Diff for /imach/src/imach.c between versions 1.308 and 1.330

version 1.308, 2021/03/31 13:11:57 version 1.330, 2022/08/06 07:18:25
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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
     Summary: some test with nres=1
   
     Revision 1.325  2022/07/25 14:27:23  brouard
     Summary: r30
   
     * imach.c (Module): Error cptcovn instead of nsd in bmij (was
     coredumped, revealed by Feiuno, thank you.
   
     Revision 1.324  2022/07/23 17:44:26  brouard
     *** empty log message ***
   
     Revision 1.323  2022/07/22 12:30:08  brouard
     *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
   
     Revision 1.322  2022/07/22 12:27:48  brouard
     *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
   
     Revision 1.321  2022/07/22 12:04:24  brouard
     Summary: r28
   
     *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
   
     Revision 1.320  2022/06/02 05:10:11  brouard
     *** empty log message ***
   
     Revision 1.319  2022/06/02 04:45:11  brouard
     * imach.c (Module): Adding the Wald tests from the log to the main
     htm for better display of the maximum likelihood estimators.
   
     Revision 1.318  2022/05/24 08:10:59  brouard
     * imach.c (Module): Some attempts to find a bug of wrong estimates
     of confidencce intervals with product in the equation modelC
   
     Revision 1.317  2022/05/15 15:06:23  brouard
     * imach.c (Module):  Some minor improvements
   
     Revision 1.316  2022/05/11 15:11:31  brouard
     Summary: r27
   
     Revision 1.315  2022/05/11 15:06:32  brouard
     *** empty log message ***
   
     Revision 1.314  2022/04/13 17:43:09  brouard
     * imach.c (Module): Adding link to text data files
   
     Revision 1.313  2022/04/11 15:57:42  brouard
     * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
   
     Revision 1.312  2022/04/05 21:24:39  brouard
     *** empty log message ***
   
     Revision 1.311  2022/04/05 21:03:51  brouard
     Summary: Fixed quantitative covariates
   
             Fixed covariates (dummy or quantitative)
           with missing values have never been allowed but are ERRORS and
           program quits. Standard deviations of fixed covariates were
           wrongly computed. Mean and standard deviations of time varying
           covariates are still not computed.
   
     Revision 1.310  2022/03/17 08:45:53  brouard
     Summary: 99r25
   
     Improving detection of errors: result lines should be compatible with
     the model.
   
     Revision 1.309  2021/05/20 12:39:14  brouard
     Summary: Version 0.99r24
   
   Revision 1.308  2021/03/31 13:11:57  brouard    Revision 1.308  2021/03/31 13:11:57  brouard
   Summary: Version 0.99r23    Summary: Version 0.99r23
   
Line 811 Line 895
   
   The same imach parameter file can be used but the option for mle should be -3.    The same imach parameter file can be used but the option for mle should be -3.
   
   Agnès, who wrote this part of the code, tried to keep most of the    Agnès, who wrote this part of the code, tried to keep most of the
   former routines in order to include the new code within the former code.    former routines in order to include the new code within the former code.
   
   The output is very simple: only an estimate of the intercept and of    The output is very simple: only an estimate of the intercept and of
Line 990  Important routines Line 1074  Important routines
 - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)  - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
   and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.    and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
 - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables  - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
   o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if    o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
     race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.      race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
   
   
       
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
Line 1060  Important routines Line 1144  Important routines
 #define POWELLNOF3INFF1TEST /* Skip test */  #define POWELLNOF3INFF1TEST /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 1115  typedef struct { Line 1200  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 1126  typedef struct { Line 1211  typedef struct {
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20  /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 30  /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */
 #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
Line 1154  typedef struct { Line 1239  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="March 2021,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, INED 2000-2021";  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 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 */
 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 cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
 int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */  int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates 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 1336  double ***cotvar; /* Time varying covari Line 1422  double ***cotvar; /* Time varying covari
 double ***cotqvar; /* Time varying quantitative covariate itqv */  double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  /* Some documentation */
 /*k          1  2   3   4     5    6    7     8    9 */        /*   Design original data
 /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */         *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 
 /* Tndvar[k]    1   2   3               4          5 */         *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
 /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */         *                                                             ntv=3     nqtv=1
 /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */         *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
 /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */         * For time varying covariate, quanti or dummies
 /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */         *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
 /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */         *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
 /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */         *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
 /* Tprod[i]=k           4               7            */         *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
 /* Tage[i]=k                  5               8      */         *       covar[k,i], value of kth fixed covariate dummy or quanti :
 /* */         *       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
          *   k=  1    2      3       4     5       6      7        8   9     10       11 
          */
   /* According to the model, more columns can be added to covar by the product of covariates */
   /* 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
     # 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 */
   /*    k        1  2   3   4     5    6    7     8    9 */
   /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/
                                                            /* fixed or varying), 1 for age product, 2 for*/
                                                            /* product */
   /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
                                                            /*(single or product without age), 2 dummy*/
                                                            /* with age product, 3 quant with age product*/
   /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
   /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
   /*TnsdVar[Tvar]   1   2                              3 */ 
   /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
   /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
   /*    nsq      1                     2                 */ /* Counting single quantit tv */
   /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
   /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
   /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */
   /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
   /* 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 */
   /* 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 */
   /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
 /* Type                    */  /* Type                    */
 /* V         1  2  3  4  5 */  /* V         1  2  3  4  5 */
 /*           F  F  V  V  V */  /*           F  F  V  V  V */
 /*           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;
   
 #define MAXRESULTLINES 10  #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[MAXRESULTLINES];  int TKresult[MAXRESULTLINESPONE];
 int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */
 int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
 int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */  int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
 double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */  int TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable or quanti value (output) */
 double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */  int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
 int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */  double Tqresult[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) */
   
   /* 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
     # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
   */
 /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */  /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
 int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
 int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
Line 1401  int *TmodelInvQind; /** Tmodelqind[1]=1 Line 1525  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 1571  char *cutl(char *blocc, char *alocc, cha Line 1696  char *cutl(char *blocc, char *alocc, cha
 {  {
   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'     /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      gives blocc="abcdef" and alocc="ghi2j".       gives alocc="abcdef" and blocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
   char *s, *t;    char *s, *t;
Line 1853  char *subdirf(char fileres[]) Line 1978  char *subdirf(char fileres[])
 /*************** function subdirf2 ***********/  /*************** function subdirf2 ***********/
 char *subdirf2(char fileres[], char *preop)  char *subdirf2(char fileres[], char *preop)
 {  {
       /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
    Errors in subdirf, 2, 3 while printing tmpout is
    rewritten within the same printf. Workaround: many printfs */
   /* Caution optionfilefiname is hidden */    /* Caution optionfilefiname is hidden */
   strcpy(tmpout,optionfilefiname);    strcpy(tmpout,optionfilefiname);
   strcat(tmpout,"/");    strcat(tmpout,"/");
Line 2224  void linmin(double p[], double xi[], int Line 2351  void linmin(double p[], double xi[], int
 #endif  #endif
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
         if(fb == fx){ /* Flat function in the direction */    if(fb == fx){ /* Flat function in the direction */
                 xmin=xx;      xmin=xx;
     *flat=1;      *flat=1;
         }else{    }else{
     *flat=0;      *flat=0;
 #endif  #endif
                 /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */                  /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
Line 2285  void linmin(double p[], double xi[], int Line 2412  void linmin(double p[], double xi[], int
   
 /*************** powell ************************/  /*************** powell ************************/
 /*  /*
 Minimization of a function func of n variables. Input consists of an initial starting point  Minimization of a function func of n variables. Input consists in an initial starting point
 p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-  p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
 rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value  rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
 such that failure to decrease by more than this amount on one iteration signals doneness. On  such that failure to decrease by more than this amount in one iteration signals doneness. On
 output, p is set to the best point found, xi is the then-current direction set, fret is the returned  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 function value at p , and iter is the number of iterations taken. The routine linmin is used.  function value at p , and iter is the number of iterations taken. The routine linmin is used.
  */   */
Line 2313  void powell(double p[], double **xi, int Line 2440  void powell(double p[], double **xi, int
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
 #ifdef LINMINORIGINAL  
 #else  
   
   flatdir=ivector(1,n);   
   for (j=1;j<=n;j++) flatdir[j]=0;   
 #endif  
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
Line 2328  void powell(double p[], double **xi, int Line 2449  void powell(double p[], double **xi, int
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
   rcurr_time = time(NULL);      rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret); /* From former iteration or initial value */  
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     rlast_time=rcurr_time;      rlast_time=rcurr_time;
     /* (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 %ld sec. %ld sec.",*iter,*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 %ld sec. %ld sec.",*iter,*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);
 /*     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 */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
Line 2442  void powell(double p[], double **xi, int Line 2563  void powell(double p[], double **xi, int
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
     /* New value of last point Pn is not computed, P(n-1) */      /* New value of last point Pn is not computed, P(n-1) */
       for(j=1;j<=n;j++) {      for(j=1;j<=n;j++) {
         if(flatdir[j] >0){        if(flatdir[j] >0){
           printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);          printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
           fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);          fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
         }  
         /* printf("\n"); */  
         /* fprintf(ficlog,"\n"); */  
       }        }
         /* printf("\n"); */
         /* fprintf(ficlog,"\n"); */
       }
     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */      /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */      if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
Line 2487  void powell(double p[], double **xi, int Line 2608  void powell(double p[], double **xi, int
       }        }
 #endif  #endif
   
 #ifdef LINMINORIGINAL  
 #else  
       free_ivector(flatdir,1,n);   
 #endif  
       free_vector(xit,1,n);         free_vector(xit,1,n); 
       free_vector(xits,1,n);         free_vector(xits,1,n); 
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
Line 2604  void powell(double p[], double **xi, int Line 2721  void powell(double p[], double **xi, int
           }            }
           printf("\n");            printf("\n");
           fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
   #ifdef FLATSUP
             free_vector(xit,1,n); 
             free_vector(xits,1,n); 
             free_vector(ptt,1,n); 
             free_vector(pt,1,n); 
             return;
   #endif
         }          }
 #endif  #endif
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
Line 2688  void powell(double p[], double **xi, int Line 2812  void powell(double p[], double **xi, int
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     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 (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 */                          /* 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,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];
         /* 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)); */        /* 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 varying covariates only */      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
         /* 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]); */        /* 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 */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       if(Dummy[Tvar[Tage[k]]]){        if(Dummy[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,Tvar[Tage[k]])]*cov[2];
       } else{          /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];         } 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]); */        /* 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 */      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]); */        /* 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][1]]==0){
         if(Dummy[Tvard[k][2]==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)];            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{          }else{
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];            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{        }else{
         if(Dummy[Tvard[k][2]==0]){          if(Dummy[Tvard[k][2]]==0){
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];            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{          }else{
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];            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]]; */
         }          }
       }        }
     }      }
Line 2729  void powell(double p[], double **xi, int Line 2862  void powell(double p[], double **xi, int
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                 /* age and covariate values of ij are in 'cov' */      /* age and covariate values of ij are in 'cov' */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           
     savm=oldm;      savm=oldm;
Line 2769  void powell(double p[], double **xi, int Line 2902  void powell(double p[], double **xi, int
   if(!first){    if(!first){
     first=1;      first=1;
     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);      printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
     }else if (first >=1 && first <10){
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       first++;
     }else if (first ==10){
       fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
       printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
       fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
       first++;
   }    }
   fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);  
   
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
Line 2844  void powell(double p[], double **xi, int Line 2985  void powell(double p[], double **xi, int
                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     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 (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 */                          /* 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,k)];        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)); */        /* 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++) { */      /* for (k=1; k<=cptcovn;k++) { */
Line 2866  void powell(double p[], double **xi, int Line 3008  void powell(double p[], double **xi, int
     /*   /\* 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,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+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 */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       if(Dummy[Tvar[Tage[k]]]){        /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        if(Dummy[Tage[k]]== 2){ /* dummy with age */
       } else{          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];         } 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]); */        /* 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 */      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]); */        /* 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][1]]==0){
         if(Dummy[Tvard[k][2]==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)];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
         }else{          }else{
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k];
         }          }
       }else{        }else{
         if(Dummy[Tvard[k][2]==0]){          if(Dummy[Tvard[k][2]]==0){
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]];
         }else{          }else{
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
         }          }
Line 2939  void powell(double p[], double **xi, int Line 3082  void powell(double p[], double **xi, int
                                   
     maxmax=0.;      maxmax=0.;
     for(i=1; i<=nlstate; i++){      for(i=1; i<=nlstate; i++){
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
       maxmax=FMAX(maxmax,meandiff[i]);        maxmax=FMAX(maxmax,meandiff[i]);
       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
     } /* i loop */      } /* i loop */
Line 2999  double **pmij(double **ps, double *cov, Line 3142  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 3008  double **pmij(double **ps, double *cov, Line 3151  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 3015  double **pmij(double **ps, double *cov, Line 3159  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.);
     /* Computing other pijs */      /* Computing other pijs */
     for(j=1; j<i; j++)      for(j=1; j<i; j++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];/* Bug valgrind */
     for(j=i+1; j<=nlstate+ndeath; j++)      for(j=i+1; j<=nlstate+ndeath; j++)
       ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
Line 3073  double **pmij(double **ps, double *cov, Line 3217  double **pmij(double **ps, double *cov,
   doldm=ddoldms; /* global pointers */    doldm=ddoldms; /* global pointers */
   dnewm=ddnewms;    dnewm=ddnewms;
   dsavm=ddsavms;    dsavm=ddsavms;
     
     /* Debug */
     /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
   agefin=cov[2];    agefin=cov[2];
   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */    /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
   /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
Line 3081  double **pmij(double **ps, double *cov, Line 3227  double **pmij(double **ps, double *cov,
   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   
   /* P_x */    /* P_x */
   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */    pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm *//* Bug valgrind */
   /* outputs pmmij which is a stochastic matrix in row */    /* outputs pmmij which is a stochastic matrix in row */
   
   /* Diag(w_x) */    /* Diag(w_x) */
Line 3273  double ***hpxij(double ***po, int nhstep Line 3419  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 3293  double ***hpxij(double ***po, int nhstep Line 3439  double ***hpxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=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,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++){  
         if(Dummy[Tvar[Tage[k]]]){  
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         } else{  
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];   
         }  
         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovprod;k++){ /*  */  
         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */  
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
       }        }
         /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
         /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
         for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
           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);
           }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]]);
           }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]=Tinvresult[nres][Tvar[k1]];
             printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d Tinvresult[nres][%d]=%d,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],Tinvresult[nres][Tvar[k1]],nagesqr,k1,cov[2+nagesqr+k1]);
             /* 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]==2 ){ /* 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]]);
             /* 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,Tvard[k1][1], k1,Tvard[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]);
             /* 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 3327  double ***hpxij(double ***po, int nhstep Line 3538  double ***hpxij(double ***po, int nhstep
               
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                         /* right multiplication of oldm by the current matrix */        /* right multiplication of oldm by the current matrix */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
Line 3397  double ***hbxij(double ***po, int nhstep Line 3608  double ***hbxij(double ***po, int nhstep
       cov[1]=1.;        cov[1]=1.;
       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
           /* Debug */
         /* 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<=cptcovn;k++){        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,k)]; */
       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */        /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,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)); */          /* 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 */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
Line 3411  double ***hbxij(double ***po, int nhstep Line 3624  double ***hbxij(double ***po, int nhstep
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];           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]); */          /* 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 (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */
         if(Dummy[Tvar[Tage[k]]]){          /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];          if(Dummy[Tage[k]]== 2){ /* dummy with age */
         } else{            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];             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]); */          /* 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 */        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)];          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("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
Line 3430  double ***hbxij(double ***po, int nhstep Line 3657  double ***hbxij(double ***po, int nhstep
       /* 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),\ */
       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                    1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
       /*        for(i=1; i<=nlstate+ndeath; i++) { */        /*        for(i=1; i<=nlstate+ndeath; i++) { */
Line 3516  double func( double *x) Line 3743  double func( double *x)
       */        */
       ioffset=2+nagesqr ;        ioffset=2+nagesqr ;
    /* Fixed */     /* Fixed */
       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */        for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant 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 (k=6)*/          /* # 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 */
           /*  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)  */
           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)*/
           /* 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] 
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 
          has been calculated etc */           has been calculated etc */
       /* For an individual i, wav[i] gives the number of effective waves */        /* For an individual i, wav[i] gives the number of effective waves */
       /* We compute the contribution to Likelihood of each effective transition        /* We compute the contribution to Likelihood of each effective transition
Line 3532  double func( double *x) Line 3764  double func( double *x)
          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++){
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/          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]; */            /* 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];
         }          }
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
Line 3548  double func( double *x) Line 3780  double func( double *x)
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;  /* Should be changed here */              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
           if(!FixedV[Tvar[Tage[kk]]])              if(!FixedV[Tvar[Tage[kk]]])
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */                cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
           else              else
             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;                cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 3659  double func( double *x) Line 3891  double func( double *x)
     } /* end of individual */      } /* end of individual */
   }  else if(mle==2){    }  else if(mle==2){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];        ioffset=2+nagesqr ;
         for (k=1; k<=ncovf;k++)
           cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(k=1; k <= ncovv ; k++){
             cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
           }
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 3838  double funcone( double *x) Line 4075  double funcone( double *x)
     /* 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 */      for (k=1; k<=ncovf;k++){ /* 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[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[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];  */
Line 4017  void likelione(FILE *ficres,double p[], Line 4254  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter=0;    int i,j,k, jk, jkk=0, iter=0;
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
Line 4051  void mlikeli(FILE *ficres,double p[], in Line 4288  void mlikeli(FILE *ficres,double p[], in
       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficrespow,"\n");    fprintf(ficrespow,"\n");
 #ifdef POWELL  #ifdef POWELL
   #ifdef LINMINORIGINAL
   #else /* LINMINORIGINAL */
     
     flatdir=ivector(1,npar); 
     for (j=1;j<=npar;j++) flatdir[j]=0; 
   #endif /*LINMINORIGINAL */
   
   #ifdef FLATSUP
     powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
     /* reorganizing p by suppressing flat directions */
     for(i=1, jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
           if(flatdir[jk]==1){
             printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
           }
           for(j=1; j <=ncovmodel; j++){
             printf("%12.7f ",p[jk]);
             jk++; 
           }
           printf("\n");
         }
       }
     }
   /* skipping */
     /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
     for(i=1, jk=1, jkk=1;i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
           if(flatdir[jk]==1){
             printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
             for(j=1; j <=ncovmodel;  jk++,j++){
               printf(" p[%d]=%12.7f",jk, p[jk]);
               /*q[jjk]=p[jk];*/
             }
           }else{
             printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
             for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
               printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
               /*q[jjk]=p[jk];*/
             }
           }
           printf("\n");
         }
         fflush(stdout);
       }
     }
     powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
   #else  /* FLATSUP */
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
 #endif  #endif  /* FLATSUP */
   
   #ifdef LINMINORIGINAL
   #else
         free_ivector(flatdir,1,npar); 
   #endif  /* LINMINORIGINAL*/
   #endif /* POWELL */
   
 #ifdef NLOPT  #ifdef NLOPT
 #ifdef NEWUOA  #ifdef NEWUOA
Line 4080  void mlikeli(FILE *ficres,double p[], in Line 4374  void mlikeli(FILE *ficres,double p[], in
   }    }
   nlopt_destroy(opt);    nlopt_destroy(opt);
 #endif  #endif
   #ifdef FLATSUP
     /* npared = npar -flatd/ncovmodel; */
     /* xired= matrix(1,npared,1,npared); */
     /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
     /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
     /* free_matrix(xire,1,npared,1,npared); */
   #else  /* FLATSUP */
   #endif /* FLATSUP */
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
Line 4531  void  freqsummary(char fileres[], double Line 4833  void  freqsummary(char fileres[], double
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);    fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
       
   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4541  Title=%s <br>Datafile=%s Firstpass=%d La Line 4843  Title=%s <br>Datafile=%s Firstpass=%d La
     exit(70);       exit(70); 
   } else{    } else{
     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \      fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%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",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
       
   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);    x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
Line 4554  Title=%s <br>Datafile=%s Firstpass=%d La Line 4856  Title=%s <br>Datafile=%s Firstpass=%d La
       
   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
   j=cptcoveff;  /* Only dummy covariates of the model */    j=cptcoveff;  /* Only dummy covariates of the model */
     /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
       
Line 4561  Title=%s <br>Datafile=%s Firstpass=%d La Line 4864  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 4573  Title=%s <br>Datafile=%s Firstpass=%d La Line 4876  Title=%s <br>Datafile=%s Firstpass=%d La
   
   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */    /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
   /* Loop on nj=1 or 2 if dummy covariates j!=0    /* Loop on nj=1 or 2 if dummy covariates j!=0
    *   Loop on j1(1 to 2**cptcoveff) covariate combination     *   Loop on j1(1 to 2**cptcovn) covariate combination
    *     freq[s1][s2][iage] =0.     *     freq[s1][s2][iage] =0.
    *     Loop on iind     *     Loop on iind
    *       ++freq[s1][s2][iage] weighted     *       ++freq[s1][s2][iage] weighted
Line 4598  Title=%s <br>Datafile=%s Firstpass=%d La Line 4901  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=cptcovs; /* Other passes for the covariate values */
     }      }
     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 covariates combination of the model, 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 4634  Title=%s <br>Datafile=%s Firstpass=%d La Line 4937  Title=%s <br>Datafile=%s Firstpass=%d La
         bool=1;          bool=1;
         if(j !=0){          if(j !=0){
           if(anyvaryingduminmodel==0){ /* If All fixed covariates */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */              if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */                for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */
                 /* if(Tvaraff[z1] ==-20){ */                  /* if(Tvaraff[z1] ==-20){ */
                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                 /* }else  if(Tvaraff[z1] ==-10){ */                  /* }else  if(Tvaraff[z1] ==-10){ */
                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                 /* }else  */                  /* }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 (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,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", 
Line 4659  Title=%s <br>Datafile=%s Firstpass=%d La Line 4962  Title=%s <br>Datafile=%s Firstpass=%d La
             m=mw[mi][iind];              m=mw[mi][iind];
             if(j!=0){              if(j!=0){
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                 for (z1=1; z1<=cptcoveff; z1++) {                  for (z1=1; z1<=cptcovn; 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,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)]) {                      if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]) {
                       bool=0;                        bool=0;
                     }                      }
                   }                    }
Line 4693  Title=%s <br>Datafile=%s Firstpass=%d La Line 4996  Title=%s <br>Datafile=%s Firstpass=%d La
                   if(s[m][iind]==-1)                    if(s[m][iind]==-1)
                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));                      printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */                    for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
                     idq[z1]=idq[z1]+weight[iind];                      if(!isnan(covar[ncovcol+z1][iind])){
                     meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */                          idq[z1]=idq[z1]+weight[iind];
                     stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[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];*/  /* Computes mean of quantitative with selected filter */
                       }
                   }                    }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */                    /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
Line 4720  Title=%s <br>Datafile=%s Firstpass=%d La Line 5026  Title=%s <br>Datafile=%s Firstpass=%d La
           /* } */            /* } */
         } /* end bool */          } /* end bool */
       } /* end iind = 1 to imx */        } /* end iind = 1 to imx */
       /* prop[s][age] is feeded for any initial and valid live state as well as        /* prop[s][age] is fed for any initial and valid live state as well as
          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */           freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
               
               
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       if(cptcoveff==0 && nj==1) /* no covariate and first pass */        if(cptcovn==0 && nj==1) /* no covariate and first pass */
         pstamp(ficresp);          pstamp(ficresp);
       if  (cptcoveff>0 && j!=0){        if  (cptcovn>0 && j!=0){
         pstamp(ficresp);          pstamp(ficresp);
         printf( "\n#********** Variable ");           printf( "\n#********** Variable "); 
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         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 4759  Title=%s <br>Datafile=%s Firstpass=%d La Line 5065  Title=%s <br>Datafile=%s Firstpass=%d La
         Printing means of quantitative variables if any          Printing means of quantitative variables if any
       */        */
       for (z1=1; z1<= nqfveff; z1++) {        for (z1=1; z1<= nqfveff; z1++) {
         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);          fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);          fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
         if(weightopt==1){          if(weightopt==1){
           printf(" Weighted mean and standard deviation of");            printf(" Weighted mean and standard deviation of");
           fprintf(ficlog," Weighted mean and standard deviation of");            fprintf(ficlog," Weighted mean and standard deviation of");
           fprintf(ficresphtmfr," Weighted mean and standard deviation of");            fprintf(ficresphtmfr," Weighted mean and standard deviation of");
         }          }
         printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));          /* mu = \frac{w x}{\sum w}
         fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));             var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 
         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));          */
           printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
           fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
           fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
       }        }
       /* for (z1=1; z1<= nqtveff; z1++) { */        /* for (z1=1; z1<= nqtveff; z1++) { */
       /*        for(m=1;m<=lastpass;m++){ */        /*        for(m=1;m<=lastpass;m++){ */
Line 4777  Title=%s <br>Datafile=%s Firstpass=%d La Line 5086  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((cptcovn==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<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }        }
       if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");        if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");        fprintf(ficresphtm, "\n");
               
       /* Header of frequency table by age */        /* Header of frequency table by age */
Line 4852  Title=%s <br>Datafile=%s Firstpass=%d La Line 5161  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
                   
         /* Writing ficresp */          /* Writing ficresp */
         if(cptcoveff==0 && nj==1){ /* no covariate and first pass */          if(cptcovn==0 && nj==1){ /* no covariate and first pass */
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
           }            }
         }else if( nj==2){          }else if( nj==2){
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]);
           }            }
         }          }
         for(s1=1; s1 <=nlstate ; s1++){          for(s1=1; s1 <=nlstate ; s1++){
Line 4874  Title=%s <br>Datafile=%s Firstpass=%d La Line 5183  Title=%s <br>Datafile=%s Firstpass=%d La
           }            }
           if( iage <= iagemax){            if( iage <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               if(cptcoveff==0 && nj==1){ /* no covariate and first pass */                if(cptcovn==0 && nj==1){ /* no covariate and first pass */
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               }else if( nj==2){                }else if( nj==2){
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
Line 4883  Title=%s <br>Datafile=%s Firstpass=%d La Line 5192  Title=%s <br>Datafile=%s Firstpass=%d La
               /*probs[iage][s1][j1]= pp[s1]/pos;*/                /*probs[iage][s1][j1]= pp[s1]/pos;*/
               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/                /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
             } else{              } else{
               if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);                if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);                fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
             }              }
           }            }
Line 4909  Title=%s <br>Datafile=%s Firstpass=%d La Line 5218  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
         fprintf(ficresphtmfr,"</tr>\n ");          fprintf(ficresphtmfr,"</tr>\n ");
         fprintf(ficresphtm,"</tr>\n");          fprintf(ficresphtm,"</tr>\n");
         if((cptcoveff==0 && nj==1)|| nj==2 ) {          if((cptcovn==0 && nj==1)|| nj==2 ) {
           if(iage <= iagemax)            if(iage <= iagemax)
             fprintf(ficresp,"\n");              fprintf(ficresp,"\n");
         }          }
Line 5185  void prevalence(double ***probs, double Line 5494  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,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,Tvaraff[z1])]) {
               bool=0;                bool=0;
             }              }
         }          }
Line 5271  void  concatwav(int wav[], int **dh, int Line 5580  void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */      mi=0;  /* First valid wave */
     mli=0; /* Last valid wave */      mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;  /* Loop on waves */
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state or unknown state  */
       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
         mli=m-1;/* mw[++mi][i]=m-1; */          mli=m-1;/* mw[++mi][i]=m-1; */
       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
         mw[++mi][i]=m;          mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
         mli=m;          mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */        if(m < lastpass){ /* m < lastpass, standard case */
         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
       else{ /* m >= lastpass, eventual special issue with warning */        else{ /* m = lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
         break;          break;
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);              printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
             }else if(firsthree >=1 && firsthree < 10){
               fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
               firsthree++;
             }else if(firsthree == 10){
               printf("Information, too many Information flags: no more reported to log either\n");
               fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
               firsthree++;
             }else{
               firsthree++;
           }            }
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);            mw[++mi][i]=m; /* Valid transition with unknown status */
           mw[++mi][i]=m;  
           mli=m;            mli=m;
         }          }
         if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
           nbwarn++;            nbwarn++;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
           }            }
Line 5322  void  concatwav(int wav[], int **dh, int Line 5639  void  concatwav(int wav[], int **dh, int
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) {  /* Date of death is known */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
           nbwarn++;            nbwarn++;
           if(firstfiv==0){            if(firstfiv==0){
             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             firstfiv=1;              firstfiv=1;
           }else{            }else{
             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
           }            }
         }else{ /* Death occured afer last wave potential bias */              s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
           }else{ /* Month of Death occured afer last wave month, potential bias */
           nberr++;            nberr++;
           if(firstwo==0){            if(firstwo==0){
             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );              printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
             firstwo=1;              firstwo=1;
           }            }
           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
         }          }
       }else{ /* if date of interview is unknown */        }else{ /* if date of interview is unknown */
         /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){          if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
           firstfour=1;            firstfour=1;
         }          }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );          fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
       }        }
     } /* end if date of death is known */      } /* end if date of death is known */
 #endif  #endif
     wav[i]=mi; /* mi should be the last effective wave (or mli) */      wav[i]=mi; /* mi should be the last effective wave (or mli),  */
     /* wav[i]=mw[mi][i]; */      /* wav[i]=mw[mi][i];   */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
Line 5363  void  concatwav(int wav[], int **dh, int Line 5681  void  concatwav(int wav[], int **dh, int
   } /* End individuals */    } /* End individuals */
   /* wav and mw are no more changed */    /* wav and mw are no more changed */
                   
       printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
     fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
   
   
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
Line 5484  void  concatwav(int wav[], int **dh, int Line 5805  void  concatwav(int wav[], int **dh, int
      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]) {
        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
            modmaxcovj=0;
            modmincovj=0;
          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*/
            ij=(int)(covar[Tvar[k]][i]);             ij=(int)(covar[Tvar[k]][i]);
            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 5497  void  concatwav(int wav[], int **dh, int Line 5820  void  concatwav(int wav[], int **dh, int
            else if (ij < modmincovj)              else if (ij < modmincovj) 
              modmincovj=ij;                modmincovj=ij; 
            if (ij <0 || ij >1 ){             if (ij <0 || ij >1 ){
              printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);               printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
              fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);               fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
                fflush(ficlog);
                exit(1);
            }             }
            if ((ij < -1) || (ij > NCOVMAX)){             if ((ij < -1) || (ij > NCOVMAX)){
              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
Line 5573  void  concatwav(int wav[], int **dh, int Line 5898  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 */ 
          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(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);
              fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
              fflush(ficlog);
              exit(1);
            }
          }
        }
    } /* 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 5608  void  concatwav(int wav[], int **dh, int Line 5943  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 covariates: 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 5629  void  concatwav(int wav[], int **dh, int Line 5964  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 5697  void  concatwav(int wav[], int **dh, int Line 6034  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 5886  void  concatwav(int wav[], int **dh, int Line 6223  void  concatwav(int wav[], int **dh, int
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                       /* if((int)age ==50){ */
       /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
       /* } */
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
Line 6009  void  concatwav(int wav[], int **dh, int Line 6348  void  concatwav(int wav[], int **dh, int
      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);       fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[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,Tvaraff[j])]);
    fprintf(ficresprobmorprev,"\n");     fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
Line 6549  void varprob(char optionfilefiname[], do Line 6888  void varprob(char optionfilefiname[], do
    int k2, l2, j1,  z1;     int k2, l2, j1,  z1;
    int k=0, l;     int k=0, l;
    int first=1, first1, first2;     int first=1, first1, first2;
      int nres=0; /* New */
    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
    double **dnewm,**doldm;     double **dnewm,**doldm;
    double *xp;     double *xp;
Line 6637  To be simple, these graphs help to under Line 6977  To be simple, these graphs help to under
    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(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)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]);
        fprintf(ficresprob, "**********\n#\n");         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)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]);
        fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficresprobcov, "**********\n#\n");
                                                   
        fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "\n#********** Variable "); 
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]);
        fprintf(ficgp, "**********\n#\n");         fprintf(ficgp, "**********\n#\n");
                                                   
                                                   
        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          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(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,Tvaraff[z1])]);
        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                                                   
        fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "\n#********** Variable ");    
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[z1])]);
        fprintf(ficresprobcor, "**********\n#");             fprintf(ficresprobcor, "**********\n#");    
        if(invalidvarcomb[j1]){         if(invalidvarcomb[j1]){
          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
Line 6671  To be simple, these graphs help to under Line 7014  To be simple, these graphs help to under
        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++) {         /* for (k=1; k<=cptcovn;k++) { */
          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,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,TvarsD[k])];
          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                     * 1  1 1 1 1                                                                      * 1  1 1 1 1
                                                                     * 2  2 1 1 1                                                                      * 2  2 1 1 1
Line 6680  To be simple, these graphs help to under Line 7026  To be simple, these graphs help to under
                                                                     */                                                                      */
          /* nbcode[1][1]=0 nbcode[1][2]=1;*/           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
        }         }
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */         /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];         /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
        for (k=1; k<=cptcovprod;k++)         /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[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[Tage[k]]==2){ /* dummy with age */
                                      cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,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]);
              exit(1);
                /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(j1,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,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(j1,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]]; */
              }
            }
            /* 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(theta=1; theta <=npar; theta++){         for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
Line 6870  To be simple, these graphs help to under Line 7246  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 */
    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);
Line 6892  void printinghtml(char fileresu[], char Line 7269  void printinghtml(char fileresu[], char
                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, i1, cpt, k4, nres;
     /* In fact some results are already printed in fichtm which is open */
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li> model=1+age+%s\n \  /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
 </ul>", model);  /* </ul>", model); */
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 6930  void printinghtml(char fileresu[], char Line 7307  void printinghtml(char fileresu[], char
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
   
    jj1=0;     jj1=0;
   
Line 6965  void printinghtml(char fileresu[], char Line 7342  void printinghtml(char fileresu[], char
        fprintf(fichtm,"</a></li>");         fprintf(fichtm,"</a></li>");
      } /* cptcovn >0 */       } /* cptcovn >0 */
    }     }
      fprintf(fichtm," \n</ul>");     fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
Line 6999  void printinghtml(char fileresu[], char Line 7376  void printinghtml(char fileresu[], char
       }        }
                 
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
          printf("\nCombination (%d) ignored because no cases \n",k1);            printf("\nCombination (%d) ignored because no cases \n",k1); 
Line 7020  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7397  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 7044  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7425  divided by h: <sub>h</sub>P<sub>ij</sub>
      if(prevfcast==1){       if(prevfcast==1){
        /* Projection of prevalence up to period (forward stable) prevalence in each health state */         /* Projection of prevalence up to period (forward stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
            fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
                    subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
        }         }
      }       }
      if(prevbcast==1){       if(prevbcast==1){
Line 7054  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7437  divided by h: <sub>h</sub>P<sub>ij</sub>
          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \           fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \   from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \   account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
 with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \  with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
            fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
        }         }
      }       }
                     
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);         fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
Line 7113  See page 'Matrix of variance-covariance Line 7498  See page 'Matrix of variance-covariance
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);     fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
   
     jj1=0;
   
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
          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,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          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]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
      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 */
Line 7127  See page 'Matrix of variance-covariance Line 7548  See page 'Matrix of variance-covariance
      /* 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");
          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,"\"</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<=cptcoveff;cpt++){  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* 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 */         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," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }        }
   
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
   
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
Line 7144  See page 'Matrix of variance-covariance Line 7576  See page 'Matrix of variance-covariance
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional 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>\n <br>\  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);
 <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
 <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);       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);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
   }/* End nres */    }/* End nres */
Line 7269  void printinggnuplot(char fileresu[], ch Line 7703  void printinggnuplot(char fileresu[], ch
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
         fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);          fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */          /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
       /* k1-1 error should be nres-1*/        /* k1-1 error should be nres-1*/
Line 7690  set ter svg size 640, 480\nunset log y\n Line 8124  set ter svg size 640, 480\nunset log y\n
             fprintf(ficgp,", '' ");              fprintf(ficgp,", '' ");
           /* l=(nlstate+ndeath)*(i-1)+1; */            /* l=(nlstate+ndeath)*(i-1)+1; */
           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */            l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
           /* for (j=2; j<= nlstate ; j ++) */            /* for (j=2; j<= nlstate ; j ++) */
           /*    fprintf(ficgp,"+$%d",k+l+j-1); */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
Line 8040  set ter svg size 640, 480\nunset log y\n Line 8474  set ter svg size 640, 480\nunset log y\n
             /* 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!!*/                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){                    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){
Line 8100  set ter svg size 640, 480\nunset log y\n Line 8547  set ter svg size 640, 480\nunset log y\n
                 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 8119  set ter svg size 640, 480\nunset log y\n Line 8627  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 8464  void prevforecast(char fileres[], double Line 8972  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])]);
     }      }
     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 8494  void prevforecast(char fileres[], double Line 9002  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])]);
         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 8604  void prevforecast(char fileres[], double Line 9112  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,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 8640  void prevforecast(char fileres[], double Line 9148  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,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 8707  void prevforecast(char fileres[], double Line 9215  void prevforecast(char fileres[], double
       printf("\n#****** ");        printf("\n#****** ");
       fprintf(ficlog,"\n#****** ");        fprintf(ficlog,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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,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][j]);
Line 8764  void prevforecast(char fileres[], double Line 9272  void prevforecast(char fileres[], double
        printf("\n#****** ");         printf("\n#****** ");
        fprintf(ficlog,"\n#****** ");         fprintf(ficlog,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {         for(j=1;j<=cptcoveff;j++) {
          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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,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][j]);
Line 9233  int readdata(char datafile[], int firsto Line 9741  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 9373  int readdata(char datafile[], int firsto Line 9885  int readdata(char datafile[], int firsto
         }          }
         if(lval <-1 || lval >1){          if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \            printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n                 \   For example, for multinomial values like 1, 2 and 3,\n                 \
  build V1=0 V2=0 for the reference value (1),\n                         \   build V1=0 V2=0 for the reference value (1),\n                         \
         V1=1 V2=0 for (2) \n                                            \          V1=1 V2=0 for (2) \n                                            \
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n                                \   output of IMaCh is often meaningless.\n                                \
  Exiting.\n",lval,linei, i,line,j);   Exiting.\n",lval,linei, i,line,iv,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \            fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n                 \   For example, for multinomial values like 1, 2 and 3,\n                 \
  build V1=0 V2=0 for the reference value (1),\n                         \   build V1=0 V2=0 for the reference value (1),\n                         \
         V1=1 V2=0 for (2) \n                                            \          V1=1 V2=0 for (2) \n                                            \
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n                                \   output of IMaCh is often meaningless.\n                                \
  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);   Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
           return 1;            return 1;
         }          }
         cotvar[j][iv][i]=(double)(lval);          cotvar[j][iv][i]=(double)(lval);
Line 9497  int readdata(char datafile[], int firsto Line 10009  int readdata(char datafile[], int firsto
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing value */        if(strb[0]=='.') { /* Missing value */
         lval=-1;          lval=-1;
           coqvar[iv][i]=NAN; 
           covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ 
       }else{        }else{
         errno=0;          errno=0;
         /* what_kind_of_number(strb); */          /* what_kind_of_number(strb); */
Line 9590  void removefirstspace(char **stri){/*, c Line 10104  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];
   
Line 9615  int decoderesult ( char resultline[], in Line 10129  int decoderesult ( char resultline[], in
     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 variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      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);
     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      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);
   }    }
   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 ' '         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" */
                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */        cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */  
     }else      }else
       cutl(strc,strd,resultsav,'=');        cutl(strc,strd,resultsav,'=');
     Tvalsel[k]=atof(strc); /* 1 */      Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
           
     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;      cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
     Tvarsel[k]=atoi(strc);      Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */      /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
     /* cptcovsel++;     */      /* cptcovsel++;     */
     if (nbocc(stra,'=') >0)      if (nbocc(stra,'=') >0)
       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++){ /* 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 covariate in model */      if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
       match=0;        match=0;
       for(k2=1; k2 <=j;k2++){/* 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[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[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
           match=1;            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: %d value missing; result: %s, model=%s\n",k1, resultline, model);          printf("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: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
           return 1;
       }        }
     }      }
   }    }
   /* 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++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    for(k2=1; k2 <=j;k2++){ /* 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++){ /* 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 */
         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;  /* 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 */
           ++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: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         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);
         fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
         return 1;
     }      }
   }    }
               
   /* 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++){ /* model line */    for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop k1 on position in the model line (excluding product) */
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */        /* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */        /* modelresult[k3]=k1: k3th position in the result line correspond to the k1 position in the model line */
       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */        /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */        /* 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: Name of the variable at the k3th position in the result line Tvarsel[k3].                                                  */
         /* Tvalsel: Value of the variable at the k3th position in the result line Tvarsel[k3].                                                 */
         /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                                 */
         /* Tvresult[nres][result_position]= id of the dummy variable at the result_position in the nres resultline                                   */
         /* 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]; /* 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)*/
         k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
         Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */        Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */        Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
         TinvDoQresult[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);        printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, 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 ){ /* Single quantitative */
       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */        /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */        /* Tqvresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
         /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
         k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);        printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
       k4q++;;        k4q++;;
       }else{
         printf("Decodemodel probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
         fprintf(ficlog,"Decodemodel probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
     }      }
   }    }
       
Line 9721  int decodemodel( char model[], int lasto Line 10259  int decodemodel( char model[], int lasto
         * - cptcovs number of simple covariates          * - cptcovs number of simple covariates
         * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10          * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
         *     which is a new column after the 9 (ncovcol) variables.           *     which is a new column after the 9 (ncovcol) variables. 
         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual          * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.          *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
         */          */
   /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
 {  {
   int i, j, k, ks, v;    int i, j, k, ks, v;
   int  j1, k1, k2, k3, k4;    int  j1, k1, k2, k3, k4;
Line 9803  int decodemodel( char model[], int lasto Line 10342  int decodemodel( char model[], int lasto
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8         *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}         * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}         * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}         *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8            * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];         *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?         *How to reorganize? Tvars(orted)
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age         * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}         * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}         *       {2,   1,     4,      8,    5,      6,     3,       7}
Line 9833  int decodemodel( char model[], int lasto Line 10372  int decodemodel( char model[], int lasto
         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
       }        }
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */                                            modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */          if (nbocc(modelsav,'+')==0)
             strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/          /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */          if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */            cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */            if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */              /* covar is not filled and then is empty */
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */              cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */              Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             Typevar[k]=1;  /* 1 for age product */              Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Counts the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */            } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;              cptcovprod--;
Line 9865  int decodemodel( char model[], int lasto Line 10405  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
                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                  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 */
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */              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 9885  int decodemodel( char model[], int lasto Line 10428  int decodemodel( char model[], int lasto
             }              }
           } /* End age is not in the model */            } /* End age is not in the model */
         } /* End if model includes a product */          } /* End if model includes a product */
         else { /* no more sum */          else { /* not a product */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
Line 9916  int decodemodel( char model[], int lasto Line 10459  int decodemodel( char model[], int lasto
    model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place     model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
    k =           1    2   3     4       5       6      7      8        9     k =           1    2   3     4       5       6      7      8        9
    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5     Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
    Typevar[k]=   0    0   0     2       1       0      2      1        1     Typevar[k]=   0    0   0     2       1       0      2      1        0
    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3     Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
    Dummy[k]      1    0   0     0       3       1      1      2        3     Dummy[k]      1    0   0     0       3       1      1      2        3
           Tmodelind[combination of covar]=k;            Tmodelind[combination of covar]=k;
Line 9925  int decodemodel( char model[], int lasto Line 10468  int decodemodel( char model[], int lasto
   /* If Tvar[k] >ncovcol it is a product */    /* If Tvar[k] >ncovcol it is a product */
   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
         /* Computing effective variables, ie used by the model, that is from the cptcovt variables */          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
   printf("Model=%s\n\    printf("Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   fprintf(ficlog,"Model=%s\n\    fprintf(ficlog,"Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
Line 9944  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10487  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 9955  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10499  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 9981  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10526  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 9996  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10542  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];        TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
       TvarsQind[nsq]=k;        TvarsQind[nsq]=k;
       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 */
Line 10566  int prevalence_limit(double *p, double * Line 11112  int prevalence_limit(double *p, double *
       printf("#******");        printf("#******");
       fprintf(ficlog,"#******");        fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
         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,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,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 */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 10587  int prevalence_limit(double *p, double * Line 11133  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,Tvaraff[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");
Line 10597  int prevalence_limit(double *p, double * Line 11143  int prevalence_limit(double *p, double *
         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
         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,Tvaraff[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 10657  int back_prevalence_limit(double *p, dou Line 11203  int back_prevalence_limit(double *p, dou
       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,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,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,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][j]);
Line 10678  int back_prevalence_limit(double *p, dou Line 11224  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,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 10702  int back_prevalence_limit(double *p, dou Line 11248  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,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 10760  int hPijx(double *p, int bage, int fage) Line 11306  int hPijx(double *p, int bage, int fage)
         continue;          continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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 */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 10839  int hPijx(double *p, int bage, int fage) Line 11385  int hPijx(double *p, int bage, int fage)
         continue;          continue;
       fprintf(ficrespijb,"\n#****** ");        fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       }        }
Line 10862  int hPijx(double *p, int bage, int fage) Line 11408  int hPijx(double *p, int bage, int fage)
   
         /* oldm=oldms;savm=savms; */          /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);          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); */          /* 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=");          fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
Line 10875  int hPijx(double *p, int bage, int fage) Line 11421  int hPijx(double *p, int bage, int fage)
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */            /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);                fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
           fprintf(ficrespijb,"\n");            fprintf(ficrespijb,"\n");
         }          }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 10928  int main(int argc, char *argv[]) Line 11474  int main(int argc, char *argv[])
   double dum=0.; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
     double wald;
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
Line 10964  int main(int argc, char *argv[]) Line 11511  int main(int argc, char *argv[])
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double **bprlim;    double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel) 
                       state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
   double ***paramstart; /* Matrix of starting parameter values */    double ***paramstart; /* Matrix of starting parameter values */
   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */    double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
Line 11558  Please run with mle=-1 to get a correct Line 12106  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));
   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 11577  Please run with mle=-1 to get a correct Line 12126  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); /*  */
   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 11619  Please run with mle=-1 to get a correct Line 12169  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 11726  Please run with mle=-1 to get a correct Line 12279  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 11835  Title=%s <br>Datafile=%s Firstpass=%d La Line 12388  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<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>  \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <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\
Line 11891  Title=%s <br>Datafile=%s Firstpass=%d La Line 12444  Title=%s <br>Datafile=%s Firstpass=%d La
 <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));  <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
       
   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
   imx,agemin,agemax,jmin,jmax,jmean);    imx,agemin,agemax,jmin,jmax,jmean);
Line 12171  Please run with mle=-1 to get a correct Line 12724  Please run with mle=-1 to get a correct
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   
       printf("#model=  1      +     age ");
       fprintf(ficres,"#model=  1      +     age ");
       fprintf(ficlog,"#model=  1      +     age ");
       fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
   </ul>", model);
   
       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
       fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
       if(nagesqr==1){
         printf("  + age*age  ");
         fprintf(ficres,"  + age*age  ");
         fprintf(ficlog,"  + age*age  ");
         fprintf(fichtm, "<th>+ age*age</th>");
       }
       for(j=1;j <=ncovmodel-2;j++){
         if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);
           fprintf(ficres,"  +      V%d  ",Tvar[j]);
           fprintf(ficlog,"  +      V%d  ",Tvar[j]);
           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
         }else if(Typevar[j]==1) {
           printf("  +    V%d*age ",Tvar[j]);
           fprintf(ficres,"  +    V%d*age ",Tvar[j]);
           fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
         }else if(Typevar[j]==2) {
           printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }
       }
       printf("\n");
       fprintf(ficres,"\n");
       fprintf(ficlog,"\n");
       fprintf(fichtm, "</tr>");
       fprintf(fichtm, "\n");
       
       
     for(i=1,jk=1; i <=nlstate; i++){      for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){        for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {          if (k != i) {
             fprintf(fichtm, "<tr>");
           printf("%d%d ",i,k);            printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficres,"%1d%1d ",i,k);
             fprintf(fichtm, "<td>%1d%1d</td>",i,k);
           for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
             printf("%12.7f ",p[jk]);              printf("%12.7f ",p[jk]);
             fprintf(ficlog,"%12.7f ",p[jk]);              fprintf(ficlog,"%12.7f ",p[jk]);
             fprintf(ficres,"%12.7f ",p[jk]);              fprintf(ficres,"%12.7f ",p[jk]);
               fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
             jk++;               jk++; 
           }            }
           printf("\n");            printf("\n");
           fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
             fprintf(fichtm, "</tr>\n");
         }          }
       }        }
     }      }
       /* fprintf(fichtm,"</tr>\n"); */
       fprintf(fichtm,"</table>\n");
       fprintf(fichtm, "\n");
   
     if(mle != 0){      if(mle != 0){
       /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, hess, p, npar, delti, ftolhess, func);        hesscov(matcov, hess, p, npar, delti, ftolhess, func);
       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
         fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
         fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
         fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
         if(nagesqr==1){
           printf("  + age*age  ");
           fprintf(ficres,"  + age*age  ");
           fprintf(ficlog,"  + age*age  ");
           fprintf(fichtm, "<th>+ age*age</th>");
         }
         for(j=1;j <=ncovmodel-2;j++){
           if(Typevar[j]==0) {
             printf("  +      V%d  ",Tvar[j]);
             fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
           }else if(Typevar[j]==1) {
             printf("  +    V%d*age ",Tvar[j]);
             fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
           }else if(Typevar[j]==2) {
             fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           }
         }
         fprintf(fichtm, "</tr>\n");
    
       for(i=1,jk=1; i <=nlstate; i++){        for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){          for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {            if (k != i) {
               fprintf(fichtm, "<tr valign=top>");
             printf("%d%d ",i,k);              printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);              fprintf(ficlog,"%d%d ",i,k);
               fprintf(fichtm, "<td>%1d%1d</td>",i,k);
             for(j=1; j <=ncovmodel; j++){              for(j=1; j <=ncovmodel; j++){
               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                wald=p[jk]/sqrt(matcov[jk][jk]);
               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                 fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                 if(fabs(wald) > 1.96){
                   fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
                 }else{
                   fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
                 }
                 fprintf(fichtm,"W=%8.3f</br>",wald);
                 fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               jk++;                 jk++; 
             }              }
             printf("\n");              printf("\n");
             fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
               fprintf(fichtm, "</tr>\n");
           }            }
         }          }
       }        }
     } /* end of hesscov and Wald tests */      } /* end of hesscov and Wald tests */
       fprintf(fichtm,"</table>\n");
           
     /*  */      /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
Line 12462  Please run with mle=-1 to get a correct Line 13097  Please run with mle=-1 to get a correct
           prvforecast = 1;            prvforecast = 1;
         }           } 
         else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/          else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
           printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);            printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
           fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);            fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
           fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);            fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
           prvforecast = 2;            prvforecast = 2;
         }          }
         else {          else {
Line 12485  Please run with mle=-1 to get a correct Line 13120  Please run with mle=-1 to get a correct
           prvbackcast = 1;            prvbackcast = 1;
         }           } 
         else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/          else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
           printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);            printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
           fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);            fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
           fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);            fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
           prvbackcast = 2;            prvbackcast = 2;
         }          }
         else {          else {
Line 12500  Please run with mle=-1 to get a correct Line 13135  Please run with mle=-1 to get a correct
         num_filled=sscanf(line,"result:%[^\n]\n",resultline);          num_filled=sscanf(line,"result:%[^\n]\n",resultline);
         nresult++; /* Sum of resultlines */          nresult++; /* Sum of resultlines */
         printf("Result %d: result:%s\n",nresult, resultline);          printf("Result %d: result:%s\n",nresult, resultline);
         if(nresult > MAXRESULTLINES){          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. ",MAXRESULTLINES,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. ",MAXRESULTLINES,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;
         }          }
         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);
         fprintf(ficlog,"result: %s\n",resultline);            fprintf(ficlog,"result: %s\n",resultline);
           } else
             goto end;
         break;          break;
       case 14:        case 14:
         printf("Error: Unknown command '%s'\n",line);          printf("Error: Unknown command '%s'\n",line);
         fprintf(ficlog,"Error: Unknown command '%s'\n",line);          fprintf(ficlog,"Error: Unknown command '%s'\n",line);
           if(line[0] == ' ' || line[0] == '\n'){
             printf("It should not be an empty line '%s'\n",line);
             fprintf(ficlog,"It should not be an empty line '%s'\n",line);
           }         
         if(ncovmodel >=2 && nresult==0 ){          if(ncovmodel >=2 && nresult==0 ){
           printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);            printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
           fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);            fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
Line 12732  Please run with mle=-1 to get a correct Line 13373  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,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,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][j]);
Line 12744  Please run with mle=-1 to get a correct Line 13385  Please run with mle=-1 to get a correct
               
       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 12797  Please run with mle=-1 to get a correct Line 13439  Please run with mle=-1 to get a correct
     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("\n#****** Result for:");        printf("\n# model %s \n#****** Result for:", model);
       fprintf(ficrest,"\n#****** Result for:");        fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
       fprintf(ficlog,"\n#****** Result for:");        fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
       for(j=1;j<=cptcoveff;j++){         for(j=1;j<=cptcoveff;j++){ 
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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,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][j]);
Line 12817  Please run with mle=-1 to get a correct Line 13459  Please run with mle=-1 to get a correct
       fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
       fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
Line 12830  Please run with mle=-1 to get a correct Line 13472  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 ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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]);
       }         } 
Line 12920  Please run with mle=-1 to get a correct Line 13562  Please run with mle=-1 to get a correct
   
           
     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 12967  Please run with mle=-1 to get a correct Line 13610  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);

Removed from v.1.308  
changed lines
  Added in v.1.330


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