ */
         }          /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /* } */
           /* 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]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         }          }
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         /* printf("\n#\n"); */          /* printf("\n#\n"); */
Line 7812  void printinggnuplot(char fileresu[], ch Line 7986  void printinggnuplot(char fileresu[], ch
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
         fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);          fprintf(ficgp,"set title \"Alive state %d %s model=1+age+%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */          /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
       /* k1-1 error should be nres-1*/        /* k1-1 error should be nres-1*/
Line 7911  void printinggnuplot(char fileresu[], ch Line 8085  void printinggnuplot(char fileresu[], ch
         /* fprintf(ficgp,"\nset out ;unset label;\n"); */          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
         fprintf(ficgp,"\nset out ;unset title;\n");          fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
     } /* k1 */      /* } /\* k1 *\/ */
   } /* cpt */    } /* cpt */
   
       
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++){      /* for (k1=1; k1<= m ; k1 ++){   */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       }        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
       /* for(k=1; k <= ncovds; k++){ */        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* } */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* /\* for(k=1; k <= ncovds; k++){ *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* 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]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       }        }
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
Line 7979  void printinggnuplot(char fileresu[], ch Line 8158  void printinggnuplot(char fileresu[], ch
       } /* vpopbased */        } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */        fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
     } /* end nres */      } /* end nres */
   } /* k1 end 2 eme*/    /* } /\* k1 end 2 eme*\/ */
                   
                   
   /*3eme*/    /*3eme*/
   for (k1=1; k1<= m ; k1 ++){    /* for (k1=1; k1<= m ; k1 ++){ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
   
       for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */        for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);          fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
         }                 /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
           }
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
Line 8036  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 8220  plot [%.f:%.f] \"%s\" every :::%d::%d u
       }        }
       fprintf(ficgp,"\nunset label;\n");        fprintf(ficgp,"\nunset label;\n");
     } /* end nres */      } /* end nres */
   } /* end kl 3eme */    /* } /\* 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 covariate and each value */    /* for (k1=1; k1<=m; k1++){    /\* For each covariate and each value *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state %d : 'LIJ_' files, cov=%d state=%d", cpt, k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end nres */      } /* end nres */
   } /* end covariate k1 */      /* } /\* end covariate k1 *\/   */
   
 /* 5eme */  /* 5eme */
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */    /* for (k1=1; k1<= m ; k1++){ /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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         }          }
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        /* } /\* end covariate *\/   */
   } /* end nres */    } /* end nres */
       
 /* 6eme */  /* 6eme */
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */    /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
       continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
        /* if(m != 1 && TKresult[nres]!= k1) */
        /*  continue; */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
       strcpy(gplotlabel,"(");              strcpy(gplotlabel,"(");      
       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       }        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /* } */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
       }         } 
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
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 /* 7eme */  /* 7eme */
   if(prevbcast == 1){    if(prevbcast == 1){
     /* CV backward prevalence  for each covariate */      /* CV backward prevalence  for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */      /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
Line 8382  set ter svg size 640, 480\nunset log y\n Line 8591  set ter svg size 640, 480\nunset log y\n
   if(prevbcast==1){    if(prevbcast==1){
     /* Back projection from cross-sectional to stable (mixed) for each covariate */      /* Back projection from cross-sectional to stable (mixed) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
         continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
          /* if(m != 1 && TKresult[nres]!= k1) */
          /*       continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
Line 8457  set ter svg size 640, 480\nunset log y\n Line 8671  set ter svg size 640, 480\nunset log y\n
             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              for (k=1; k<=cptcovs; k++){    /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */                if(Dummy[modelresult[nres][k]]==0){  /* To be verified */
               lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* 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 */                  /* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                  lv=Tvresult[nres][k];
               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */                  vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               kl++;                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               kl++;                  /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
               if(k <cptcoveff && cptcoveff>1)                  /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  kl++;
                   /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
                   sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
                   kl++;
                   if(k <cptcovs && cptcovs>1)
                     sprintf(gplotcondition+strlen(gplotcondition)," && ");
                 }
             }              }
             strcpy(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 *\/ */              /* 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 *\/ */
Line 8534  set ter svg size 640, 480\nunset log y\n Line 8754  set ter svg size 640, 480\nunset log y\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,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#model=%s \n",model);      fprintf(ficgp,"#model=1+age+%s \n",model);
     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */      /* for(k1=1; k1 <=m; k1++)  /\* For each combination of covariate *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       /* k1=nres; */
         continue;        k1=TKresult[nres];
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/        /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */        for (k=1; k<=cptcovs; k++){  /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */          /* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
         lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */             TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        }
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /* if(m != 1 && TKresult[nres]!= k1) */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        continue; */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /* strcpy(gplotlabel,"("); */
       }        /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
       }         /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         /*        /\* decodtabm(1,2,4) = 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]; *\/ */
         /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," 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][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /* }       */
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
Line 8774  set ter svg size 640, 480\nunset log y\n Line 9006  set ter svg size 640, 480\nunset log y\n
       } /* end k2 */        } /* end k2 */
       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
       fprintf(ficgp,"\n set out; unset title;set key default;\n");        fprintf(ficgp,"\n set out; unset title;set key default;\n");
     } /* end k1 */      } /* end resultline */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
   fflush(ficgp);     fflush(ficgp); 
Line 9343  void prevforecast(char fileres[], double Line 9575  void prevforecast(char fileres[], double
     i1=pow(2,cptcoveff);      i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       for(k=1; k<=i1;k++){ /* We find the combination equivalent to result line values of dummies */         k=TKresult[nres];
          if(TKresult[nres]==0) k=1; /* To be checked for noresult */
        /* for(k=1; k<=i1;k++){ /\* We find the combination equivalent to result line values of dummies *\/ */
       if(i1 != 1 && TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       fprintf(ficlog,"\n#****** ");        fprintf(ficlog,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficresvpl,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }          /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */          /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        }
         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
       }         /*        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* }       */
       fprintf(ficresvpl,"******\n");        fprintf(ficresvpl,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 9400  void prevforecast(char fileres[], double Line 9636  void prevforecast(char fileres[], double
    i1=pow(2,cptcoveff);     i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}     if (cptcovn < 1){i1=1;}
         
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
      for(k=1; k<=i1;k++){       k=TKresult[nres];
        if(i1 != 1 && TKresult[nres]!= k)       if(TKresult[nres]==0) k=1; /* To be checked for noresult */
          continue;      /* for(k=1; k<=i1;k++){ */
       /*    if(i1 != 1 && TKresult[nres]!= k) */
       /*   continue; */
        fprintf(ficresvbl,"\n#****** ");         fprintf(ficresvbl,"\n#****** ");
        printf("\n#****** ");         printf("\n#****** ");
        fprintf(ficlog,"\n#****** ");         fprintf(ficlog,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {         for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */
          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);           printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);           fprintf(ficresvbl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);           fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
        }         /* for(j=1;j<=cptcoveff;j++) { */
        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */         /*        fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);         /*        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);         /*        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);         /* } */
          /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
          /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
          /*        fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
          /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
        }         }
        fprintf(ficresvbl,"******\n");         fprintf(ficresvbl,"******\n");
        printf("******\n");         printf("******\n");
Line 10246  int decoderesult( char resultline[], int Line 10488  int decoderesult( char resultline[], int
   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;    int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
   char resultsav[MAXLINE];    char resultsav[MAXLINE];
   /* int resultmodel[MAXLINE]; */    /* int resultmodel[MAXLINE]; */
   int modelresult[MAXLINE];    /* int modelresult[MAXLINE]; */
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   removefirstspace(&resultline);    removefirstspace(&resultline);
Line 10255  int decoderesult( char resultline[], int Line 10497  int decoderesult( char resultline[], int
   strcpy(resultsav,resultline);    strcpy(resultsav,resultline);
   printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);    printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */
   }    }
   if(j == 0){ /* Resultline but no = */    if(j == 0){ /* Resultline but no = */
     TKresult[nres]=0; /* Combination for the nresult and the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     return (0);      return (0);
   }    }
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);      printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
     fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);      fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
     /* return 1;*/      /* return 1;*/
   }    }
   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */    for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */
     if(nbocc(resultsav,'=') >1){      if(nbocc(resultsav,'=') >1){
       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
       /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */        /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
Line 10290  int decoderesult( char resultline[], int Line 10532  int decoderesult( char resultline[], int
   }    }
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/    /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */    for(k1=1; k1<= cptcovt ;k1++){ /* Loop on MODEL LINE V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     if(Typevar[k1]==0){ /* Single covariate in model */      if(Typevar[k1]==0){ /* Single covariate in model */
       /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */        /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
       match=0;        match=0;
       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */        for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */          if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */            modelresult[nres][k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */            match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
           break;            break;
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);          printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
         fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);          fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s\n",Tvar[k1], resultline, model);
         return 1;          return 1;
       }        }
     }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/      }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
Line 10311  int decoderesult( char resultline[], int Line 10553  int decoderesult( char resultline[], int
       match=0;        match=0;
       for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */        for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */          if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
           modelresult[k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */            modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
           resultmodel[nres][k1]=k2; /* Added here */            resultmodel[nres][k1]=k2; /* Added here */
           printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);            printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);
           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */            match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
Line 10319  int decoderesult( char resultline[], int Line 10561  int decoderesult( char resultline[], int
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);          printf("Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
         fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);          fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
       return 1;        return 1;
       }        }
     }else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/      }else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/
Line 10335  int decoderesult( char resultline[], int Line 10577  int decoderesult( char resultline[], int
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);          printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
         fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",k1,Tvardk[k1][1], resultline, model);          fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
         return 1;          return 1;
       }        }
       match=0;        match=0;
Line 10349  int decoderesult( char resultline[], int Line 10591  int decoderesult( char resultline[], int
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);          printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
         fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",k1,Tvardk[k1][2], resultline, model);          fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
         return 1;          return 1;
       }        }
     }/* End of testing */      }/* End of testing */
   }/* End loop cptcovt    }/* End loop cptcovt */
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */    /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
   for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    for(k2=1; k2 <=j;k2++){ /* j or cptcovs is the number of single covariates used either in the model line as well as in the result line (dummy or quantitative)
                              * Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     match=0;      match=0;
     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */      for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single only */        if(Typevar[k1]==0){ /* Single only */
         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */          if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
           resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */            resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             modelresult[nres][k2]=k1; /* k1th position in the model equation corresponds to k2th position in the result line. modelresult[1]=2 modelresult[2]=1  modelresult[3]=3  remodelresult[4]=6 modelresult[5]=9 */
           ++match;            ++match;
         }          }
       }        }
     }      }
     if(match == 0){      if(match == 0){
       printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);        printf("Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
       fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);        fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
       return 1;        return 1;
     }else if(match > 1){      }else if(match > 1){
       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);        printf("Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);        fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
       return 1;        return 1;
     }      }
   }    }
           /* cptcovres=j /\* Number of variables in the resultline is equal to cptcovs and thus useless *\/     */
   /* We need to deduce which combination number is chosen and save quantitative values */    /* 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 */    /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /* nres=1st result line: V4=1 V5=25.1 V3=0  V2=8 V1=1 */    /* nres=1st result line: V4=1 V5=25.1 V3=0  V2=8 V1=1 */
Line 10396  int decoderesult( char resultline[], int Line 10640  int decoderesult( char resultline[], int
   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */    /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
   /* V5*age V5 known which value for nres?  */    /* V5*age V5 known which value for nres?  */
   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */    /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop k1 on position in the model line (excluding product) */    for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* cptcovt number of covariates (excluding 1 and age or age*age) in the MODEL equation.
                                                      * loop on position k1 in the MODEL LINE */
     /* k counting number of combination of single dummies in the equation model */      /* k counting number of combination of single dummies in the equation model */
     /* k4 counting single dummies in the equation model */      /* k4 counting single dummies in the equation model */
     /* k4q counting single quantitatives in the equation model */      /* k4q counting single quantitatives in the equation model */
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */
        /* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */         /* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
       /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/        /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
       /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */        /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
       /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */        /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */
Line 10409  int decoderesult( char resultline[], int Line 10654  int decoderesult( char resultline[], int
       /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */        /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */
       /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */        /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */
       /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */        /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
       /* Tvresult[nres][result_position]= id of the dummy variable at the result_position in the nres resultline                     */        /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline                     */
       /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */        /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */
       /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */        /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
       k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */        k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
       /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/        /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
       k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/        k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
       k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */        k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Stores the value into the name of the variable. */        TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
       /* Tinvresult[nres][4]=1 */        /* Tinvresult[nres][4]=1 */
       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */        /* Tresult[nres][k4+1]=Tvalsel[k3];/\* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) *\/ */
       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */        Tresult[nres][k3]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
         /* Tvresult[nres][k4+1]=(int)Tvarsel[k3];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
         Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */        Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
       precov[nres][k1]=Tvalsel[k3];        precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
       printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);        printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);
       k4++;;        k4++;;
     }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
Line 10431  int decoderesult( char resultline[], int Line 10678  int decoderesult( char resultline[], int
       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
       k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */        k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
       /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        /* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 *\/ */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        /* Tvresult[nres][k4q+1]=(int)Tvarsel[k3q];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
         /* Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /\* Tvqresult[nres][1]=5 *\/ */
         Tqresult[nres][k3q]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvresult[nres][k3q]=(int)Tvarsel[k3q];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tvqresult[nres][k3q]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
       precov[nres][k1]=Tvalsel[k3q];        precov[nres][k1]=Tvalsel[k3q];
Line 10444  int decoderesult( char resultline[], int Line 10695  int decoderesult( char resultline[], int
               
       k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/        k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
       k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/        k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */        TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
       precov[nres][k1]=Tvalsel[k3];        precov[nres][k1]=Tvalsel[k3];
       printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);        printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);
     }else if( Dummy[k1]==3 ){ /* For quant with age product */      }else if( Dummy[k1]==3 ){ /* For quant with age product */
       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
       precov[nres][k1]=Tvalsel[k3q];        precov[nres][k1]=Tvalsel[k3q];
       printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);        printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
     }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */      }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
       precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];              precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
       printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);        printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);
Line 10462  int decoderesult( char resultline[], int Line 10713  int decoderesult( char resultline[], int
     }      }
   }    }
       
   TKresult[nres]=++k; /* Combination for the nresult and the model */    TKresult[nres]=++k; /* Number of combinations of dummies for the nresult and the model =Tvalsel[k3]*pow(2,k4) + 1*/
   return (0);    return (0);
 }  }
   
Line 10498  int decodemodel( char model[], int lasto Line 10749  int decodemodel( char model[], int lasto
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' model=%s ",model);        printf("Error. 'v' must be in upper case 'V' model=1+age+%s ",model);
       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. 'v' must be in upper case model=1+age+%s ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=1+age+%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;          return 1;
Line 10622  int decodemodel( char model[], int lasto Line 10873  int decodemodel( char model[], int lasto
             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
                                                 thus after V4 we invent V5 and V6 because age*V3 will be computed in 4                                                  thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
                                                 Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */                                                  Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
               /* Please remark that the new variables are model dependent */
               /* If we have 4 variable but the model uses only 3, like in
                * model= V1 + age*V1 + V2 + V3 + age*V2 + age*V3 + V1*V2 + V1*V3
                *  k=     1     2       3   4     5        6        7       8
                * Tvar[k]=1     1       2   3     2        3       (5       6) (and not 4 5 because of V4 missing)
                * Tage[kk]    [1]= 2           [2]=5      [3]=6                  kk=1 to cptcovage=3
                * Tvar[Tage[kk]][1]=2          [2]=2      [3]=3
                */
             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  */
Line 10727  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10986  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
       modell[k].subtype= FQ;        modell[k].subtype= FQ;
       nsq++;        nsq++;
       TvarsQ[nsq]=Tvar[k];        TvarsQ[nsq]=Tvar[k]; /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary see below */
       TvarsQind[nsq]=k;        TvarsQind[nsq]=k;    /* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
       ncovf++;        ncovf++;
       TvarF[ncovf]=Tvar[k];        TvarF[ncovf]=Tvar[k];
       TvarFind[ncovf]=k;        TvarFind[ncovf]=k;
Line 10759  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11018  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].subtype= VQ;        modell[k].subtype= VQ;
       ncovv++; /* Only simple time varying variables */        ncovv++; /* Only simple time varying variables */
       nsq++;        nsq++;
       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */        TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */ /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary here) */
       TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate */        TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate *//* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
       TvarV[ncovv]=Tvar[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 */        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 */        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 */
Line 10950  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11209  Dummy[k] 0=dummy (0 1), 1 quantitative (
       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){        if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
           if(Tvar[k1]==Tvar[k2]){            if(Tvar[k1]==Tvar[k2]){
             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);              printf("Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);              fprintf(ficlog,"Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
             return(1);              return(1);
           }            }
         }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
           k3=Tposprod[k1];            k3=Tposprod[k1];
           k4=Tposprod[k2];            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])) ){            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]]);              printf("Error duplication in the model=1+age+%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);              fprintf(ficlog,"Error duplication in the model=1+age+%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);              return(1);
           }            }
         }          }
Line 11315  int prevalence_limit(double *p, double * Line 11574  int prevalence_limit(double *p, double *
   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */    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 each combination k of dummy covariates in the model */    /* for(k=1; k<=i1;k++){ /\* For each combination k of dummy covariates in the model *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(i1 != 1 && TKresult[nres]!= k)        k=TKresult[nres];
         continue;        if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         /* if(i1 != 1 && TKresult[nres]!= k) /\* We found the combination k corresponding to the resultline value of dummies *\/ */
         /*        continue; */
   
       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
Line 11329  int prevalence_limit(double *p, double * Line 11590  int prevalence_limit(double *p, double *
       fprintf(ficrespl,"#******");        fprintf(ficrespl,"#******");
       printf("#******");        printf("#******");
       fprintf(ficlog,"#******");        fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */        for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
         /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */          /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* Here problem for varying dummy*/          /* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          /* fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficrespl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        }
         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       }        /*        fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /* } */
       fprintf(ficrespl,"******\n");        fprintf(ficrespl,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 11351  int prevalence_limit(double *p, double * Line 11614  int prevalence_limit(double *p, double *
       }        }
   
       fprintf(ficrespl,"#Age ");        fprintf(ficrespl,"#Age ");
       for(j=1;j<=cptcoveff;j++) {        /* for(j=1;j<=cptcoveff;j++) { */
         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);        /*        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         /* } */
         for(j=1;j<=cptcovs;j++) { /* New the quanti variable is added */
           fprintf(ficrespl,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
       fprintf(ficrespl,"Total Years_to_converge\n");        fprintf(ficrespl,"Total Years_to_converge\n");
           
       for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);          /**< Computes the prevalence limit in each live state at age x and for covariate combination (k and) nres */
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); /* Nicely done */
         fprintf(ficrespl,"%.0f ",age );          fprintf(ficrespl,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          /* for(j=1;j<=cptcoveff;j++) */
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          /*   fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           for(j=1;j<=cptcovs;j++)
             fprintf(ficrespl,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         tot=0.;          tot=0.;
         for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
           tot +=  prlim[i][i];            tot +=  prlim[i][i];
Line 11371  int prevalence_limit(double *p, double * Line 11640  int prevalence_limit(double *p, double *
         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);          fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
       } /* Age */        } /* Age */
       /* was end of cptcod */        /* was end of cptcod */
     } /* cptcov */      } /* nres */
   } /* nres */    /* } /\* for each combination *\/ */
   return 0;    return 0;
 }  }
   
Line 11414  int back_prevalence_limit(double *p, dou Line 11683  int back_prevalence_limit(double *p, dou
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
      if(i1 != 1 && TKresult[nres]!= k)        k=TKresult[nres];
         continue;        if(TKresult[nres]==0) k=1; /* To be checked for noresult */
      /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/       /* if(i1 != 1 && TKresult[nres]!= k) */
        /*         continue; */
        /* /\*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*\/ */
       fprintf(ficresplb,"#******");        fprintf(ficresplb,"#******");
       printf("#******");        printf("#******");
       fprintf(ficlog,"#******");        fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */        for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficresplb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        /* for(j=1;j<=cptcoveff ;j++) {/\* all covariates *\/ */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        /*        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        /*        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        /*        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        /* } */
         /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* } */
       fprintf(ficresplb,"******\n");        fprintf(ficresplb,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 11442  int back_prevalence_limit(double *p, dou Line 11718  int back_prevalence_limit(double *p, dou
       }        }
           
       fprintf(ficresplb,"#Age ");        fprintf(ficresplb,"#Age ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++) {
         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficresplb,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
       fprintf(ficresplb,"Total Years_to_converge\n");        fprintf(ficresplb,"Total Years_to_converge\n");
Line 11466  int back_prevalence_limit(double *p, dou Line 11742  int back_prevalence_limit(double *p, dou
           /* exit(1); */            /* exit(1); */
         }          }
         fprintf(ficresplb,"%.0f ",age );          fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcovs;j++)
           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);            fprintf(ficresplb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         tot=0.;          tot=0.;
         for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
           tot +=  bprlim[i][i];            tot +=  bprlim[i][i];
Line 11477  int back_prevalence_limit(double *p, dou Line 11753  int back_prevalence_limit(double *p, dou
       } /* Age */        } /* Age */
       /* was end of cptcod */        /* was end of cptcod */
       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */        /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
     } /* end of any combination */      /* } /\* end of any combination *\/ */
   } /* end of nres */      } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
   /* fclose(ficrespijb); */    /* fclose(ficrespijb); */
Line 11487  int back_prevalence_limit(double *p, dou Line 11763  int back_prevalence_limit(double *p, dou
     
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /* to be optimized with precov */
   int stepsize;    int stepsize;
   int agelim;    int agelim;
   int hstepm;    int hstepm;
Line 11497  int hPijx(double *p, int bage, int fage) Line 11773  int hPijx(double *p, int bage, int fage)
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
   
     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);    strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {    if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;      printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;      fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
     }    }
     printf("Computing pij: result on file '%s' \n", filerespij);    printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
       
     stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
     
     agelim=AGESUP;    agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                     
     /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);    pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");    fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);    i1= pow(2,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(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){      k=TKresult[nres];
       if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         continue;      /* for(k=1; k<=i1;k++){ */
       fprintf(ficrespij,"\n#****** ");      /* if(i1 != 1 && TKresult[nres]!= k) */
       for(j=1;j<=cptcoveff;j++)       /*  continue; */
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);      fprintf(ficrespij,"\n#****** ");
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      for(j=1;j<=cptcovs;j++){
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
       fprintf(ficrespij,"******\n");        /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
               /*        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      }
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       fprintf(ficrespij,"******\n");
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
               for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                 nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
         oldm=oldms;savm=savms;        /*          nhstepm=nhstepm*YEARM; aff par mois*/
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);          
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespij," %1d-%1d",i,j);
         fprintf(ficrespij,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespij,"%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(ficrespij," %1d-%1d",i,j);              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
         fprintf(ficrespij,"\n");  
         for (h=0; h<=nhstepm; h++){  
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/  
           fprintf(ficrespij,"%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(ficrespij," %.5f", p3mat[i][j][h]);  
           fprintf(ficrespij,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespij,"\n");          fprintf(ficrespij,"\n");
       }        }
       /*}*/        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"\n");
     }      }
     return 0;    }
     /*}*/
     return 0;
 }  }
     
  int hBijx(double *p, int bage, int fage, double ***prevacurrent){   int hBijx(double *p, int bage, int fage, double ***prevacurrent){
     /*------------- h Bij x at various ages ------------*/      /*------------- h Bij x at various ages ------------*/
       /* To be optimized with precov */
   int stepsize;    int stepsize;
   /* int agelim; */    /* int agelim; */
         int ageminl;          int ageminl;
Line 11599  int hPijx(double *p, int bage, int fage) Line 11878  int hPijx(double *p, int bage, int fage)
   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      k=TKresult[nres];
       if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         continue;      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
       fprintf(ficrespijb,"\n#****** ");      /*    if(i1 != 1 && TKresult[nres]!= k) */
       for(j=1;j<=cptcoveff;j++)      /*  continue; */
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);      fprintf(ficrespijb,"\n#****** ");
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */      for(j=1;j<=cptcovs;j++){
         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        fprintf(ficrespijb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        /* for(j=1;j<=cptcoveff;j++) */
       fprintf(ficrespijb,"******\n");        /*        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       if(invalidvarcomb[k]){  /* Is it necessary here? */        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);         /*        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         continue;      }
       }      fprintf(ficrespijb,"******\n");
             if(invalidvarcomb[k]){  /* Is it necessary here? */
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        continue;
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */      }
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */      
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/      /* 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) */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
                 nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */        nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
         /* and memory limitations if stepm is small */        
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         /* oldm=oldms;savm=savms; */        
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */        /* and memory limitations if stepm is small */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */        
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");        /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           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," %1d-%1d",i,j);              fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
         fprintf(ficrespijb,"\n");  
         for (h=0; h<=nhstepm; h++){  
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/  
           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]);/* Bug valgrind */  
           fprintf(ficrespijb,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       } /* end age deb */        }
     } /* end combination */        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       } /* end age deb */
       /* } /\* end combination *\/ */
   } /* end nres */    } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
Line 11703  int main(int argc, char *argv[]) Line 11986  int main(int argc, char *argv[])
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/    /* int firstobs=1, lastobs=10; /\* nobs = lastobs-firstobs declared globally ;*\/ */
   int c,  h , cpt, c2;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 12042  int main(int argc, char *argv[]) Line 12325  int main(int argc, char *argv[])
         strcpy(model,modeltemp);           strcpy(model,modeltemp); 
       }        }
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=1+age+%s\n",model, modeltemp, model);fflush(stdout); */
     printf("model=1+age+%s\n",model);fflush(stdout);      printf("model=1+age+%s\n",model);fflush(stdout);
     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);      fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);      fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
Line 12326  Please run with mle=-1 to get a correct Line 12609  Please run with mle=-1 to get a correct
   mint=matrix(1,maxwav,firstobs,lastobs);    mint=matrix(1,maxwav,firstobs,lastobs);
   anint=matrix(1,maxwav,firstobs,lastobs);    anint=matrix(1,maxwav,firstobs,lastobs);
   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */    s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
   printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));    /* printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel)); */
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
Line 12346  Please run with mle=-1 to get a correct Line 12629  Please run with mle=-1 to get a correct
   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
   TvarsDind=ivector(1,NCOVMAX); /*  */    TvarsDind=ivector(1,NCOVMAX); /*  */
   TnsdVar=ivector(1,NCOVMAX); /*  */    TnsdVar=ivector(1,NCOVMAX); /*  */
       /* for(i=1; i<=NCOVMAX;i++) TnsdVar[i]=3; */
   TvarsD=ivector(1,NCOVMAX); /*  */    TvarsD=ivector(1,NCOVMAX); /*  */
   TvarsQind=ivector(1,NCOVMAX); /*  */    TvarsQind=ivector(1,NCOVMAX); /*  */
   TvarsQ=ivector(1,NCOVMAX); /*  */    TvarsQ=ivector(1,NCOVMAX); /*  */
Line 12468  Please run with mle=-1 to get a correct Line 12752  Please run with mle=-1 to get a correct
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   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]; as well as calculate cptcoveff or number of total effective dummy covariates*/
   }    }
       
   ncovcombmax=pow(2,cptcoveff);    ncovcombmax=pow(2,cptcoveff);
   invalidvarcomb=ivector(1, ncovcombmax);     invalidvarcomb=ivector(0, ncovcombmax); 
   for(i=1;i<ncovcombmax;i++)    for(i=0;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
Line 12607  Title=%s <br>Datafile=%s Firstpass=%d La Line 12891  Title=%s <br>Datafile=%s Firstpass=%d La
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \    fprintf(fichtm,"<html><head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n\
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <title>IMaCh %s</title></head>\n\
    <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n\
   <font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>\
   -EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 \
   (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - \
   <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \n", optionfilehtm);
     
     fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\
 <font size=\"2\">IMaCh-%s <br> %s</font> \  <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\  This file: <a href=\"%s\">%s</a></br>Title=%s <br>Datafile=<a href=\"%s\">%s</a> Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
Line 12620  Title=%s <br>Datafile=%s Firstpass=%d La Line 12911  Title=%s <br>Datafile=%s Firstpass=%d La
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\   - Date and time at start: %s</ul>\n",\
           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\            version,fullversion,optionfilehtm,optionfilehtm,title,datafile,datafile,firstpass,lastpass,stepm, weightopt, model, \
           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\            optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
           fileres,fileres,\            fileres,fileres,\
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
Line 12934  Please run with mle=-1 to get a correct Line 13225  Please run with mle=-1 to get a correct
     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */      globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
             /* exit(0); */
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
Line 13612  Please run with mle=-1 to get a correct Line 13904  Please run with mle=-1 to get a correct
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
       }        }
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);          printf(" V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */
         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);          fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
       printf("******\n");        printf("******\n");
Line 13631  Please run with mle=-1 to get a correct Line 13923  Please run with mle=-1 to get a correct
   
                                   
     /*---------- State-specific expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                       /* Should be moved in a function */         
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
     strcat(filerest,fileresu);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
Line 13670  Please run with mle=-1 to get a correct Line 13962  Please run with mle=-1 to get a correct
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
     if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline, find the combination and output results according to the values of dummies and then quanti.  */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying. For each nres and each value at position k
       if(i1 != 1 && TKresult[nres]!= k)                            * we know Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline
                             * Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline 
                             * and Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
         /* */
         if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */
         continue;          continue;
       printf("\n# model %s \n#****** Result for:", model);        printf("\n# model %s \n#****** Result for:", model);
       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);        fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);        fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
       for(j=1;j<=cptcoveff;j++){         /* It might not be a good idea to mix dummies and quantitative */
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);        /* for(j=1;j<=cptcoveff;j++){ /\* j=resultpos. Could be a loop on cptcovs: number of single dummy covariate in the result line as well as in the model *\/ */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);        for(j=1;j<=cptcovs;j++){ /* j=resultpos. Could be a loop on cptcovs: number of single covariate (dummy or quantitative) in the result line as well as in the model */
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* Output by variables in the resultline *\/ */
       }          /* Tvaraff[j] is the name of the dummy variable in position j in the equation model:
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */           * Tvaraff[1]@9={4, 3, 0, 0, 0, 0, 0, 0, 0}, in model=V5+V4+V3+V4*V3+V5*age
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);           * (V5 is quanti) V4 and V3 are dummies
         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);           * TnsdVar[4] is the position 1 and TnsdVar[3]=2 in codtabm(k,l)(V4  V3)=V4  V3
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);           *                                                              l=1 l=2
       }            *                                                           k=1  1   1   0   0
            *                                                           k=2  2   1   1   0
            *                                                           k=3 [1] [2]  0   1
            *                                                           k=4  2   2   1   1
            * If nres=1 result: V3=1 V4=0 then k=3 and outputs
            * If nres=2 result: V4=1 V3=0 then k=2 and outputs
            * nres=1 =>k=3 j=1 V4= nbcode[4][codtabm(3,1)=1)=0; j=2  V3= nbcode[3][codtabm(3,2)=2]=1
            * nres=2 =>k=2 j=1 V4= nbcode[4][codtabm(2,1)=2)=1; j=2  V3= nbcode[3][codtabm(2,2)=1]=0
            */
           /* Tvresult[nres][j] Name of the variable at position j in this resultline */
           /* Tresult[nres][j] Value of this variable at position j could be a float if quantitative  */
   /* We give up with the combinations!! */
           printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]);  /* end if dummy  or quanti */
   
           if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline  */
             printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
               printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
             }else{
               printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
             }
             /* fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
             /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           }else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
             /* For each selected (single) quantitative value */
             printf(" V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             fprintf(ficrest," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
               printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
             }else{
               printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
             }
           }else{
             printf("Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
             fprintf(ficlog,"Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
             exit(1);
           }
         } /* End loop for each variable in the resultline */
         /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /\* Wrong j is not in the equation model *\/ */
         /*        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* }       */
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
       printf("******\n");        printf("******\n");
               
       fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
       fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
         /* It could have been: for(j=1;j<=cptcoveff;j++) {printf("V=%d=%lg",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);} */
         /* But it won't be sorted and depends on how the resultline is ordered */
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          /* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }          /* fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        }
         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation  */
         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);          fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
           fprintf(ficrescveij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
       }         } 
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
Line 13707  Please run with mle=-1 to get a correct Line 14051  Please run with mle=-1 to get a correct
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       /* pstamp(ficresvij); */        /* 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,TnsdVar[TnsdVar[Tvaraff[j]]])]);          fprintf(ficresvij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
           /* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */          /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */          fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
       }         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
Line 13741  Please run with mle=-1 to get a correct Line 14086  Please run with mle=-1 to get a correct
           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 forward period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# Age popbased mobilav e.. (std) "); /* Adding covariate values? */
         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"); */
Line 13788  Please run with mle=-1 to get a correct Line 14133  Please run with mle=-1 to get a correct
       printf("done selection\n");fflush(stdout);        printf("done selection\n");fflush(stdout);
       fprintf(ficlog,"done selection\n");fflush(ficlog);        fprintf(ficlog,"done selection\n");fflush(ficlog);
               
     } /* End k selection */      } /* End k selection or end covariate selection for nres */
   
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /* variance-covariance of forward period prevalence*/      /* variance-covariance of forward period prevalence */
     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);      varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
           
Line 13867  Please run with mle=-1 to get a correct Line 14212  Please run with mle=-1 to get a correct
   free_ivector(Tposprod,1,NCOVMAX);    free_ivector(Tposprod,1,NCOVMAX);
   free_ivector(Tprod,1,NCOVMAX);    free_ivector(Tprod,1,NCOVMAX);
   free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(Tvaraff,1,NCOVMAX);
   free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(invalidvarcomb,0,ncovcombmax);
   free_ivector(Tage,1,NCOVMAX);    free_ivector(Tage,1,NCOVMAX);
   free_ivector(Tmodelind,1,NCOVMAX);    free_ivector(Tmodelind,1,NCOVMAX);
   free_ivector(TmodelInvind,1,NCOVMAX);    free_ivector(TmodelInvind,1,NCOVMAX);
Removed from v.1.332  
changed lines
  Added in v.1.338

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