Diff for /imach/src/imach.c between versions 1.326 and 1.337

version 1.326, 2022/07/26 17:33:55 version 1.337, 2022/09/02 14:26:02
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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
     Summary: Version 0.99r33
   
     * 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 1.331  2022/08/07 05:40:09  brouard
     *** empty log message ***
   
     Revision 1.330  2022/08/06 07:18:25  brouard
     Summary: last 0.99r31
   
     *  imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function
   
     Revision 1.329  2022/08/03 17:29:54  brouard
     *  imach.c (Module): Many errors in graphs fixed with Vn*age covariates.
   
     Revision 1.328  2022/07/27 17:40:48  brouard
     Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage
   
     Revision 1.327  2022/07/27 14:47:35  brouard
     Summary: Still a problem for one-step probabilities in case of quantitative variables
   
   Revision 1.326  2022/07/26 17:33:55  brouard    Revision 1.326  2022/07/26 17:33:55  brouard
   Summary: some test with nres=1    Summary: some test with nres=1
   
Line 1186  typedef struct { Line 1259  typedef struct {
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 132  #define FILENAMELENGTH 256
   
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
Line 1225  typedef struct { Line 1298  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="July 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];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 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=V2+V1+ V3*age+V2*V4 */  /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
 int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */  /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */  int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
 int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */  int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
 int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */  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 cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of 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 1249  int nqfveff=0; /**< nqfveff Number of Qu Line 1323  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 1388  int *ncodemaxwundef;  /* ncodemax[j]= Nu Line 1463  int *ncodemaxwundef;  /* ncodemax[j]= Nu
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs; /* Global pointer */  double **pmmij, ***probs; /* Global pointer */
 double ***mobaverage, ***mobaverages; /* New global variable */  double ***mobaverage, ***mobaverages; /* New global variable */
   double **precov; /* New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up)  */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   double anprojd, mprojd, jprojd; /* For eventual projections */    double anprojd, mprojd, jprojd; /* For eventual projections */
Line 1412  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1488  int **nbcode, *Tvar; /**< model=V2 => Tv
        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12          *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 
        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv         *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
        *                                                             ntv=3     nqtv=1         *                                                             ntv=3     nqtv=1
        *  cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11         *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
        * For time varying covariate, quanti or dummies         * For time varying covariate, quanti or dummies
        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti         *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
        *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti         *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1         *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1         *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
        *       covar[k,i], value of kth fixed covariate dummy or quanti :         *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
        *   k=  1    2      3       4     5       6      7        8   9     10       11          *   k=  1    2      3       4     5       6      7        8   9     10       11 
Line 1438  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1514  int **nbcode, *Tvar; /**< model=V2 => Tv
                                                          /* with age product, 3 quant with age product*/                                                           /* with age product, 3 quant with age product*/
 /*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 */ 
   /*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[k]    2   3                              9 */ /* position K of single dummy cova */
 /*    nsq      1                     2                 */ /* Counting single quantit tv */  /*    nsq      1                     2                 */ /* Counting single quantit tv */
Line 1447  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1525  int **nbcode, *Tvar; /**< model=V2 => Tv
 /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */  /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
 /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */  /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */
 /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */  /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */
   /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
 /* TvarF 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 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)  */
 /* Type                    */  /* Type                    */
Line 1455  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1534  int **nbcode, *Tvar; /**< model=V2 => Tv
 /*           D  Q  D  D  Q */  /*           D  Q  D  D  Q */
 /*                         */  /*                         */
 int *TvarsD;  int *TvarsD;
   int *TnsdVar;
 int *TvarsDind;  int *TvarsDind;
 int *TvarsQ;  int *TvarsQ;
 int *TvarsQind;  int *TvarsQind;
Line 1462  int *TvarsQind; Line 1542  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 Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */  int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
 int Tinvresult[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 Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */  int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
 double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  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 */
   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 Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
 int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */  int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
   
 /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1  /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
   # States 1=Coresidence, 2 Living alone, 3 Institution    # States 1=Coresidence, 2 Living alone, 3 Institution
Line 1505  int *TmodelInvQind; /** Tmodelqind[1]=1 Line 1588  int *TmodelInvQind; /** Tmodelqind[1]=1
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard;  int **Tvard;
   int **Tvardk;
 int *Tprod;/**< Gives the k position of the k1 product */  int *Tprod;/**< Gives the k position of the k1 product */
 /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */  /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
 int *Tposprod; /**< Gives the k1 product from the k position */  int *Tposprod; /**< Gives the k1 product from the k position */
Line 2434  void powell(double p[], double **xi, int Line 2518  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 2763  void powell(double p[], double **xi, int Line 2849  void powell(double p[], double **xi, int
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
           
   int i, ii,j,k;      int i, ii,j,k, k1;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
Line 2794  void powell(double p[], double **xi, int Line 2880  void powell(double p[], double **xi, int
      if(nagesqr==1){       if(nagesqr==1){
       cov[3]= agefin*agefin;        cov[3]= agefin*agefin;
      }       }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
       /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */         if(Typevar[k1]==1){ /* A product with age */
       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
     }         }else{
     for (k=1; k<=nsq;k++) { /* For single varying covariates only */           cov[2+nagesqr+k1]=precov[nres][k1];
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */         }
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];       }/* End of loop on model equation */
       /* cov[++k1]=Tqresult[nres][k];  */       
       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  /* Start of old code (replaced by a loop on position in the model equation */
     }      /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model *\/ */
     for (k=1; k<=cptcovage;k++){  /* For product with age */      /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
       if(Dummy[Tage[k]]==2){ /* dummy with age */      /*   /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; *\/ */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];      /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
         /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */      /*   /\* model = 1 +age + V1*V3 + age*V1 + V2 + V1 + age*V2 + V3 + V3*age + V1*V2  */
       } else if(Dummy[Tage[k]]==3){ /* quantitative with age */      /*    * k                  1        2      3    4      5      6     7        8 */
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];      /*    *cov[]   1    2      3        4      5    6      7      8     9       10 */
         /* cov[++k1]=Tqresult[nres][k];  */      /*    *TypeVar[k]          2        1      0    0      1      0     1        2 */
       }      /*    *Dummy[k]            0        2      0    0      2      0     2        0 */
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */      /*    *Tvar[k]             4        1      2    1      2      3     3        5 */
     }      /*    *nsd=3                              (1)  (2)           (3) */
     for (k=1; k<=cptcovprod;k++){ /* For product without age */      /*    *TvarsD[nsd]                      [1]=2    1             3 */
       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */      /*    *TnsdVar                          [2]=2 [1]=1         [3]=3 */
       if(Dummy[Tvard[k][1]==0]){      /*    *TvarsDind[nsd](=k)               [1]=3 [2]=4         [3]=6 */
         if(Dummy[Tvard[k][2]==0]){      /*    *Tage[]                  [1]=1                  [2]=2      [3]=3 */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];      /*    *Tvard[]       [1][1]=1                                           [2][1]=1 */
           /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */      /*    *                   [1][2]=3                                           [2][2]=2 */
         }else{      /*    *Tprod[](=k)     [1]=1                                              [2]=8 */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];      /*    *TvarsDp(=Tvar)   [1]=1            [2]=2             [3]=3          [4]=5 */
           /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */      /*    *TvarD (=k)       [1]=1            [2]=3 [3]=4       [3]=6          [4]=6 */
         }      /*    *TvarsDpType */
       }else{      /*    *si model= 1 + age + V3 + V2*age + V2 + V3*age */
         if(Dummy[Tvard[k][2]==0]){      /*    * nsd=1              (1)           (2) */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];      /*    *TvarsD[nsd]          3             2 */
           /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */      /*    *TnsdVar           (3)=1          (2)=2 */
         }else{      /*    *TvarsDind[nsd](=k)  [1]=1        [2]=3 */
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];      /*    *Tage[]                  [1]=2           [2]= 3    */
           /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */      /*    *\/ */
         }      /*   /\* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; *\/ */
       }      /*   /\* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
     }      /* } */
       /* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model *\/ */
       /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
       /*   /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 *\/ */
       /*   /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
       /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
       /*   /\* cov[++k1]=Tqresult[nres][k];  *\/ */
       /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
       /*   if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,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 *\/ */
       /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
       /*  /\* cov[++k1]=Tqresult[nres][k];  *\/ */
       /*   } */
       /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
       /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
       /*   if(Dummy[Tvard[k][1]]==0){ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
       /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[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(ij,Tvard[k][2])] * Tqinvresult[nres][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][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
       /*    /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
       /*  } */
       /*   } */
       /* } /\* End product without age *\/ */
   /* ENd of old code */
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
Line 2927  void powell(double p[], double **xi, int Line 3052  void powell(double p[], double **xi, int
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k, k1;
   int first=0;    int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
Line 2967  void powell(double p[], double **xi, int Line 3092  void powell(double p[], double **xi, int
     if(nagesqr==1){      if(nagesqr==1){
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     }      }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */      for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */        if(Typevar[k1]==1){ /* A product with age */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
       /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */  
     }  
     /* for (k=1; k<=cptcovn;k++) { */  
     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */  
     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */  
     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */  
     /* } */  
     for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];   
       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
     }  
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */  
     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */  
     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */  
     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
     for (k=1; k<=cptcovage;k++){  /* For product with age */  
       /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/  
       if(Dummy[Tage[k]]== 2){ /* dummy with age */  
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
       } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  
       }  
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
     }  
     for (k=1; k<=cptcovprod;k++){ /* For product without age */  
       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */  
       if(Dummy[Tvard[k][1]==0]){  
         if(Dummy[Tvard[k][2]==0]){  
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
         }else{  
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
         }  
       }else{        }else{
         if(Dummy[Tvard[k][2]==0]){          cov[2+nagesqr+k1]=precov[nres][k1];
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
         }else{  
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
         }  
       }        }
     }      }/* End of loop on model equation */
   
   /* Old code */ 
   
       /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
       /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
       /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; */
       /*   /\* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
       /* } */
       /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
       /* /\*   /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
       /* /\*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
       /* /\*   /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\\/ *\/ */
       /* /\* } *\/ */
       /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
       /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
       /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
       /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* /\* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; *\/ */
       /* /\* for (k=1; k<=cptcovprod;k++) /\\* Useless *\\/ *\/ */
       /* /\*   /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\\/ *\/ */
       /* /\*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
       /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
       /*   /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ ERROR ???*\/ */
       /*   if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       /*   } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
       /*   } */
       /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
       /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
       /*   if(Dummy[Tvard[k][1]]==0){ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
       /*  } */
       /*   }else{ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
       /*  } */
       /*   } */
       /* } */
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 3121  double **pmij(double **ps, double *cov, Line 3256  double **pmij(double **ps, double *cov,
         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }        }
       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
     }      }
     for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
Line 3130  double **pmij(double **ps, double *cov, Line 3265  double **pmij(double **ps, double *cov,
         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       }        }
       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
     }      }
   }    }
       
Line 3137  double **pmij(double **ps, double *cov, Line 3273  double **pmij(double **ps, double *cov,
     s1=0;      s1=0;
     for(j=1; j<i; j++){      for(j=1; j<i; j++){
       s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /* printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     }      }
     for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
       s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /* printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     }      }
     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
Line 3385  double **matprod2(double **out, double * Line 3521  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 combination of covariate values corresponding to ij 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 3397  double ***hpxij(double ***po, int nhstep Line 3534  double ***hpxij(double ***po, int nhstep
   
      */       */
   
   int i, j, d, h, k;    int i, j, d, h, k, k1;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   double agexact;    double agexact;
Line 3420  double ***hpxij(double ***po, int nhstep Line 3557  double ***hpxij(double ***po, int nhstep
       if(nagesqr==1){        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       }        }
       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */        /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */        /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
         /* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 */        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */          if(Typevar[k1]==1){ /* A product with age */
 /*    k        1  2   3   4     5    6    7     8    9 */            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];  
         /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */  
       }  
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1*age +V4 +age*V3 */  
         /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/  
         /* */  
         if(Dummy[Tage[k]]== 2){ /* dummy with age */  
         /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ */  
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  
         }  
         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovprod;k++){ /*  For product without age */  
         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */  
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
         if(Dummy[Tvard[k][1]==0]){  
           if(Dummy[Tvard[k][2]==0]){  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
           }  
         }else{          }else{
           if(Dummy[Tvard[k][2]==0]){            cov[2+nagesqr+k1]=precov[nres][k1];
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
           }  
         }          }
       }        }/* End of loop on model equation */
           /* Old code */ 
   /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
   /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
   /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
   /* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\\/ *\/ */
   /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
   /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
   /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
   /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
   /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
   /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
   /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
   /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
   /*        /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); *\/ */
   /*        printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
   /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
   /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
   /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
   /*        /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only *\\/ *\/ */
   /*        /\*   /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
   /*        printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
   /*        printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
   /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
   /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
   /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
   /*        printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
   /*        printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
   
   /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
   /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
   /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
   /*        /\* *\/ */
   /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
   /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
   /* /\*cptcovage=2                   1               2      *\/ */
   /* /\*Tage[k]=                      5               8      *\/   */
   /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
   /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];        */
   /*        printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
   /*        printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
   /*        /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age *\\/ *\/ */
   /*        /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age *\\\/ *\\/ *\/ */
   /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\\/ *\/ */
   /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */
   /*        /\*   printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); *\/ */
   /*        /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; *\/ */
   /*        /\* } *\/ */
   /*        /\* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
   /*      }else if(Typevar[k1]==2 ){ /\* For product (not with age) *\/ */
   /* /\*       for (k=1; k<=cptcovprod;k++){ /\\*  For product without age *\\/ *\/ */
   /* /\* /\\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\\/ *\/ */
   /* /\* /\\*    k        1  2   3   4     5    6    7     8    9 *\\/ *\/ */
   /* /\* /\\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\\/ *\/ */
   /* /\* /\\*cptcovprod=1            1               2            *\\/ *\/ */
   /* /\* /\\*Tprod[]=                4               7            *\\/ *\/ */
   /* /\* /\\*Tvard[][1]             4               1             *\\/ *\/ */
   /* /\* /\\*Tvard[][2]               3               2           *\\/ *\/ */
             
   /*        /\* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])],nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]); *\/ */
   /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
   /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];     */
   /*        printf("hPxij Prod ij=%d k1=%d  cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
   /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   
   /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
   /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
   /*            /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];   *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; *\/ */
   /*          /\* }else{ /\\* Product of dummy by quantitative *\\/ *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; *\/ */
   /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
   /*        /\*   } *\/ */
   /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
   /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
   /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
   /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
   /*        /\*   }else{ /\\* Product of two quant *\\/ *\/ */
   /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\\/ *\/ */
   /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
   /*        /\*   } *\/ */
   /*        /\* }/\\*end of products quantitative *\\/ *\/ */
   /*      }/\*end of products *\/ */
         /* } /\* End of loop on model equation *\/ */
       /* for (k=1; k<=cptcovn;k++)  */        /* for (k=1; k<=cptcovn;k++)  */
       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */        /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
Line 3510  double ***hpxij(double ***po, int nhstep Line 3702  double ***hpxij(double ***po, int nhstep
 /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
 double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
 {  {
   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over    /* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
        computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
      nhstepm*hstepm matrices.       nhstepm*hstepm matrices.
Line 3522  double ***hbxij(double ***po, int nhstep Line 3715  double ***hbxij(double ***po, int nhstep
      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output       The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
   */    */
   
   int i, j, d, h, k;    int i, j, d, h, k, k1;
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
   double **newm, ***newmm;    double **newm, ***newmm;
   double agexact;    double agexact;
Line 3548  double ***hbxij(double ***po, int nhstep Line 3741  double ***hbxij(double ***po, int nhstep
         /* Debug */          /* Debug */
       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */        /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=nsd;k++){ /* For single dummy covariates only *//* cptcovn error */        }
       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */        /** New code */
       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];/* Bug valgrind */          if(Typevar[k1]==1){ /* A product with age */
         /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
       }  
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];   
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */  
         /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */  
         if(Dummy[Tage[k]]== 2){ /* dummy with age */  
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];   
         }  
         /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */  
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];  
         if(Dummy[Tvard[k][1]==0]){  
           if(Dummy[Tvard[k][2]==0]){  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
           }  
         }else{          }else{
           if(Dummy[Tvard[k][2]==0]){            cov[2+nagesqr+k1]=precov[nres][k1];
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
           }  
         }          }
       }                         }/* End of loop on model equation */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /** End of new code */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    /** This was old code */
         /* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only *\//\* cptcovn error *\/ */
         /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
         /* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
         /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind *\/ */
         /*   /\* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
         /* } */
         /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
         /*        /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
         /*        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
         /*        /\* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
         /* } */
         /* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 *\//\* For product with age *\/ */
         /*        /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!*\\/ *\/ */
         /*        if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
         /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
         /*        } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
         /*          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  */
         /*        } */
         /*        /\* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
         /* } */
         /* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn *\/ */
         /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         /*        if(Dummy[Tvard[k][1]]==0){ */
         /*          if(Dummy[Tvard[k][2]]==0){ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
         /*          }else{ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
         /*          } */
         /*        }else{ */
         /*          if(Dummy[Tvard[k][2]]==0){ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
         /*          }else{ */
         /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
         /*          } */
         /*        } */
         /* }                       */
         /* /\*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*\/ */
         /* /\*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*\/ */
   /** End of old code */
         
       /* Careful transposed matrix */        /* Careful transposed matrix */
       /* age is in cov[2], prevacurrent at beginning of transition. */        /* age is in cov[2], prevacurrent at beginning of transition. */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
Line 3648  double ***hbxij(double ***po, int nhstep Line 3853  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 3680  double func( double *x) Line 3886  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 3700  double func( double *x) Line 3906  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 3710  double func( double *x) Line 3917  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 3800  double func( double *x) Line 4010  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 3984  double func( double *x) Line 4194  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 4007  double funcone( double *x) Line 4217  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 4024  double funcone( double *x) Line 4239  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 4081  double funcone( double *x) Line 4309  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 4113  double funcone( double *x) Line 4353  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 4724  void  freqsummary(char fileres[], double Line 4970  void  freqsummary(char fileres[], double
                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies as well as proposing some starting values */  {  /* Some frequencies as well as proposing some starting values */
       /* Frequencies of any combination of dummy covariate used in the model equation */ 
   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
Line 4792  Title=%s <br>Datafile=%s Firstpass=%d La Line 5038  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 *\/ */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
       
Line 4800  Title=%s <br>Datafile=%s Firstpass=%d La Line 5047  Title=%s <br>Datafile=%s Firstpass=%d La
      reference=low_education V1=0,V2=0       reference=low_education V1=0,V2=0
      med_educ                V1=1 V2=0,        med_educ                V1=1 V2=0, 
      high_educ               V1=0 V2=1       high_educ               V1=0 V2=1
      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn 
   */    */
   dateintsum=0;    dateintsum=0;
   k2cpt=0;    k2cpt=0;
Line 4837  Title=%s <br>Datafile=%s Firstpass=%d La Line 5084  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=cptcoveff; /* 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 covariates combination of the model, 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 */
       posproptt=0.;        posproptt=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-5; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (s2=-5; s2<=nlstate+ndeath; s2++)            for (s2=-5; s2<=nlstate+ndeath; s2++)  
Line 4879  Title=%s <br>Datafile=%s Firstpass=%d La Line 5126  Title=%s <br>Datafile=%s Firstpass=%d La
                 /*       /\* 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  */                  /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */                  /* 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=%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 */
                   /* 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 */
                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",                     /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                    /*   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
                      j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                    /*   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                   /* 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 4901  Title=%s <br>Datafile=%s Firstpass=%d La Line 5151  Title=%s <br>Datafile=%s Firstpass=%d La
                 for (z1=1; z1<=cptcoveff; 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,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 
                                                                                       value is -1, we don't select. It differs from the                                                                                         value is -1, we don't select. It differs from the 
                                                                                       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,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 4934  Title=%s <br>Datafile=%s Firstpass=%d La Line 5189  Title=%s <br>Datafile=%s Firstpass=%d La
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */                    for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
                     if(!isnan(covar[ncovcol+z1][iind])){                      if(!isnan(covar[ncovcol+z1][iind])){
                         idq[z1]=idq[z1]+weight[iind];                        idq[z1]=idq[z1]+weight[iind];
                         meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */                        meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                         /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/                        /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
                         stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */                        stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                     }                      }
                   }                    }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
Line 4976  Title=%s <br>Datafile=%s Firstpass=%d La Line 5231  Title=%s <br>Datafile=%s Firstpass=%d La
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficlog, "\n#********** Variable ");           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++){          for (z1=1; z1<=cptcovs; z1++){
           if(!FixedV[Tvaraff[z1]]){            if(!FixedV[Tvaraff[z1]]){
             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }else{            }else{
             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }            }
         }          }
         printf( "**********\n#");          printf( "**********\n#");
Line 5024  Title=%s <br>Datafile=%s Firstpass=%d La Line 5279  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((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");          fprintf(ficresp, " Age");
       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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((cptcoveff==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);
Line 5104  Title=%s <br>Datafile=%s Firstpass=%d La Line 5362  Title=%s <br>Datafile=%s Firstpass=%d La
         }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<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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 5412  void prevalence(double ***probs, double Line 5670  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 5430  void prevalence(double ***probs, double Line 5688  void prevalence(double ***probs, double
         for (z1=1; z1<=cptcoveff; 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][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */              if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
               bool=0;                bool=0;
           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
               bool=0;                bool=0;
             }              }
         }          }
Line 5736  void  concatwav(int wav[], int **dh, int Line 5994  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 5834  void  concatwav(int wav[], int **dh, int Line 6092  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 5843  void  concatwav(int wav[], int **dh, int Line 6105  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 5857  void  concatwav(int wav[], int **dh, int Line 6119  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 5879  void  concatwav(int wav[], int **dh, int Line 6150  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; /*Number of total real effective covariates: effective     *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 5900  void  concatwav(int wav[], int **dh, int Line 6171  void  concatwav(int wav[], int **dh, int
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
     /* cij is the combination in the list of combination of dummy covariates */
     /* strstart is a string of time at start of computing */
   int i, j, nhstepm, hstepm, h, nstepm;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
Line 5968  void  concatwav(int wav[], int **dh, int Line 6241  void  concatwav(int wav[], int **dh, int
     /* If stepm=6 months */      /* If stepm=6 months */
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
Line 6010  void  concatwav(int wav[], int **dh, int Line 6283  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 6278  void  concatwav(int wav[], int **dh, int Line 6552  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][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,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 6910  To be simple, these graphs help to under Line 7189  To be simple, these graphs help to under
    tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,cptcoveff);
    if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    j1=0;     j1=0;
    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/  
      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 *\/ */     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 cptcovs=%d\n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs);
        if(tj != 1 && TKresult[nres]!= j1)
          continue;
   
      /* for(j1=1; j1<=tj;j1++){  /\* For each valid combination of covariates or only once*\/ */
        /* for(nres=1;nres <=1; 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,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,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=%s \n",nres, z1, modelresult[nres][z1], model);
            fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);
            /* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%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,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,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,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 6944  To be simple, these graphs help to under Line 7268  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,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,k)]*cov[2];  
            /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */  
          } else if(Dummy[Tage[k]]==3){ /* quantitative with age */  
            cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  
            /* 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,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)];  
              /* 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,k)] * Tqresult[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,k)] * Tqinvresult[nres][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][Tvard[k][1]]*  Tqinvresult[nres][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 7178  To be simple, these graphs help to under Line 7513  To be simple, these graphs help to under
          } /* k12 */           } /* k12 */
        } /*l1 */         } /*l1 */
      }/* k1 */       }/* k1 */
    } /* loop on nres */  
    }  /* loop on combination of covariates j1 */     }  /* loop on combination of covariates j1 */
      } /* loop on nres */
    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
Line 7210  void printinghtml(char fileresu[], char Line 7545  void printinghtml(char fileresu[], char
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",     fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));     fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
Line 7244  void printinghtml(char fileresu[], char Line 7579  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;     /* 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 7278  void printinghtml(char fileresu[], char Line 7622  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;     /* 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=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
Line 7329  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7670  divided by h: <sub>h</sub>P<sub>ij</sub>
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);         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,"LIJ_"),cpt,k1,nres);
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\         fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
  And probability to be observed in various states (up to %d) being in state %d at different ages.       \   And probability to be observed in various states (up to %d) being in state %d at different ages.       \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
          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,"LIJT_"),cpt,k1,nres);
      }       }
      /* 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> \         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);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));
         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 */
Line 7377  with weights corresponding to observed p Line 7722  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 7435  See page 'Matrix of variance-covariance Line 7780  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 7464  See page 'Matrix of variance-covariance Line 7805  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;       /* 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=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
   
Line 7501  See page 'Matrix of variance-covariance Line 7838  See page 'Matrix of variance-covariance
          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 7516  true period expectancies (those weighted Line 7853  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 7594  void printinggnuplot(char fileresu[], ch Line 7930  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];
         /* 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]]);
           /* decodtabm(1,1,4) = 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(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 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* printf(" V%d=%d ",Tvaraff[k],vlv); */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */          /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* 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 7657  void printinggnuplot(char fileresu[], ch Line 7999  void printinggnuplot(char fileresu[], ch
         }else{          }else{
           kl=0;            kl=0;
           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */              /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 7685  void printinggnuplot(char fileresu[], ch Line 8028  void printinggnuplot(char fileresu[], ch
           }else{            }else{
             kl=0;              kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */              for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */                /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
                 lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];                /* vlv= nbcode[Tvaraff[k]][lv]; */
                 vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
               kl++;                kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */                /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
Line 7699  void printinggnuplot(char fileresu[], ch Line 8044  void printinggnuplot(char fileresu[], ch
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \                  fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/                          2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{                }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);                  fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
                 kl++;                  kl++;
               }                }
             } /* end covariate */              } /* end covariate */
Line 7727  void printinggnuplot(char fileresu[], ch Line 8072  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(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]]);
         /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* 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];        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* 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 *\/ */
       /* for(k=1; k <= ncovds; k++){ */        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         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(k=1; k <= ncovds; k++){ *\/ */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        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 7793  void printinggnuplot(char fileresu[], ch Line 8144  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(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {        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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* 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];          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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][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 7848  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 8205  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(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= 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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           vlv= nbcode[Tvaraff[k]][lv];          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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");
Line 7899  set ter svg size 640, 480\nunset log y\n Line 8262  set ter svg size 640, 480\nunset log y\n
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end 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(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= 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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           vlv= nbcode[Tvaraff[k]][lv];          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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");
Line 7957  set ter svg size 640, 480\nunset log y\n Line 8326  set ter svg size 640, 480\nunset log y\n
         }          }
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        /* } /\* end covariate *\/   */
   } /* end 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(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]]);
         /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* 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];        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* 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 *\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        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");
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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(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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* 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];          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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");
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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(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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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");
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             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<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
                 lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */                /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
                 vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
               kl++;                kl++;
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
               kl++;                kl++;
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   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(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]]);
           /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* 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 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   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");
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             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[Tvresult[nres][k]]==0){  /* To be verified */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                  /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
               /* 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 combination k1 and covariate k *\/ */
               /* 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]; /* Value of the modality of Tvaraff[k] */                  lv=Tvresult[nres][k];
               kl++;                  vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               kl++;                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               if(k <cptcoveff && cptcoveff>1)                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
                   /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
                   kl++;
                   /* sprintf(gplotcondition+strlen(gplotcondition),"$%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 <cptcoveff && cptcoveff>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 *\/ */
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     fprintf(ficgp,"#model=%s \n",model);      fprintf(ficgp,"#model=%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);        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
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */             TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         vlv= nbcode[Tvaraff[k]][lv];        }
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /* if(m != 1 && TKresult[nres]!= k1) */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        continue; */
       }        /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /* strcpy(gplotlabel,"("); */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
       }         /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
         /*        lv= 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);
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             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */              /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */              for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                switch(Typevar[j]){
                 if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */                case 1:
                   if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                  if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     if(DummyV[j]==0){/* Bug valgrind */                    if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
                       fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;                      if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     }else{ /* quantitative */                        if(DummyV[j]==0){/* Bug valgrind */
                       fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */                          fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                        }else{ /* quantitative */
                           fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                           /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                         }
                         ij++;
                     }                      }
                     ij++;  
                   }                    }
                 }                   }
               }else if(cptcovprod >0){                  break;
                 if(j==Tprod[ijp]) { /* */                 case 2:
                   /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */                  if(cptcovprod >0){
                   if(ijp <=cptcovprod) { /* Product */                    if(j==Tprod[ijp]) { /* */ 
                     if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */                      /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                       if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */                      if(ijp <=cptcovprod) { /* Product */
                         /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */                        if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);                          if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                       }else{ /* Vn is dummy and Vm is quanti */                            /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                         /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */                            fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                          }else{ /* Vn is dummy and Vm is quanti */
                       }                            /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                     }else{ /* Vn*Vm Vn is quanti */                            fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                       if(DummyV[Tvard[ijp][2]]==0){                          }
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);                        }else{ /* Vn*Vm Vn is quanti */
                       }else{ /* Both quanti */                          if(DummyV[Tvard[ijp][2]]==0){
                         fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                            fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                           }else{ /* Both quanti */
                             fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                           }
                       }                        }
                         ijp++;
                     }                      }
                     ijp++;                    } /* end Tprod */
                   }                  }
                 } /* end Tprod */                  break;
               } else{  /* simple covariate */                case 0:
                   /* simple covariate */
                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */                  /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                 if(Dummy[j]==0){                  if(Dummy[j]==0){
                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */                    fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
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                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */                    fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                 }                  }
               } /* end simple */                 /* end simple */
                   break;
                 default:
                   break;
                 } /* end switch */
             } /* end j */              } /* end j */
           }else{            }else{ /* k=k2 */
             i=i-ncovmodel;              if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */                fprintf(ficgp," (1.");i=i-ncovmodel;
               fprintf(ficgp," (1.");              }else
                 i=i-ncovmodel;
           }            }
                       
           if(ng != 1){            if(ng != 1){
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                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                                 
               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                ijp=1;
                  if(cptcovage >0){                 /* for(j=3; j <=ncovmodel-nagesqr; j++){ */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */                for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                      if(ij <=cptcovage) { /* Bug valgrind */                  switch(Typevar[j]){
                        fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);                  case 1:
                        /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                    if(cptcovage >0){ 
                        ij++;                      if(j==Tage[ij]) { /* Bug valgrind */
                      }                        if(ij <=cptcovage) { /* Bug valgrind */
                    }                          if(DummyV[j]==0){/* Bug valgrind */
                  }else                            /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */
                    fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */                            /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */
                             fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
                             /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
                             /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                           }else{ /* quantitative */
                             /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
                             fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                             /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
                             /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                           }
                           ij++;
                         }
                       }
                     }
                     break;
                   case 2:
                     if(cptcovprod >0){
                       if(j==Tprod[ijp]) { /* */ 
                         /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                         if(ijp <=cptcovprod) { /* Product */
                           if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                             if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                               fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
                             }else{ /* Vn is dummy and Vm is quanti */
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             }
                           }else{ /* Vn*Vm Vn is quanti */
                             if(DummyV[Tvard[ijp][2]]==0){
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
                             }else{ /* Both quanti */
                               fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             } 
                           }
                           ijp++;
                         }
                       } /* end Tprod */
                     } /* end if */
                     break;
                   case 0: 
                     /* simple covariate */
                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                     if(Dummy[j]==0){
                       /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
                       fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /*  */
                       /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
                     }else{ /* quantitative */
                       fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
                       /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */
                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                     }
                     /* end simple */
                     /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */
                     break;
                   default:
                     break;
                   } /* end switch */
               }                }
               fprintf(ficgp,")");                fprintf(ficgp,")");
             }              }
Line 8481  set ter svg size 640, 480\nunset log y\n Line 8971  set ter svg size 640, 480\nunset log y\n
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             else /* ng= 3 */              else /* ng= 3 */
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
             if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }            }
Line 8494  set ter svg size 640, 480\nunset log y\n Line 8984  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 8817  void prevforecast(char fileres[], double Line 9307  void prevforecast(char fileres[], double
       
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   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(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */
     if(i1 != 1 && TKresult[nres]!= k)      if(i1 != 1 && TKresult[nres]!= k)
       continue;        continue;
     if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
Line 8826  void prevforecast(char fileres[], double Line 9316  void prevforecast(char fileres[], double
     }      }
     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
     }      }
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 8856  void prevforecast(char fileres[], double Line 9347  void prevforecast(char fileres[], double
         }          }
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
             fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff]  correct */
         fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);          fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
                   
         for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j<=nlstate+ndeath;j++) {
Line 8966  void prevforecast(char fileres[], double Line 9458  void prevforecast(char fileres[], double
     }      }
     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
     }      }
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 9002  void prevforecast(char fileres[], double Line 9494  void prevforecast(char fileres[], double
         }          }
         fprintf(ficresfb,"\n");          fprintf(ficresfb,"\n");
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
         fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);          fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
         for(i=1; i<=nlstate+ndeath;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
           ppij=0.;ppi=0.;            ppij=0.;ppi=0.;
Line 9061  void prevforecast(char fileres[], double Line 9553  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];
        /* 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,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,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,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][j]);        }
         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[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 9118  void prevforecast(char fileres[], double Line 9613  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)      /* for(k=1; k<=i1;k++){ */
          continue;      /*    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,j)]);           printf(" V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           fprintf(ficresvbl," V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           fprintf(ficlog," V%d=%lg ",Tvqresult[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][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][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][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 9595  int readdata(char datafile[], int firsto Line 10095  int readdata(char datafile[], int firsto
   
   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */    DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */    FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
     for(v=1;v<NCOVMAX;v++){
       DummyV[v]=0;
       FixedV[v]=0;
     }
   
   for(v=1; v <=ncovcol;v++){    for(v=1; v <=ncovcol;v++){
     DummyV[v]=0;      DummyV[v]=0;
Line 9954  void removefirstspace(char **stri){/*, c Line 10458  void removefirstspace(char **stri){/*, c
   *stri=p2;     *stri=p2; 
 }  }
   
 int decoderesult ( char resultline[], int nres)  int decoderesult( char resultline[], int nres)
 /**< This routine decode one result line and returns the combination # of dummy covariates only **/  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
 {  {
   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;    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);
     printf("decoderesult:%s\n",resultline);
   
   if (strstr(resultline,"v") !=0){    strcpy(resultsav,resultline);
     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);    printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);  
     return 1;  
   }  
   trimbb(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 this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);      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, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);      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;*/
   }    }
   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" */
       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */        cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
         /* If a blank, then strc="V4=" and strd='\0' */
         if(strc[0]=='\0'){
         printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
           fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
           return 1;
         }
     }else      }else
       cutl(strc,strd,resultsav,'=');        cutl(strc,strd,resultsav,'=');
     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */      Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
Line 9998  int decoderesult ( char resultline[], in Line 10507  int decoderesult ( char resultline[], in
       strcpy(resultsav,stra); /* and analyzes it */        strcpy(resultsav,stra); /* and analyzes it */
   }    }
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */    /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
     if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */    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 */
         /* 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: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);          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]);
         fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);          fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%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*/
   }        /* We feed resultmodel[k1]=k2; */
         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 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=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 */
             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 */
             break;
           }
         }
         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]);
           fprintf(ficlog,"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]);
         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*/
         /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */ 
         match=0;
         printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);
         for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
             /* modelresult[k2]=k1; */
             printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);
             match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
           }
         }
         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);
           fprintf(ficlog,"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);
           return 1;
         }
         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 */
           if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
             /* modelresult[k2]=k1;*/
             printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);
             match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
             break;
           }
         }
         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);
           fprintf(ficlog,"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);
           return 1;
         }
       }/* End of testing */
     }/* 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 */
   for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
     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 */        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[k1]=k2;  /* k2th variable of the model corresponds to k1 variable of the model. 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: %d value missing; result: %s, model=%s\n",k1, resultline, model);        printf("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: %d value missing; result: %s, model=%s\n",k1, resultline, model);        fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%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=%s\n",k2, resultline, model);
Line 10036  int decoderesult ( char resultline[], in Line 10597  int decoderesult ( char resultline[], in
       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 */
   /* 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 */
   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/    /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/
   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    /* nres=2nd result line: V4=1 V5=24.1 V3=1  V2=8 V1=0 */
   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/    /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
   /*    1 0 0 0 */    /*    1 0 0 0 */
   /*    2 1 0 0 */    /*    2 1 0 0 */
   /*    3 0 1 0 */     /*    3 0 1 0 */ 
   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */    /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/
   /*    5 0 0 1 */    /*    5 0 0 1 */
   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */    /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=1)*/
   /*    7 0 1 1 */    /*    7 0 1 1 */
   /*    8 1 1 1 */    /*    8 1 1 1 */
   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */    /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */    /* 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 on model line */    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.
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */                                                     * loop on position k1 in the MODEL LINE */
       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */      /* k counting number of combination of single dummies in the equation model */
       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */      /* k4 counting single dummies in the equation model */
       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */      /* k4q counting single quantitatives in the equation model */
       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */
       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */         /* 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)*/
         /* 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                        */
         /*      k3 is the position in the nres result line of the k1th variable of the model equation                                  */
         /* 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.                                                 */
         /* Tresult[nres][result_position]= value 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                                        */
         /* 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 */
         /* 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)*/
         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]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
         /* 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][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 */
       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);        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);
       k4++;;        k4++;;
     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
       k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */        /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
         k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
         /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
         /* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 *\/ */
         /* 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 */
       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);        TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         precov[nres][k1]=Tvalsel[k3q];
         printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
       k4q++;;        k4q++;;
       }else if( Dummy[k1]==2 ){ /* For dummy with age product */
         /* Tvar[k1]; */ /* Age variable */
         /* Wrong we want the value of variable name Tvar[k1] */
         
         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)*/
         TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
         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]);
       }else if( Dummy[k1]==3 ){ /* For quant with age product */
         k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
         TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
         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]);
       }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]];      
         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]]);
       }else{
         printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
         fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
     }      }
   }    }
       
   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 10236  int decodemodel( char model[], int lasto Line 10849  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  */
             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */              Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvardk[k][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               Tvardk[k][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */              /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */              /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
Line 10316  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10939  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
       TvarsD[nsd]=Tvar[k];        TvarsD[nsd]=Tvar[k];
       TvarsDind[nsd]=k;        TvarsDind[nsd]=k;
         TnsdVar[Tvar[k]]=nsd;
       TvarF[ncovf]=Tvar[k];        TvarF[ncovf]=Tvar[k];
       TvarFind[ncovf]=k;        TvarFind[ncovf]=k;
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
Line 10327  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10951  Dummy[k] 0=dummy (0 1), 1 quantitative (
       ncovf++;        ncovf++;
       modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
       TvarF[ncovf]=Tvar[k];        TvarF[ncovf]=Tvar[k];
         /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
       TvarFind[ncovf]=k;        TvarFind[ncovf]=k;
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
Line 10337  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10962  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 10353  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10978  Dummy[k] 0=dummy (0 1), 1 quantitative (
       nsd++;        nsd++;
       TvarsD[nsd]=Tvar[k];        TvarsD[nsd]=Tvar[k];
       TvarsDind[nsd]=k;        TvarsDind[nsd]=k;
         TnsdVar[Tvar[k]]=nsd; /* To be verified */
       ncovv++; /* Only simple time varying variables */        ncovv++; /* Only simple time varying variables */
       TvarV[ncovv]=Tvar[k];        TvarV[ncovv]=Tvar[k];
       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */        TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
Line 10368  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10994  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;        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 10895  void syscompilerinfo(int logged) Line 11521  void syscompilerinfo(int logged)
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
     /* Computes the prevalence limit for each combination of the dummy covariates */
   int i, j, k, i1, k4=0, nres=0 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
Line 10923  int prevalence_limit(double *p, double * Line 11550  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(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++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       /* k=k+1; */        /* k=k+1; */
       /* to clean */        /* to clean */
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
       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,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*\/ */
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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]]);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        }
         fprintf(ficlog," 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(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 10958  int prevalence_limit(double *p, double * Line 11589  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,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,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 10978  int prevalence_limit(double *p, double * Line 11615  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 11024  int back_prevalence_limit(double *p, dou Line 11661  int back_prevalence_limit(double *p, dou
     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)       if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));       /*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<=cptcoveff ;j++) {/* all covariates */
         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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 */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[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][j]);          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
       }        }
       fprintf(ficresplb,"******\n");        fprintf(ficresplb,"******\n");
       printf("******\n");        printf("******\n");
Line 11050  int back_prevalence_limit(double *p, dou Line 11687  int back_prevalence_limit(double *p, dou
           
       fprintf(ficresplb,"#Age ");        fprintf(ficresplb,"#Age ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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 11074  int back_prevalence_limit(double *p, dou Line 11711  int back_prevalence_limit(double *p, dou
         }          }
         fprintf(ficresplb,"%.0f ",age );          fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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 11094  int back_prevalence_limit(double *p, dou Line 11731  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 11104  int hPijx(double *p, int bage, int fage) Line 11741  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)      /* for(k=1; k<=i1;k++){ */
         continue;      /* if(i1 != 1 && TKresult[nres]!= k) */
       fprintf(ficrespij,"\n#****** ");      /*  continue; */
       for(j=1;j<=cptcoveff;j++)       fprintf(ficrespij,"\n#****** ");
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      for(j=1;j<=cptcovs;j++){
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficrespij," 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(ficrespij,"******\n");        /*        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
             }
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      fprintf(ficrespij,"******\n");
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                 nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*          nhstepm=nhstepm*YEARM; aff par mois*/
         oldm=oldms;savm=savms;        
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");        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 11206  int hPijx(double *p, int bage, int fage) Line 11845  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)      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
         continue;      /*    if(i1 != 1 && TKresult[nres]!= k) */
       fprintf(ficrespijb,"\n#****** ");      /*  continue; */
       for(j=1;j<=cptcoveff;j++)      fprintf(ficrespijb,"\n#****** ");
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      for(j=1;j<=cptcovs;j++){
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /* for(j=1;j<=cptcoveff;j++) */
       }        /*        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 *\/ */
       if(invalidvarcomb[k]){  /* Is it necessary here? */        /*        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);       }
         continue;      fprintf(ficrespijb,"******\n");
       }      if(invalidvarcomb[k]){  /* Is it necessary here? */
               fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        continue;
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */      }
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */      
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */      /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/      for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
                 /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        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*/
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */        
         /* and memory limitations if stepm is small */        /*          nhstepm=nhstepm*YEARM; aff par mois*/
         
         /* oldm=oldms;savm=savms; */        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,nlstate,stepm,oldm,savm, k);   */        /* and memory limitations if stepm is small */
         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); */        /* oldm=oldms;savm=savms; */
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");        /* 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 11306  int main(int argc, char *argv[]) Line 11948  int main(int argc, char *argv[])
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char  modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
   char resultline[MAXLINE];    char resultline[MAXLINE], resultlineori[MAXLINE];
       
   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 11933  Please run with mle=-1 to get a correct Line 12575  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 11952  Please run with mle=-1 to get a correct Line 12594  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); /*  */
       /* 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 11994  Please run with mle=-1 to get a correct Line 12638  Please run with mle=-1 to get a correct
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tvardk=imatrix(1,NCOVMAX,1,2);
   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age    Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                               */  
     for(i=1;i<NCOVMAX;i++)
       Tage[i]=0;
   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an    Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                 * individual dummy, fixed or varying:                                  * individual dummy, fixed or varying:
                                 * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,                                  * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
Line 12071  Please run with mle=-1 to get a correct Line 12718  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);
Line 12101  Please run with mle=-1 to get a correct Line 12748  Please run with mle=-1 to get a correct
            * For k=4 covariates, h goes from 1 to m=2**k             * For k=4 covariates, h goes from 1 to m=2**k
            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;             * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1             * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
            *     h\k   1     2     3     4             *     h\k   1     2     3     4   *  h-1\k-1  4  3  2  1          
            *______________________________               *______________________________   *______________________
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1   *     0     0  0  0  0 
            *     2     2     1     1     1             *     2     2     1     1     1   *     1     0  0  0  1 
            *     3 i=2 1     2     1     1             *     3 i=2 1     2     1     1   *     2     0  0  1  0 
            *     4     2     2     1     1             *     4     2     2     1     1   *     3     0  0  1  1 
            *     5 i=3 1 i=2 1     2     1             *     5 i=3 1 i=2 1     2     1   *     4     0  1  0  0 
            *     6     2     1     2     1             *     6     2     1     2     1   *     5     0  1  0  1 
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1   *     6     0  1  1  0 
            *     8     2     2     2     1             *     8     2     2     2     1   *     7     0  1  1  1 
            *     9 i=5 1 i=3 1 i=2 1     2             *     9 i=5 1 i=3 1 i=2 1     2   *     8     1  0  0  0 
            *    10     2     1     1     2             *    10     2     1     1     2   *     9     1  0  0  1 
            *    11 i=6 1     2     1     2             *    11 i=6 1     2     1     2   *    10     1  0  1  0 
            *    12     2     2     1     2             *    12     2     2     1     2   *    11     1  0  1  1 
            *    13 i=7 1 i=4 1     2     2                 *    13 i=7 1 i=4 1     2     2   *    12     1  1  0  0  
            *    14     2     1     2     2             *    14     2     1     2     2   *    13     1  1  0  1 
            *    15 i=8 1     2     2     2             *    15 i=8 1     2     2     2   *    14     1  1  1  0 
            *    16     2     2     2     2             *    16     2     2     2     2   *    15     1  1  1  1          
            */             */                                     
   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
      * and the value of each covariate?       * and the value of each covariate?
Line 12210  Title=%s <br>Datafile=%s Firstpass=%d La Line 12857  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-2013-2016-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 12223  Title=%s <br>Datafile=%s Firstpass=%d La Line 12877  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 12537  Please run with mle=-1 to get a correct Line 13191  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 12881  Please run with mle=-1 to get a correct Line 13536  Please run with mle=-1 to get a correct
     }      }
             
     /* Results */      /* Results */
       /* Value of covariate in each resultine will be compututed (if product) and sorted according to model rank */
       /* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */  
       precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
     endishere=0;      endishere=0;
     nresult=0;      nresult=0;
     parameterline=0;      parameterline=0;
Line 12954  Please run with mle=-1 to get a correct Line 13612  Please run with mle=-1 to get a correct
         }          }
         break;          break;
       case 13:        case 13:
         num_filled=sscanf(line,"result:%[^\n]\n",resultline);          num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
         nresult++; /* Sum of resultlines */          nresult++; /* Sum of resultlines */
         printf("Result %d: result:%s\n",nresult, resultline);          printf("Result %d: result:%s\n",nresult, resultlineori);
           /* removefirstspace(&resultlineori); */
           
           if(strstr(resultlineori,"v") !=0){
             printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
             fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
             return 1;
           }
           trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
           printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);
         if(nresult > MAXRESULTLINESPONE-1){          if(nresult > MAXRESULTLINESPONE-1){
           printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);            printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
           fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);            fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
           goto end;            goto end;
         }          }
           
         if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */          if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
           fprintf(ficparo,"result: %s\n",resultline);            fprintf(ficparo,"result: %s\n",resultline);
           fprintf(ficres,"result: %s\n",resultline);            fprintf(ficres,"result: %s\n",resultline);
Line 13065  Please run with mle=-1 to get a correct Line 13733  Please run with mle=-1 to get a correct
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
       /* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
       /** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
       /* calls hpxij with combination k */
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
           
     /* ncovcombmax=  pow(2,cptcoveff); */      /* ncovcombmax=  pow(2,cptcoveff); */
     /*-------------- Variance of one-step probabilities---*/      /*-------------- Variance of one-step probabilities for a combination ij or for nres ?---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
           
Line 13195  Please run with mle=-1 to get a correct Line 13866  Please run with mle=-1 to get a correct
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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][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][j]);          fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
       printf("******\n");        printf("******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
         /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
               
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 13217  Please run with mle=-1 to get a correct Line 13889  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 13256  Please run with mle=-1 to get a correct Line 13928  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,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,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,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][j]);           * (V5 is quanti) V4 and V3 are dummies
         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[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][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,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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][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][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 13293  Please run with mle=-1 to get a correct Line 14017  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,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]);          /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
           fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
       }         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
Line 13326  Please run with mle=-1 to get a correct Line 14052  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 13373  Please run with mle=-1 to get a correct Line 14099  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);
   
           
     free_vector(weight,firstobs,lastobs);      free_vector(weight,firstobs,lastobs);
       free_imatrix(Tvardk,1,NCOVMAX,1,2);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,firstobs,lastobs);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,firstobs,lastobs);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
Line 13430  Please run with mle=-1 to get a correct Line 14157  Please run with mle=-1 to get a correct
   free_ivector(TvarsQ,1,NCOVMAX);    free_ivector(TvarsQ,1,NCOVMAX);
   free_ivector(TvarsQind,1,NCOVMAX);    free_ivector(TvarsQind,1,NCOVMAX);
   free_ivector(TvarsD,1,NCOVMAX);    free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TnsdVar,1,NCOVMAX);
   free_ivector(TvarsDind,1,NCOVMAX);    free_ivector(TvarsDind,1,NCOVMAX);
   free_ivector(TvarFD,1,NCOVMAX);    free_ivector(TvarFD,1,NCOVMAX);
   free_ivector(TvarFDind,1,NCOVMAX);    free_ivector(TvarFDind,1,NCOVMAX);
Line 13455  Please run with mle=-1 to get a correct Line 14183  Please run with mle=-1 to get a correct
   free_ivector(Tmodelind,1,NCOVMAX);    free_ivector(Tmodelind,1,NCOVMAX);
   free_ivector(TmodelInvind,1,NCOVMAX);    free_ivector(TmodelInvind,1,NCOVMAX);
   free_ivector(TmodelInvQind,1,NCOVMAX);    free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/
   
   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
   /* free_imatrix(codtab,1,100,1,10); */    /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);

Removed from v.1.326  
changed lines
  Added in v.1.337


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