Diff for /imach/src/imach.c between versions 1.191 and 1.227

version 1.191, 2015/07/14 10:00:33 version 1.227, 2016/07/21 08:43:33
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 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.227  2016/07/21 08:43:33  brouard
     Summary: 0.99 working (more or less) for Asian Workshop on multitate methods
   
     Revision 1.226  2016/07/12 18:42:34  brouard
     Summary: temp
   
     Revision 1.225  2016/07/12 08:40:03  brouard
     Summary: saving but not running
   
     Revision 1.224  2016/07/01 13:16:01  brouard
     Summary: Fixes
   
     Revision 1.223  2016/02/19 09:23:35  brouard
     Summary: temporary
   
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
     Revision 1.221  2016/02/15 23:35:36  brouard
     Summary: minor bug
   
     Revision 1.219  2016/02/15 00:48:12  brouard
     *** empty log message ***
   
     Revision 1.218  2016/02/12 11:29:23  brouard
     Summary: 0.99 Back projections
   
     Revision 1.217  2015/12/23 17:18:31  brouard
     Summary: Experimental backcast
   
     Revision 1.216  2015/12/18 17:32:11  brouard
     Summary: 0.98r4 Warning and status=-2
   
     Version 0.98r4 is now:
      - displaying an error when status is -1, date of interview unknown and date of death known;
      - permitting a status -2 when the vital status is unknown at a known date of right truncation.
     Older changes concerning s=-2, dating from 2005 have been supersed.
   
     Revision 1.215  2015/12/16 08:52:24  brouard
     Summary: 0.98r4 working
   
     Revision 1.214  2015/12/16 06:57:54  brouard
     Summary: temporary not working
   
     Revision 1.213  2015/12/11 18:22:17  brouard
     Summary: 0.98r4
   
     Revision 1.212  2015/11/21 12:47:24  brouard
     Summary: minor typo
   
     Revision 1.211  2015/11/21 12:41:11  brouard
     Summary: 0.98r3 with some graph of projected cross-sectional
   
     Author: Nicolas Brouard
   
     Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
     Revision 1.209  2015/11/17 22:12:03  brouard
     Summary: Adding ftolpl parameter
     Author: N Brouard
   
     We had difficulties to get smoothed confidence intervals. It was due
     to the period prevalence which wasn't computed accurately. The inner
     parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
     computation are long.
   
     Revision 1.208  2015/11/17 14:31:57  brouard
     Summary: temporary
   
     Revision 1.207  2015/10/27 17:36:57  brouard
     *** empty log message ***
   
     Revision 1.206  2015/10/24 07:14:11  brouard
     *** empty log message ***
   
     Revision 1.205  2015/10/23 15:50:53  brouard
     Summary: 0.98r3 some clarification for graphs on likelihood contributions
   
     Revision 1.204  2015/10/01 16:20:26  brouard
     Summary: Some new graphs of contribution to likelihood
   
     Revision 1.203  2015/09/30 17:45:14  brouard
     Summary: looking at better estimation of the hessian
   
     Also a better criteria for convergence to the period prevalence And
     therefore adding the number of years needed to converge. (The
     prevalence in any alive state shold sum to one
   
     Revision 1.202  2015/09/22 19:45:16  brouard
     Summary: Adding some overall graph on contribution to likelihood. Might change
   
     Revision 1.201  2015/09/15 17:34:58  brouard
     Summary: 0.98r0
   
     - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
   
     Revision 1.200  2015/09/09 16:53:55  brouard
     Summary: Big bug thanks to Flavia
   
     Even model=1+age+V2. did not work anymore
   
     Revision 1.199  2015/09/07 14:09:23  brouard
     Summary: 0.98q6 changing default small png format for graph to vectorized svg.
   
     Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
   
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
     Revision 1.194  2015/08/18 13:32:00  brouard
     Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
     Revision 1.193  2015/08/04 07:17:42  brouard
     Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
   Revision 1.191  2015/07/14 10:00:33  brouard    Revision 1.191  2015/07/14 10:00:33  brouard
   Summary: Some fixes    Summary: Some fixes
   
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   Short summary of the programme:    Short summary of the programme:
       
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies or State-specific
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (if states aren't health statuses) Expectancies from
   first survey ("cross") where individuals from different ages are    cross-longitudinal data. Cross-longitudinal data consist in: 
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    -1- a first survey ("cross") where individuals from different ages
   second wave of interviews ("longitudinal") which measure each change    are interviewed on their health status or degree of disability (in
   (if any) in individual health status.  Health expectancies are    the case of a health survey which is our main interest)
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    -2- at least a second wave of interviews ("longitudinal") which
   Maximum Likelihood of the parameters involved in the model.  The    measure each change (if any) in individual health status.  Health
   simplest model is the multinomial logistic model where pij is the    expectancies are computed from the time spent in each health state
   probability to be observed in state j at the second wave    according to a model. More health states you consider, more time is
   conditional to be observed in state i at the first wave. Therefore    necessary to reach the Maximum Likelihood of the parameters involved
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    in the model.  The simplest model is the multinomial logistic model
   'age' is age and 'sex' is a covariate. If you want to have a more    where pij is the probability to be observed in state j at the second
   complex model than "constant and age", you should modify the program    wave conditional to be observed in state i at the first
   where the markup *Covariates have to be included here again* invites    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
   you to do it.  More covariates you add, slower the    etc , where 'age' is age and 'sex' is a covariate. If you want to
     have a more complex model than "constant and age", you should modify
     the program where the markup *Covariates have to be included here
     again* invites you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
Line 545 Line 681
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the period (stable) prevalence.     of the life expectancies. It also computes the period (stable) prevalence.
   
   Back prevalence and projections:
   
    - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
      double agemaxpar, double ftolpl, int *ncvyearp, double
      dateprev1,double dateprev2, int firstpass, int lastpass, int
      mobilavproj)
   
       Computes the back prevalence limit for any combination of
       covariate values k at any age between ageminpar and agemaxpar and
       returns it in **bprlim. In the loops,
   
      - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
          **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
   
      - hBijx Back Probability to be in state i at age x-h being in j at x
      Computes for any combination of covariates k and any age between bage and fage 
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                           oldm=oldms;savm=savms;
   
      - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
        Computes the transition matrix starting at age 'age' over
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
        nhstepm*hstepm matrices. 
   
        Returns p3mat[i][j][h] after calling
        p3mat[i][j][h]=matprod2(newm,
        bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
        dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
        oldm);
   
   Important routines
   
   - func (or funcone), computes logit (pij) distinguishing
     o fixed variables (single or product dummies or quantitative);
     o varying variables by:
      (1) wave (single, product dummies, quantitative), 
      (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
          % fixed dummy (treated) or quantitative (not done because time-consuming);
          % varying dummy (not done) or quantitative (not done);
   - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
     and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
   - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
     o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
       race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
   
   
       
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
Line 604 Line 788
   
 /* #define DEBUG */  /* #define DEBUG */
 /* #define DEBUGBRENT */  /* #define DEBUGBRENT */
   /* #define DEBUGLINMIN */
   /* #define DEBUGHESS */
   #define DEBUGHESSIJ
   /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
   #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 *\/ */
   
Line 612 Line 801
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   #include <ctype.h>
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
Line 673  typedef struct { Line 863  typedef struct {
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  1 & (h-1) >> (k-1) ;  #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) >> (k-1)) & 1) +1 
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  /* #define AGESUP 130 */
   #define AGESUP 150
   #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
   #define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32  #ifdef _WIN32
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
Line 691  typedef struct { Line 886  typedef struct {
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   #include "version.h"
 char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char version[]=__IMACH_VERSION__;
   char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 701  int nagesqr=0, nforce=0; /* nagesqr=1 if Line 897  int nagesqr=0, nforce=0; /* nagesqr=1 if
 /* Number of covariates model=V2+V1+ V3*age+V2*V4 */  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */  int cptcovs=0; /**< cptcovs number of simple covariates in the model 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 */
   int ncoveff=0; /* Total number of effective covariates in the model */
   int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
   int ntveff=0; /**< ntveff number of effective time varying variables */
   int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
Line 728  double jmean=1; /* Mean space between 2 Line 931  double jmean=1; /* Mean space between 2
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
   
 /*FILE *fic ; */ /* Used in readdata only */  /*FILE *fic ; */ /* Used in readdata only */
 FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
 int globpr=0; /* Global variable for printing or not */  int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
Line 752  char fileresv[FILENAMELENGTH]; Line 957  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
 char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 char command[FILENAMELENGTH];  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char fileresu[FILENAMELENGTH]; /* fileres without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
Line 827  int estepm; Line 1032  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;  int firstpass=0, lastpass=4,*cod, *cens;
   int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                      covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs; /* Global pointer */
   double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
Line 839  double *agedc; Line 1051  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * covar=matrix(0,NCOVMAX,1,n);                     * covar=matrix(0,NCOVMAX,1,n); 
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
   double **coqvar; /* Fixed quantitative covariate iqv */
   double ***cotvar; /* Time varying covariate itv */
   double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
   int *Tage;
   int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
   int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 int **codtab; /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **Tvard;
   int *Tprod;/**< Gives the k position of the k1 product */
   int *Tposprod; /**< Gives the k1 product from the k position */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
   */
   int cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
Line 876  static int split( char *path, char *dirc Line 1104  static int split( char *path, char *dirc
     }      }
     /* got dirc from getcwd*/      /* got dirc from getcwd*/
     printf(" DIRC = %s \n",dirc);      printf(" DIRC = %s \n",dirc);
   } else {                              /* strip direcotry from path */    } else {                              /* strip directory from path */
     ss++;                               /* after this, the filename */      ss++;                               /* after this, the filename */
     l2 = strlen( ss );                  /* length of filename */      l2 = strlen( ss );                  /* length of filename */
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 1284  char *subdirf3(char fileres[], char *pre Line 1512  char *subdirf3(char fileres[], char *pre
   strcat(tmpout,fileres);    strcat(tmpout,fileres);
   return tmpout;    return tmpout;
 }  }
    
   /*************** function subdirfext ***********/
   char *subdirfext(char fileres[], char *preop, char *postop)
   {
     
     strcpy(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
   
   /*************** function subdirfext3 ***********/
   char *subdirfext3(char fileres[], char *preop, char *postop)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
    
 char *asc_diff_time(long time_sec, char ascdiff[])  char *asc_diff_time(long time_sec, char ascdiff[])
 {  {
   long sec_left, days, hours, minutes;    long sec_left, days, hours, minutes;
Line 1362  double brent(double ax, double bx, doubl Line 1613  double brent(double ax, double bx, doubl
       etemp=e;         etemp=e; 
       e=d;         e=d; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));                                   d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       else {         else { 
         d=p/q;                                   d=p/q; 
         u=x+d;                                   u=x+d; 
         if (u-a < tol2 || b-u < tol2)                                   if (u-a < tol2 || b-u < tol2) 
           d=SIGN(tol1,xm-x);                                           d=SIGN(tol1,xm-x); 
       }         } 
     } else {       } else { 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
Line 1381  double brent(double ax, double bx, doubl Line 1632  double brent(double ax, double bx, doubl
     } else {       } else { 
       if (u < x) a=u; else b=u;         if (u < x) a=u; else b=u; 
       if (fu <= fw || w == x) {         if (fu <= fw || w == x) { 
         v=w;                                   v=w; 
         w=u;                                   w=u; 
         fv=fw;                                   fv=fw; 
         fw=fu;                                   fw=fu; 
       } else if (fu <= fv || v == x || v == w) {         } else if (fu <= fv || v == x || v == w) { 
         v=u;                                   v=u; 
         fv=fu;                                   fv=fu; 
       }         } 
     }       } 
   }     } 
Line 1428  values at the three points, fa, fb , and Line 1679  values at the three points, fa, fb , and
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
 #ifdef DEBUG  #ifdef DEBUG
   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);    fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
 #endif  #endif
   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
     r=(*bx-*ax)*(*fb-*fc);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
Line 1444  values at the three points, fa, fb , and Line 1695  values at the three points, fa, fb , and
       double A, fparabu;         double A, fparabu; 
       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       fparabu= *fa - A*(*ax-u)*(*ax-u);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);        printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);        fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
       /* And thus,it can be that fu > *fc even if fparabu < *fc */        /* And thus,it can be that fu > *fc even if fparabu < *fc */
       /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
Line 1478  values at the three points, fa, fb , and Line 1729  values at the three points, fa, fb , and
 /*      fu = *fc; */  /*      fu = *fc; */
 /*      *fc =dum; */  /*      *fc =dum; */
 /*       } */  /*       } */
 #ifdef DEBUG  #ifdef DEBUGMNBRAK
       printf("mnbrak34  fu < or >= fc \n");                   double A, fparabu; 
       fprintf(ficlog, "mnbrak34 fu < fc\n");       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
        printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
        fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
 #endif  #endif
       dum=u; /* Shifting c and u */        dum=u; /* Shifting c and u */
       u = *cx;        u = *cx;
Line 1491  values at the three points, fa, fb , and Line 1745  values at the three points, fa, fb , and
 #endif  #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim\n");        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
 #endif  #endif
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u after c but before ulim AND fu < fc\n");                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");                            fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
   #endif
                             SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                                   SHFT(*fb,*fc,fu,(*func)(u)) 
   #ifdef DEBUG
                                           printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
 #endif  #endif
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))   
         SHFT(*fb,*fc,fu,(*func)(u))   
       }         } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");        fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
 #endif  #endif
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else { /* u could be left to b (if r > q parabola has a maximum) */      } else { /* u could be left to b (if r > q parabola has a maximum) */
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");        fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
 #endif  #endif
       u=(*cx)+GOLD*(*cx-*bx);         u=(*cx)+GOLD*(*cx-*bx); 
       fu=(*func)(u);         fu=(*func)(u); 
   #ifdef DEBUG
         printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
         fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
   #endif
     } /* end tests */      } /* end tests */
     SHFT(*ax,*bx,*cx,u)       SHFT(*ax,*bx,*cx,u) 
     SHFT(*fa,*fb,*fc,fu)       SHFT(*fa,*fb,*fc,fu) 
 #ifdef DEBUG  #ifdef DEBUG
       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);        fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
 #endif  #endif
   } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
 }   } 
Line 1537  int ncom; Line 1798  int ncom;
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
     
   #ifdef LINMINORIGINAL
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   #else
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
   #endif
 {   { 
   double brent(double ax, double bx, double cx,     double brent(double ax, double bx, double cx, 
                double (*f)(double), double tol, double *xmin);                  double (*f)(double), double tol, double *xmin); 
Line 1548  void linmin(double p[], double xi[], int Line 1813  void linmin(double p[], double xi[], int
   double xx,xmin,bx,ax;     double xx,xmin,bx,ax; 
   double fx,fb,fa;    double fx,fb,fa;
   
   double scale=10., axs, xxs, xxss; /* Scale added for infinity */  #ifdef LINMINORIGINAL
    #else
     double scale=10., axs, xxs; /* Scale added for infinity */
   #endif
     
   ncom=n;     ncom=n; 
   pcom=vector(1,n);     pcom=vector(1,n); 
   xicom=vector(1,n);     xicom=vector(1,n); 
   nrfunc=func;     nrfunc=func; 
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     pcom[j]=p[j];       pcom[j]=p[j]; 
     xicom[j]=xi[j];       xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
   }     } 
   
   #ifdef LINMINORIGINAL
     xx=1.;
   #else
   axs=0.0;    axs=0.0;
   xxss=1; /* 1 and using scale */    xxs=1.;
   xxs=1;  
   do{    do{
     ax=0.;  
     xx= xxs;      xx= xxs;
   #endif
       ax=0.;
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
     /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
     /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */      /* xt[x,j]=pcom[j]+x*xicom[j]  f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and  f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j))   */
Line 1572  void linmin(double p[], double xi[], int Line 1843  void linmin(double p[], double xi[], int
     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
   #ifdef LINMINORIGINAL
   #else
     if (fx != fx){      if (fx != fx){
         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */                          xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);                          printf("|");
                           fprintf(ficlog,"|");
   #ifdef DEBUGLINMIN
                           printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
   #endif
     }      }
   }while(fx != fx);    }while(fx != fx && xxs > 1.e-5);
   #endif
     
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
     fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
   #endif
   #ifdef LINMINORIGINAL
   #else
           if(fb == fx){ /* Flat function in the direction */
                   xmin=xx;
       *flat=1;
           }else{
       *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) */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
   /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
   /* fmin = f(p[j] + xmin * xi[j]) */    /* fmin = f(p[j] + xmin * xi[j]) */
   /* P+lambda n in that direction (lambdamin), with TOL between abscisses */    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
   /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
 #ifdef DEBUG  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
   #endif
   #ifdef LINMINORIGINAL
   #else
                           }
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("linmin end ");    printf("linmin end ");
     fprintf(ficlog,"linmin end ");
 #endif  #endif
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     /* printf(" before xi[%d]=%12.8f", j,xi[j]); */  #ifdef LINMINORIGINAL
     xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */      xi[j] *= xmin; 
     /* if(xxs <1.0) */  #else
     /*   printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */  #ifdef DEBUGLINMIN
       if(xxs <1.0)
         printf(" before xi[%d]=%12.8f", j,xi[j]);
   #endif
       xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
   #ifdef DEBUGLINMIN
       if(xxs <1.0)
         printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
   #endif
   #endif
     p[j] += xi[j]; /* Parameters values are updated accordingly */      p[j] += xi[j]; /* Parameters values are updated accordingly */
   }     } 
   /* printf("\n"); */  
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
     printf("\n");
   printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));    printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
     printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);      printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
     if(j % ncovmodel == 0)      fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
       if(j % ncovmodel == 0){
       printf("\n");        printf("\n");
         fprintf(ficlog,"\n");
       }
   }    }
   #else
 #endif  #endif
   free_vector(xicom,1,n);     free_vector(xicom,1,n); 
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
Line 1623  such that failure to decrease by more th Line 1930  such that failure to decrease by more th
 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.
  */   */
   #ifdef LINMINORIGINAL
   #else
           int *flatdir; /* Function is vanishing in that direction */
           int flat=0, flatd=0; /* Function is vanishing in that direction */
   #endif
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
   void linmin(double p[], double xi[], int n, double *fret,   #ifdef LINMINORIGINAL
    void linmin(double p[], double xi[], int n, double *fret, 
               double (*func)(double []));                 double (*func)(double [])); 
   #else 
    void linmin(double p[], double xi[], int n, double *fret, 
                                                    double (*func)(double []),int *flat); 
   #endif
   int i,ibig,j;     int i,ibig,j; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double directest;    double directest;
   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 1641  void powell(double p[], double **xi, int Line 1964  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
     rcurr_time = time(NULL);      rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret); /* From former iteration or initial value */      fp=(*fret); /* From former iteration or initial value */
     ibig=0;       ibig=0; 
Line 1653  void powell(double p[], double **xi, int Line 1976  void powell(double p[], double **xi, int
     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 %ld sec. %ld sec.",*iter,*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 %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 1667  void powell(double p[], double **xi, int Line 1990  void powell(double p[], double **xi, int
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         strcurr[itmp-1]='\0';                                  strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);                                  rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         forecast_time = *localtime(&rforecast_time);                                  forecast_time = *localtime(&rforecast_time);
         strcpy(strfor,asctime(&forecast_time));                                  strcpy(strfor,asctime(&forecast_time));
         itmp = strlen(strfor);                                  itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')                                  if(strfor[itmp-1]=='\n')
         strfor[itmp-1]='\0';                                          strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);                                  printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);                                  fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i */
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
           printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
           printf("%d",i);fflush(stdout); /* print direction (parameter) i */        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
   #ifdef LINMINORIGINAL
       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                                     /* Outputs are fret(new point p) p is updated and xit rescaled */  #else
         linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                           flatdir[i]=flat; /* Function is vanishing in that direction i */
   #endif
                           /* Outputs are fret(new point p) p is updated and xit rescaled */
       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
         /* because that direction will be replaced unless the gain del is small */                                  /* because that direction will be replaced unless the gain del is small */
         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */                                  /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
         /* Unless the n directions are conjugate some gain in the determinant may be obtained */                                  /* Unless the n directions are conjugate some gain in the determinant may be obtained */
         /* with the new direction. */                                  /* with the new direction. */
         del=fabs(fptt-(*fret));                                   del=fabs(fptt-(*fret)); 
         ibig=i;                                   ibig=i; 
       }         } 
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %.12e",i,(*fret));        printf("%d %.12e",i,(*fret));
       fprintf(ficlog,"%d %.12e",i,(*fret));        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         printf(" x(%d)=%.12e",j,xit[j]);                                  printf(" x(%d)=%.12e",j,xit[j]);
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p(%d)=%.12e",j,p[j]);                                  printf(" p(%d)=%.12e",j,p[j]);
         fprintf(ficlog," p(%d)=%.12e",j,p[j]);                                  fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
Line 1719  void powell(double p[], double **xi, int Line 2047  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++) {
                                   if(flatdir[j] >0){
                                           printf(" 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"); */
                           }
     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? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
Line 1727  void powell(double p[], double **xi, int Line 2063  void powell(double p[], double **xi, int
       /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
       /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
       /* By adding 10 parameters more the gain should be 18.31 */        /* By adding 10 parameters more the gain should be 18.31 */
                           
       /* Starting the program with initial values given by a former maximization will simply change */        /* Starting the program with initial values given by a former maximization will simply change */
       /* the scales of the directions and the directions, because the are reset to canonical directions */        /* the scales of the directions and the directions, because the are reset to canonical directions */
       /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
Line 1755  void powell(double p[], double **xi, int Line 2091  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); 
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     }       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
Line 1769  void powell(double p[], double **xi, int Line 2108  void powell(double p[], double **xi, int
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt); /* f_3 */      fptt=(*func)(ptt); /* f_3 */
   #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   if (*iter <=4) {
   #else
   #endif
   #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
   #else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   #endif
       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       /* From x1 (P0) distance of x2 is at h and x3 is 2h */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       /* Let f"(x2) be the 2nd derivative equal everywhere.  */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
         /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
         /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         /*  Even if f3 <f1, directest can be negative and t >0 */
         /* mu² and del² are equal when f3=f1 */
                           /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                           /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                           /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                           /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
 #ifdef NRCORIGINAL  #ifdef NRCORIGINAL
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
 #else  #else
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       t= t- del*SQR(fp-fptt);        t= t- del*SQR(fp-fptt);
 #endif  #endif
       directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
 #ifdef DEBUG  #ifdef DEBUG
       printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
       fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
Line 1798  void powell(double p[], double **xi, int Line 2152  void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);                                  printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);          fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     }         } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
         printf("Before linmin in direction P%d-P0\n",n);                                  printf("Before linmin in direction P%d-P0\n",n);
         for (j=1;j<=n;j++) {                                   for (j=1;j<=n;j++) {
           printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);                                          printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           if(j % ncovmodel == 0)                                          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
             printf("\n");                                          if(j % ncovmodel == 0){
         }                                                  printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
 #endif  #endif
         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/  #ifdef LINMINORIGINAL
 #ifdef DEBUGLINMIN                                  linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
         for (j=1;j<=n;j++) {   #else
           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);                                  linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
           if(j % ncovmodel == 0)                                  flatdir[i]=flat; /* Function is vanishing in that direction i */
             printf("\n");  
         }  
 #endif  #endif
         for (j=1;j<=n;j++) {   
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */  
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */  
         }  
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);  
         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);  
   
   #ifdef DEBUGLINMIN
                                   for (j=1;j<=n;j++) { 
                                           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                           if(j % ncovmodel == 0){
                                                   printf("\n");
                                                   fprintf(ficlog,"\n");
                                           }
                                   }
   #endif
                                   for (j=1;j<=n;j++) { 
                                           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                   }
   #ifdef LINMINORIGINAL
   #else
                                   for (j=1, flatd=0;j<=n;j++) {
                                           if(flatdir[j]>0)
                                                   flatd++;
                                   }
                                   if(flatd >0){
                                           printf("%d flat directions\n",flatd);
                                           fprintf(ficlog,"%d flat directions\n",flatd);
                                           for (j=1;j<=n;j++) { 
                                                   if(flatdir[j]>0){
                                                           printf("%d ",j);
                                                           fprintf(ficlog,"%d ",j);
                                                   }
                                           }
                                           printf("\n");
                                           fprintf(ficlog,"\n");
                                   }
   #endif
                                   printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);                                  fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for(j=1;j<=n;j++){                                  for(j=1;j<=n;j++){
           printf(" %.12e",xit[j]);                                          printf(" %lf",xit[j]);
           fprintf(ficlog," %.12e",xit[j]);                                          fprintf(ficlog," %lf",xit[j]);
         }                                  }
         printf("\n");                                  printf("\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t negative */        } /* end of t or directest negative */
   #ifdef POWELLNOF3INFF1TEST
   #else
     } /* end if (fptt < fp)  */      } /* end if (fptt < fp)  */
   }   #endif
   #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                   } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
   #else
   #endif
     } /* loop iteration */ 
 }   } 
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached with precision ftolpl */
       /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {0.51571254859325999, 0.4842874514067399, */
     /*  0.51326036147820708, 0.48673963852179264} */
     /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
       
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           /* Starting with matrix unity */
   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 1865  double **prevalim(double **prlim, int nl Line 2280  double **prevalim(double **prlim, int nl
   cov[1]=1.;    cov[1]=1.;
       
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       ncvloop++;
     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<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/                          /* Here comes the value of the covariate 'ij' */
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
     for (k=1; k<=cptcovprod;k++) /* Useless */      for (k=1; k<=cptcovprod;k++) /* Useless */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[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)];
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /* 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' */
     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;
     oldm=newm;      oldm=newm;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){      for(j=1; j<=nlstate; j++){
       min=1.;        max[j]=0.;
       max=0.;        min[j]=1.;
       for(i=1; i<=nlstate; i++) {      }
         sumnew=0;      for(i=1;i<=nlstate;i++){
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for(j=1; j<=nlstate; j++){ 
         prlim[i][j]= newm[i][j]/(1-sumnew);          prlim[i][j]= newm[i][j]/(1-sumnew);
         /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/          max[j]=FMAX(max[j],prlim[i][j]);
         max=FMAX(max,prlim[i][j]);          min[j]=FMIN(min[j],prlim[i][j]);
         min=FMIN(min,prlim[i][j]);  
       }        }
       maxmin=max-min;      }
       maxmax=FMAX(maxmax,maxmin);  
       maxmax=0.;
       for(j=1; j<=nlstate; j++){
         meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[j]);
         /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
     } /* j loop */      } /* j loop */
       *ncvyear= (int)age- (int)agefin;
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
         /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* age loop */
       /* After some age loop it doesn't converge */
     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
   Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* 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(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
   return prlim; /* should not reach here */    return prlim; /* should not reach here */
 }  }
   
   
    /**** Back Prevalence limit (stable or period prevalence)  ****************/
   
    /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
    /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
   {
     /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
        matrix by transitions matrix until convergence is reached with precision ftolpl */
     /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {0.51571254859325999, 0.4842874514067399, */
     /*  0.51326036147820708, 0.48673963852179264} */
     /* If we start from prlim again, prlim tends to a constant matrix */
   
     int i, ii,j,k;
     double *min, *max, *meandiff, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **bmij();
     double **newm;
     double         **dnewm, **doldm, **dsavm;  /* for use */
     double         **oldm, **savm;  /* for use */
   
     double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
     
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
           oldm=oldms; savm=savms;
   
           /* Starting with matrix unity */
           for (ii=1;ii<=nlstate+ndeath;ii++)
                   for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
     
     cov[1]=1.;
     
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
     /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
       ncvloop++;
       newm=savm; /* oldm should be kept from previous iteration or unity at start */
                   /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
       /* Covariates have to be included here again */
       cov[2]=agefin;
       if(nagesqr==1)
         cov[3]= agefin*agefin;;
       for (k=1; k<=cptcovn;k++) {
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
       }
       /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
       for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
       for (k=1; k<=cptcovprod;k++) /* Useless */
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
       
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* 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 *\/ */
                   /* ij should be linked to the correct index of cov */
                   /* age and covariate values ij are in 'cov', but we need to pass
                    * ij for the observed prevalence at age and status and covariate
                    * number:  prevacurrent[(int)agefin][ii][ij]
                    */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
       savm=oldm;
       oldm=newm;
       for(j=1; j<=nlstate; j++){
         max[j]=0.;
         min[j]=1.;
       }
       for(j=1; j<=nlstate; j++){ 
         for(i=1;i<=nlstate;i++){
                                   /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                   bprlim[i][j]= newm[i][j];
                                   max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                   min[i]=FMIN(min[i],bprlim[i][j]);
         }
       }
                   
       maxmax=0.;
       for(i=1; i<=nlstate; i++){
         meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
         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); */
       } /* j loop */
       *ncvyear= -( (int)age- (int)agefin);
       /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
       if(maxmax < ftolpl){
         /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
         return bprlim;
       }
     } /* age loop */
       /* After some age loop it doesn't converge */
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
   Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* 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(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
     return bprlim; /* should not reach here */
   }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
Line 1932  double **pmij(double **ps, double *cov, Line 2505  double **pmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){      for(j=1; j<i;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }        }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }      }
       for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }        }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }  
     }      }
         }
     for(i=1; i<= nlstate; i++){    
       s1=0;    for(i=1; i<= nlstate; i++){
       for(j=1; j<i; j++){      s1=0;
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */      for(j=1; j<i; j++){
         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        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); */
       for(j=i+1; j<=nlstate+ndeath; j++){      }
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */      for(j=i+1; j<=nlstate+ndeath; j++){
         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        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); */
       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      }
       ps[i][i]=1./(s1+1.);      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       /* Computing other pijs */      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)      /* Computing other pijs */
         ps[i][j]= exp(ps[i][j])*ps[i][i];      for(j=1; j<i; 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];      for(j=i+1; j<=nlstate+ndeath; j++)
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        ps[i][j]= exp(ps[i][j])*ps[i][i];
     } /* end i */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         } /* end i */
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
       for(jj=1; jj<= nlstate+ndeath; jj++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         ps[ii][jj]=0;      for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][ii]=1;        ps[ii][jj]=0;
       }        ps[ii][ii]=1;
     }      }
         }
         
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     /*   } */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     /*   printf("\n "); */    /*   } */
     /* } */    /*   printf("\n "); */
     /* printf("\n ");printf("%lf ",cov[2]);*/    /* } */
     /*    /* printf("\n ");printf("%lf ",cov[2]);*/
       for(i=1; i<= npar; i++) printf("%f ",x[i]);    /*
       goto end;*/      for(i=1; i<= npar; i++) printf("%f ",x[i]);
     return ps;                  goto end;*/
     return ps;
 }  }
   
 /**************** Product of 2 matrices ******************/  /*************** backward transition probabilities ***************/ 
   
 double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
    double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    /* Computes the backward probability at age agefin and covariate ij
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */     * and returns in **ps as well as **bmij.
   /* in, b, out are matrice of pointers which should have been initialized      */
      before: only the contents of out is modified. The function returns    int i, ii, j,k;
      a pointer to pointers identical to out */    
   int i, j, k;    double **out, **pmij();
   for(i=nrl; i<= nrh; i++)    double sumnew=0.;
     for(k=ncolol; k<=ncoloh; k++){    double agefin;
       out[i][k]=0.;    
       for(j=ncl; j<=nch; j++)    double **dnewm, **dsavm, **doldm;
         out[i][k] +=in[i][j]*b[j][k];    double **bbmij;
     }    
   return out;    doldm=ddoldms; /* global pointers */
     dnewm=ddnewms;
     dsavm=ddsavms;
     
     agefin=cov[2];
     /* bmij *//* age is cov[2], ij is included in cov, but we need for
        the observed prevalence (with this covariate ij) */
     dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
     /* We do have the matrix Px in savm  and we need pij */
     for (j=1;j<=nlstate+ndeath;j++){
       sumnew=0.; /* w1 p11 + w2 p21 only on live states */
       for (ii=1;ii<=nlstate;ii++){
         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
       } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
       for (ii=1;ii<=nlstate+ndeath;ii++){
         if(sumnew >= 1.e-10){
           /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else */
           doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
         }else{
           printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
         }
       } /*End ii */
     } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
     /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
     bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
     /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
     /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /* left Product of this matrix by diag matrix of prevalences (savm) */
     for (j=1;j<=nlstate+ndeath;j++){
       for (ii=1;ii<=nlstate+ndeath;ii++){
         dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
       }
     } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
     ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
     /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
     /* end bmij */
     return ps; 
 }  }
   /*************** transition probabilities ***************/ 
   
   double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 /************* Higher Matrix Product ***************/  
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  {
   /* Computes the transition matrix starting at age 'age' over     /* According to parameters values stored in x and the covariate's values stored in cov,
      'nhstepm*hstepm*stepm' months (i.e. until       computes the probability to be observed in state j being in state i by appying the
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying        model to the ncovmodel covariates (including constant and age).
      nhstepm*hstepm matrices.        lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
      (typically every 2 years instead of every month which is too big        ncth covariate in the global vector x is given by the formula:
      for the memory).       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
      Model is determined by parameters x and covariates have to be        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
      included manually here.        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      */       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   int i, j, d, h, k;    */
   double **out, cov[NCOVMAX+1];    double s1, lnpijopii;
   double **newm;    /*double t34;*/
   double agexact;    int i,j, nc, ii, jj;
   
           for(i=1; i<= nlstate; i++){
                   for(j=1; j<i;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                   /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                   lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                           /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   }
                   for(j=i+1; j<=nlstate+ndeath;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                   /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                                   lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                                   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   }
           }
           
           for(i=1; i<= nlstate; i++){
                   s1=0;
                   for(j=1; j<i; j++){
                           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); */
                   }
                   for(j=i+1; j<=nlstate+ndeath; j++){
                           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); */
                   }
                   /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   ps[i][i]=1./(s1+1.);
                   /* Computing other pijs */
                   for(j=1; j<i; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   for(j=i+1; j<=nlstate+ndeath; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           } /* end i */
           
           for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   for(jj=1; jj<= nlstate+ndeath; jj++){
                           ps[ii][jj]=0;
                           ps[ii][ii]=1;
                   }
           }
           /* Added for backcast */ /* Transposed matrix too */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   s1=0.;
                   for(ii=1; ii<= nlstate+ndeath; ii++){
                           s1+=ps[ii][jj];
                   }
                   for(ii=1; ii<= nlstate; ii++){
                           ps[ii][jj]=ps[ii][jj]/s1;
                   }
           }
           /* Transposition */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   for(ii=jj; ii<= nlstate+ndeath; ii++){
                           s1=ps[ii][jj];
                           ps[ii][jj]=ps[jj][ii];
                           ps[jj][ii]=s1;
                   }
           }
           /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
           /*   } */
           /*   printf("\n "); */
           /* } */
           /* printf("\n ");printf("%lf ",cov[2]);*/
           /*
                   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   goto end;*/
           return ps;
   }
   
   
   /**************** Product of 2 matrices ******************/
   
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     int i, j, k;
     for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
       }
     return out;
   }
   
   
   /************* Higher Matrix Product ***************/
   
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
     /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
        for the memory).
        Model is determined by parameters x and covariates have to be 
        included manually here. 
   
        */
   
     int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     double **newm;
     double agexact;
     double agebegin, ageend;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2046  double ***hpxij(double ***po, int nhstep Line 2780  double ***hpxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=cptcovn;k++) 
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];          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]; */
       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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[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,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,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]);*/
                           /* 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){ */
         /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
         savm=oldm;
         oldm=newm;
       }
       for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
                                   po[i][j][h]=newm[i][j];
                                   /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
       /*printf("h=%d ",h);*/
     } /* end h */
           /*     printf("\n H=%d \n",h); */
     return po;
   }
   
   /************* Higher Back Matrix Product ***************/
   /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
   double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
   {
     /* Computes the transition matrix starting at age 'age' over
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
        nhstepm*hstepm matrices.
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step
        (typically every 2 years instead of every month which is too big
        for the memory).
        Model is determined by parameters x and covariates have to be
        included manually here.
   
     */
   
     int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     double **newm;
     double agexact;
     double agebegin, ageend;
     double **oldm, **savm;
   
     oldm=oldms;savm=savms;
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         newm=savm;
         /* Covariates have to be included here again */
         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;
         if(nagesqr==1)
           cov[3]= agexact*agexact;
         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,Tvar[k])]; */
         for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           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]; */
         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])]; */
                           
                           
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         /* Careful transposed matrix */
         /* age is in cov[2] */
         /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
         /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
         out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                      1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /* if((int)age == 70){ */
         /*        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++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
       savm=oldm;        savm=oldm;
       oldm=newm;        oldm=newm;
     }      }
Line 2073  double ***hpxij(double ***po, int nhstep Line 2914  double ***hpxij(double ***po, int nhstep
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
 /*     printf("\n H=%d \n",h); */    /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
   
 #ifdef NLOPT  #ifdef NLOPT
   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   double fret;    double fret;
Line 2101  double ***hpxij(double ***po, int nhstep Line 2943  double ***hpxij(double ***po, int nhstep
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
     int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   int s1, s2;    int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
   double bbh, survp;    double bbh, survp;
   long ipmx;    long ipmx;
   double agexact;    double agexact;
Line 2121  double func( double *x) Line 2965  double func( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
   if(mle==1){    if(mle==1){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* Computes the values of the ncovmodel covariates of the model        /* Computes the values of the ncovmodel covariates of the model
          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
          to be observed in j being in i according to the model.           to be observed in j being in i according to the model.
        */        */
       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */        ioffset=2+nagesqr+cptcovage;
           cov[2+nagesqr+k]=covar[Tvar[k]][i];        /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
         for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
           cov[++ioffset]=covar[Tvar[k]][i];
       }        }
         for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
           cov[++ioffset]=coqvar[iqv][i];
         }
   
       /* 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 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
          has been calculated etc */           has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
         /* We compute the contribution to Likelihood of each effective transition
            mw[mi][i] is real wave of the mi th effectve wave */
         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
            s2=s[mw[mi+1][i]][i];
            And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
            But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
            meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
         */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
             cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
           }
           for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
             if(cotqvar[mw[mi][i]][iqtv][i] == -1){
               printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
             }
             cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
           }
           /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
         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 2146  double func( double *x) Line 3015  double func( double *x)
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;            cov[2]=agexact;
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;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 */
           }            }
Line 2155  double func( double *x) Line 3024  double func( double *x)
           savm=oldm;            savm=oldm;
           oldm=newm;            oldm=newm;
         } /* end mult */          } /* end mult */
                                         
         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         /* But now since version 0.9 we anticipate for bias at large stepm.          /* But now since version 0.9 we anticipate for bias at large stepm.
          * If stepm is larger than one month (smallest stepm) and if the exact delay            * If stepm is larger than one month (smallest stepm) and if the exact delay 
Line 2183  double func( double *x) Line 3052  double func( double *x)
              which is also equal to probability to die before dh                which is also equal to probability to die before dh 
              minus probability to die before dh-stepm .                minus probability to die before dh-stepm . 
              In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
         as if date of death was unknown. Death was treated as any other               as if date of death was unknown. Death was treated as any other
         health state: the date of the interview describes the actual state               health state: the date of the interview describes the actual state
         and not the date of a change in health state. The former idea was               and not the date of a change in health state. The former idea was
         to consider that at each interview the state was recorded               to consider that at each interview the state was recorded
         (healthy, disable or death) and IMaCh was corrected; but when we               (healthy, disable or death) and IMaCh was corrected; but when we
         introduced the exact date of death then we should have modified               introduced the exact date of death then we should have modified
         the contribution of an exact death to the likelihood. This new               the contribution of an exact death to the likelihood. This new
         contribution is smaller and very dependent of the step unit               contribution is smaller and very dependent of the step unit
         stepm. It is no more the probability to die between last interview               stepm. It is no more the probability to die between last interview
         and month of death but the probability to survive from last               and month of death but the probability to survive from last
         interview up to one month before death multiplied by the               interview up to one month before death multiplied by the
         probability to die within a month. Thanks to Chris               probability to die within a month. Thanks to Chris
         Jackson for correcting this bug.  Former versions increased               Jackson for correcting this bug.  Former versions increased
         mortality artificially. The bad side is that we add another loop               mortality artificially. The bad side is that we add another loop
         which slows down the processing. The difference can be up to 10%               which slows down the processing. The difference can be up to 10%
         lower mortality.               lower mortality.
             */
             /* If, at the beginning of the maximization mostly, the
                cumulative probability or probability to be dead is
                constant (ie = 1) over time d, the difference is equal to
                0.  out[s1][3] = savm[s1][3]: probability, being at state
                s1 at precedent wave, to be dead a month before current
                wave is equal to probability, being at state s1 at
                precedent wave, to be dead at mont of the current
                wave. Then the observed probability (that this person died)
                is null according to current estimated parameter. In fact,
                it should be very low but not zero otherwise the log go to
                infinity.
           */            */
         /* If, at the beginning of the maximization mostly, the  
            cumulative probability or probability to be dead is  
            constant (ie = 1) over time d, the difference is equal to  
            0.  out[s1][3] = savm[s1][3]: probability, being at state  
            s1 at precedent wave, to be dead a month before current  
            wave is equal to probability, being at state s1 at  
            precedent wave, to be dead at mont of the current  
            wave. Then the observed probability (that this person died)  
            is null according to current estimated parameter. In fact,  
            it should be very low but not zero otherwise the log go to  
            infinity.  
         */  
 /* #ifdef INFINITYORIGINAL */  /* #ifdef INFINITYORIGINAL */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #else */  /* #else */
Line 2220  double func( double *x) Line 3089  double func( double *x)
 /*        else */  /*        else */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */  /* #endif */
             lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
             
         } else if  (s2==-2) {          } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
           lli= log(survp);            lli= log(survp);
         }          }
                   else if  (s2==-4) { 
         else if  (s2==-4) {   
           for (j=3,survp=0. ; j<=nlstate; j++)              for (j=3,survp=0. ; j<=nlstate; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
           else if  (s2==-5) { 
         else if  (s2==-5) {             for (j=1,survp=0. ; j<=2; j++)  
           for (j=1,survp=0. ; j<=2; j++)    
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
           
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
Line 2248  double func( double *x) Line 3114  double func( double *x)
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         /*if(lli ==000.0)*/          /*if(lli ==000.0)*/
         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         ipmx +=1;          ipmx +=1;
         sw += weight[i];          sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /* if (lli < log(mytinydouble)){ */          /* if (lli < log(mytinydouble)){ */
Line 2352  double func( double *x) Line 3218  double func( double *x)
         s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
         if( s2 > nlstate){           if( s2 > nlstate){ 
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
           } else if  ( s2==-1 ) { /* alive */
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= log(survp);
         }else{          }else{
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
Line 2407  double funcone( double *x) Line 3277  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
           int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
   int s1, s2;    int s1, s2;
           int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
     double agebegin, ageend;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2423  double funcone( double *x) Line 3296  double funcone( double *x)
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
   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+cptcovage;
     for(mi=1; mi<= wav[i]-1; mi++){      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
       for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
         cov[++ioffset]=covar[Tvar[k]][i];
       }
       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
         cov[++ioffset]=coqvar[Tvar[iqv]][i];
       }
       
       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
           cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
         }
         for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
           cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
         }
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=nlstate+ndeath;j++){
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           savm[ii][j]=(ii==j ? 1.0 : 0.0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
       for(d=0; d<dh[mi][i]; d++){        
         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
           /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
             and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;          newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         cov[2]=agexact;          cov[2]=agexact;
Line 2441  double funcone( double *x) Line 3333  double funcone( double *x)
         for (kk=1; kk<=cptcovage;kk++) {          for (kk=1; kk<=cptcovage;kk++) {
           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;            cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
         }          }
           /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         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 2453  double funcone( double *x) Line 3345  double funcone( double *x)
               
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];        s2=s[mw[mi+1][i]][i];
         /* if(s2==-1){ */
         /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
         /*        /\* exit(1); *\/ */
         /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
       /* bias is positive if real duration        /* bias is positive if real duration
        * is higher than the multiple of stepm and negative otherwise.         * is higher than the multiple of stepm and negative otherwise.
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);          lli=log(out[s1][s2] - savm[s1][s2]);
       } else if  (s2==-2) {        } else if  ( s2==-1 ) { /* alive */
         for (j=1,survp=0. ; j<=nlstate; j++)           for (j=1,survp=0. ; j<=nlstate; j++) 
           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         lli= log(survp);          lli= log(survp);
Line 2480  double funcone( double *x) Line 3376  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\          fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
Line 2514  void likelione(FILE *ficres,double p[], Line 3410  void likelione(FILE *ficres,double p[],
   int k;    int k;
   
   if(*globpri !=0){ /* Just counts and sums, no printings */    if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ilk");       strcpy(fileresilk,"ILK_"); 
     strcat(fileresilk,fileres);      strcat(fileresilk,fileresu);
     if((ficresilk=fopen(fileresilk,"w"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }      }
     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");      fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
Line 2531  void likelione(FILE *ficres,double p[], Line 3427  void likelione(FILE *ficres,double p[],
   *fretone=(*funcone)(p);    *fretone=(*funcone)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      if (mle ==0)
     fflush(fichtm);         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
   }       else if(mle >=1)
         fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
       fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       
         
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
       }
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
     }
   return;    return;
 }  }
   
Line 2564  void mlikeli(FILE *ficres,double p[], in Line 3474  void mlikeli(FILE *ficres,double p[], in
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(filerespow,"pow");     strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);    strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", filerespow);      printf("Problem with resultfile: %s\n", filerespow);
Line 2607  void mlikeli(FILE *ficres,double p[], in Line 3517  void mlikeli(FILE *ficres,double p[], in
 #endif  #endif
   free_matrix(xi,1,npar,1,npar);    free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("#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));
   fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
 /**** Computes Hessian and covariance matrix ***/  /**** Computes Hessian and covariance matrix ***/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    /* double **hess; */
   int i, j;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);    double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double gompertz(double p[]);    double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    /* hess=matrix(1,npar,1,npar); */
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d-",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d-",i);fflush(ficlog);
         
      hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           
Line 2643  void hesscov(double **matcov, double p[] Line 3553  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {      for (j=1;j<=npar;j++)  {
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d-%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j,func,npar);          hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
                   
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
Line 2679  void hesscov(double **matcov, double p[] Line 3589  void hesscov(double **matcov, double p[]
   fprintf(ficlog,"\n#Hessian matrix#\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
   for (i=1;i<=npar;i++) {     for (i=1;i<=npar;i++) { 
     for (j=1;j<=npar;j++) {       for (j=1;j<=npar;j++) { 
       printf("%.3e ",hess[i][j]);        printf("%.6e ",hess[i][j]);
       fprintf(ficlog,"%.3e ",hess[i][j]);        fprintf(ficlog,"%.6e ",hess[i][j]);
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   
     /* printf("\n#Covariance matrix#\n"); */
     /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
     /* for (i=1;i<=npar;i++) {  */
     /*   for (j=1;j<=npar;j++) {  */
     /*     printf("%.6e ",matcov[i][j]); */
     /*     fprintf(ficlog,"%.6e ",matcov[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
   /* Recompute Inverse */    /* Recompute Inverse */
   for (i=1;i<=npar;i++)    /* for (i=1;i<=npar;i++) */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
   ludcmp(a,npar,indx,&pd);    /* ludcmp(a,npar,indx,&pd); */
   
     /*  printf("\n#Hessian matrix recomputed#\n"); */
   
     /* for (j=1;j<=npar;j++) { */
     /*   for (i=1;i<=npar;i++) x[i]=0; */
     /*   x[j]=1; */
     /*   lubksb(a,npar,indx,x); */
     /*   for (i=1;i<=npar;i++){  */
     /*     y[i][j]=x[i]; */
     /*     printf("%.3e ",y[i][j]); */
     /*     fprintf(ficlog,"%.3e ",y[i][j]); */
     /*   } */
     /*   printf("\n"); */
     /*   fprintf(ficlog,"\n"); */
     /* } */
   
     /* Verifying the inverse matrix */
   #ifdef DEBUGHESS
     y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
   
   /*  printf("\n#Hessian matrix recomputed#\n");     printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
      fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
   
   for (j=1;j<=npar;j++) {    for (j=1;j<=npar;j++) {
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){       for (i=1;i<=npar;i++){ 
       y[i][j]=x[i];        printf("%.2f ",y[i][j]);
       printf("%.3e ",y[i][j]);        fprintf(ficlog,"%.2f ",y[i][j]);
       fprintf(ficlog,"%.3e ",y[i][j]);  
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
   }    }
   */  #endif
   
   free_matrix(a,1,npar,1,npar);    free_matrix(a,1,npar,1,npar);
   free_matrix(y,1,npar,1,npar);    free_matrix(y,1,npar,1,npar);
   free_vector(x,1,npar);    free_vector(x,1,npar);
   free_ivector(indx,1,npar);    free_ivector(indx,1,npar);
   free_matrix(hess,1,npar,1,npar);    /* free_matrix(hess,1,npar,1,npar); */
   
   
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  { /* Around values of x, computes the function func and returns the scales delti and hessian */
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2, res, fx;
   double p2[MAXPARM+1]; /* identical to x */    double p2[MAXPARM+1]; /* identical to x */
   double res;  
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;  
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
   
Line 2741  double hessii(double x[], double delta, Line 3676  double hessii(double x[], double delta,
       p2[theta]=x[theta]-delt;        p2[theta]=x[theta]-delt;
       k2=func(p2)-fx;        k2=func(p2)-fx;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
               
 #ifdef DEBUGHESS  #ifdef DEBUGHESSII
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 #endif  #endif
Line 2757  double hessii(double x[], double delta, Line 3692  double hessii(double x[], double delta,
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
       }        }
     }      } /* End loop k */
   }    }
   delti[theta]=delts;    delti[theta]=delts;
   return res;     return res; 
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k, kmax=1;
     double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
     
   fx=func(x);    fx=func(x);
   for (k=1; k<=2; k++) {    for (k=1; k<=kmax; k=k+10) {
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (i=1;i<=npar;i++) p2[i]=x[i];
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k1=func(p2)-fx;      k1=func(p2)-fx;
       
     p2[thetai]=x[thetai]+delti[thetai]/k;      p2[thetai]=x[thetai]+delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k2=func(p2)-fx;      k2=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      p2[thetaj]=x[thetaj]+delti[thetaj]*k;
     k3=func(p2)-fx;      k3=func(p2)-fx;
       
     p2[thetai]=x[thetai]-delti[thetai]/k;      p2[thetai]=x[thetai]-delti[thetai]*k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      p2[thetaj]=x[thetaj]-delti[thetaj]*k;
     k4=func(p2)-fx;      k4=func(p2)-fx;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
 #ifdef DEBUG      if(k1*k2*k3*k4 <0.){
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        firstime=1;
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        kmax=kmax+10;
       }
       if(kmax >=10 || firstime ==1){
         printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
         fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }
   #ifdef DEBUGHESSIJ
       v1=hess[thetai][thetai];
       v2=hess[thetaj][thetaj];
       cv12=res;
       /* Computing eigen value of Hessian matrix */
       lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       if ((lc2 <0) || (lc1 <0) ){
         printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
         printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }
 #endif  #endif
   }    }
   return res;    return res;
 }  }
   
       /* Not done yet: Was supposed to fix if not exactly at the maximum */
   /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
   /* { */
   /*   int i; */
   /*   int l=1, lmax=20; */
   /*   double k1,k2,k3,k4,res,fx; */
   /*   double p2[MAXPARM+1]; */
   /*   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
   /*   int k=0,kmax=10; */
   /*   double l1; */
     
   /*   fx=func(x); */
   /*   for(l=0 ; l <=lmax; l++){  /\* Enlarging the zone around the Maximum *\/ */
   /*     l1=pow(10,l); */
   /*     delts=delt; */
   /*     for(k=1 ; k <kmax; k=k+1){ */
   /*       delt = delti*(l1*k); */
   /*       for (i=1;i<=npar;i++) p2[i]=x[i]; */
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k1=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]+delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k2=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
   /*       k3=func(p2)-fx; */
         
   /*       p2[thetai]=x[thetai]-delti[thetai]/k; */
   /*       p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
   /*       k4=func(p2)-fx; */
   /*       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
   /* #ifdef DEBUGHESSIJ */
   /*       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /*       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
   /* #endif */
   /*       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
   /*      k=kmax; */
   /*       } */
   /*       else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
   /*      k=kmax; l=lmax*10; */
   /*       } */
   /*       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  */
   /*      delts=delt; */
   /*       } */
   /*     } /\* End loop k *\/ */
   /*   } */
   /*   delti[theta]=delts; */
   /*   return res;  */
   /* } */
   
   
 /************** Inverse of matrix **************/  /************** Inverse of matrix **************/
 void ludcmp(double **a, int n, int *indx, double *d)   void ludcmp(double **a, int n, int *indx, double *d) 
 {   { 
Line 2875  void lubksb(double **a, int n, int *indx Line 3887  void lubksb(double **a, int n, int *indx
   
 void pstamp(FILE *fichier)  void pstamp(FILE *fichier)
 {  {
   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                     int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                     int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, k, iv;
     int iind=0, iage=0;
     int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *meanq;
   double pos,posprop, k2, dateintsum=0,k2cpt=0;    double **meanqt;
   char fileresp[FILENAMELENGTH];    double *pp, **prop, *posprop, *pospropt;
       double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
     double agebegin, ageend;
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   strcpy(fileresp,"p");    posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
   strcat(fileresp,fileres);    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
     /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     meanqt=matrix(1,lastpass,1,nqtveff);
     strcpy(fileresp,"P_");
     strcat(fileresp,fileresu);
     /*strcat(fileresphtm,fileresu);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);  
     strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
     if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
       printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
               fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
       
     strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
     if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
       printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       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\
   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);
     }
     fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
   
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
   j1=0;    j1=0;
       
   j=cptcoveff;    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
     j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   first=1;    first=1;
   
   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */       reference=low_education V1=0,V2=0
   /*    j1++; */       med_educ                V1=1 V2=0, 
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){       high_educ               V1=0 V2=1
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
         scanf("%d", i);*/    */
       for (i=-5; i<=nlstate+ndeath; i++)    
         for (jk=-5; jk<=nlstate+ndeath; jk++)      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
           for(m=iagemin; m <= iagemax+3; m++)      posproptt=0.;
             freq[i][jk][m]=0;      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
               scanf("%d", i);*/
       for (i=1; i<=nlstate; i++)        for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-5; jk<=nlstate+ndeath; jk++)  
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;            freq[i][jk][m]=0;
               
       dateintsum=0;      for (i=1; i<=nlstate; i++)  {
       k2cpt=0;        for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i<=imx; i++) {          prop[i][m]=0;
         bool=1;        posprop[i]=0;
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */        pospropt[i]=0;
           for (z1=1; z1<=cptcoveff; z1++)             }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){      /* for (z1=1; z1<= nqfveff; z1++) {   */
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */      /*   meanq[z1]+=0.; */
               bool=0;      /*   for(m=1;m<=lastpass;m++){ */
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",       /*  meanqt[m][z1]=0.; */
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],      /*   } */
                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/      /* } */
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/        
             }       dateintsum=0;
         }      k2cpt=0;
        /* For that combination of covariate j1, we count and print the frequencies in one pass */
         if (bool==1){      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
           for(m=firstpass; m<=lastpass; m++){        bool=1;
             k2=anint[m][i]+(mint[m][i]/12.);        if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/          if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;            /* for (z1=1; z1<= nqfveff; z1++) {   */
               if(agev[m][i]==1) agev[m][i]=iagemax+2;            /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];            /* } */
               if (m<lastpass) {            for (z1=1; z1<=cptcoveff; z1++) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              /* if(Tvaraff[z1] ==-20){ */
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];              /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
               /* }else  if(Tvaraff[z1] ==-10){ */
               /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
               /* }else  */
               if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                 /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
                 bool=0;
                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                    bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                    j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
               } /* Onlyf fixed */
             } /* end z1 */
           } /* cptcovn > 0 */
         } /* end any */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
           /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[iind];mi++){ /* For that wave */
             m=mw[mi][iind];
             if(anyvaryingduminmodel==1){ /* Some are varying covariates */
               for (z1=1; z1<=cptcoveff; z1++) {
                 if( Fixed[Tmodelind[z1]]==1){
                   iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                   if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                     bool=0;
                 }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                   if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                     bool=0;
                   }
               }                }
                             }
               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {            }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
                 dateintsum=dateintsum+k2;            /* bool =0 we keep that guy which corresponds to the combination of dummy values */
                 k2cpt++;            if(bool==1){
               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                  and mw[mi+1][iind]. dh depends on stepm. */
               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
               if(m >=firstpass && m <=lastpass){
                 k2=anint[m][iind]+(mint[m][iind]/12.);
                 /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                 if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                 if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                 if (m<lastpass) {
                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                   /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                   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.));
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                   freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
               }                }
               /*}*/              } /* end if between passes */  
           }              if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
         }                dateintsum=dateintsum+k2;
       } /* end i */                k2cpt++;
                        /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/  
       pstamp(ficresp);  
       if  (cptcovn>0) {  
         fprintf(ficresp, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");  
         fprintf(ficlog, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficlog, "**********\n#");  
       }  
       for(i=1; i<=nlstate;i++)   
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");  
         
       for(i=iagemin; i <= iagemax+3; i++){  
         if(i==iagemax+3){  
           fprintf(ficlog,"Total");  
         }else{  
           if(first==1){  
             first=0;  
             printf("See log file for details...\n");  
           }  
           fprintf(ficlog,"Age %d", i);  
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];   
         }  
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  
           if(pp[jk]>=1.e-10){  
             if(first==1){  
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
             }              }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            } /* end bool 2 */
           }else{          } /* end m */
             if(first==1)        } /* end bool */
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      } /* end iind = 1 to imx */
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      /* prop[s][age] is feeded for any initial and valid live state as well as
          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
   
   
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pstamp(ficresp);
       /* if  (ncoveff>0) { */
       if  (cptcoveff>0) {
         fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++){
           fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         }
         fprintf(ficresp, "**********\n#");
         fprintf(ficresphtm, "**********</h3>\n");
         fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficlog, "**********\n");
       }
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       for(i=1; i<=nlstate;i++) {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }
       fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");
         
       /* Header of frequency table by age */
       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       fprintf(ficresphtmfr,"<th>Age</th> ");
       for(jk=-1; jk <=nlstate+ndeath; jk++){
         for(m=-1; m <=nlstate+ndeath; m++){
           if(jk!=0 && m!=0)
             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
         }
       }
       fprintf(ficresphtmfr, "\n");
         
       /* For each age */
       for(iage=iagemin; iage <= iagemax+3; iage++){
         fprintf(ficresphtm,"<tr>");
         if(iage==iagemax+1){
           fprintf(ficlog,"1");
           fprintf(ficresphtmfr,"<tr><th>0</th> ");
         }else if(iage==iagemax+2){
           fprintf(ficlog,"0");
           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
         }else if(iage==iagemax+3){
           fprintf(ficlog,"Total");
           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
         }else{
           if(first==1){
             first=0;
             printf("See log file for details...\n");
           }
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", iage);
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][iage]; 
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][iage];
           if(pp[jk]>=1.e-10){
             if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }            }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }else{
             if(first==1)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }          }
         }
   
         for(jk=1; jk <=nlstate ; jk++){        for(jk=1; jk <=nlstate ; jk++){ 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /* posprop[jk]=0; */
             pp[jk] += freq[jk][m][i];          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
         }                   pp[jk] += freq[jk][m][iage];
         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){        } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
           pos += pp[jk];  
           posprop += prop[jk][i];        for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
           pos += pp[jk]; /* pos is the total number of transitions until this age */
           posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                                             from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
                                           from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
         }
         for(jk=1; jk <=nlstate ; jk++){
           if(pos>=1.e-5){
             if(first==1)
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           }else{
             if(first==1)
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          if( iage <= iagemax){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             if(first==1)              fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              /*probs[iage][jk][j1]= pp[jk]/pos;*/
           }else{              /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
             if(first==1)            }
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            else{
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
           }              fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
           if( i <= iagemax){  
             if(pos>=1.e-5){  
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);  
               /*probs[i][jk][j1]= pp[jk]/pos;*/  
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
             }  
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);  
           }            }
         }          }
                   pospropt[jk] +=posprop[jk];
         for(jk=-1; jk <=nlstate+ndeath; jk++)        } /* end loop jk */
           for(m=-1; m <=nlstate+ndeath; m++)        /* pospropt=0.; */
             if(freq[jk][m][i] !=0 ) {        for(jk=-1; jk <=nlstate+ndeath; jk++){
             if(first==1)          for(m=-1; m <=nlstate+ndeath; m++){
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            if(freq[jk][m][iage] !=0 ) { /* minimizing output */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);              if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
             }              }
         if(i <= iagemax)              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
           fprintf(ficresp,"\n");            }
         if(first==1)            if(jk!=0 && m!=0)
           printf("Others in log...\n");              fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
         fprintf(ficlog,"\n");          }
         } /* end loop jk */
         posproptt=0.; 
         for(jk=1; jk <=nlstate; jk++){
           posproptt += pospropt[jk];
         }
         fprintf(ficresphtmfr,"</tr>\n ");
         if(iage <= iagemax){
           fprintf(ficresp,"\n");
           fprintf(ficresphtm,"</tr>\n");
       }        }
       /*}*/        if(first==1)
   }          printf("Others in log...\n");
   dateintmean=dateintsum/k2cpt;         fprintf(ficlog,"\n");
        } /* end loop age iage */
       fprintf(ficresphtm,"<tr><th>Tot</th>");
       for(jk=1; jk <=nlstate ; jk++){
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);   
         }else{
           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);    
         }
       }
       fprintf(ficresphtm,"</tr>\n");
       fprintf(ficresphtm,"</table>\n");
       fprintf(ficresphtmfr,"</table>\n");
       if(posproptt < 1.e-5){
         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
         invalidvarcomb[j1]=1;
       }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
         invalidvarcomb[j1]=0;
       }
       fprintf(ficresphtmfr,"</table>\n");
     } /* end selected combination of covariate j1 */
     dateintmean=dateintsum/k2cpt; 
                    
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);    fclose(ficresphtm);
     fclose(ficresphtmfr);
     free_vector(meanq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);    /* End of freqsummary */
   /* End of Freq */  
 }  }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
Line 3062  void prevalence(double ***probs, double Line 4257  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, iv;
     int mi; /* Effective wave */
     int iage;
     double agebegin, ageend;
   
   double **prop;    double **prop;
   double posprop;     double posprop; 
Line 3073  void prevalence(double ***probs, double Line 4271  void prevalence(double ***probs, double
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin,iagemax+3);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
Line 3081  void prevalence(double ***probs, double Line 4279  void prevalence(double ***probs, double
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;    first=1;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
     /*for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1; i<=nlstate; i++)  
       j1++;*/        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
                 prop[i][iage]=0.0;
       for (i=1; i<=nlstate; i++)        printf("Prevalence combination of varying and fixed dummies %d\n",j1);
         for(m=iagemin; m <= iagemax+3; m++)      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
           prop[i][m]=0.0;      fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
            
       for (i=1; i<=imx; i++) { /* Each individual */      for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;        bool=1;
         if  (cptcovn>0) {        /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
           for (z1=1; z1<=cptcoveff; z1++)         for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           m=mw[mi][i];
           /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
           /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
           for (z1=1; z1<=cptcoveff; z1++){
             if( Fixed[Tmodelind[z1]]==1){
               iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
               if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
               bool=0;                bool=0;
         }             }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
         if (bool==1) {               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/                bool=0;
               }
           }
           if(bool==1){ /* Otherwise we skip that wave/person */
             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
             if(m >=firstpass && m <=lastpass){
             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
               if (s[m][i]>0 && s[m][i]<=nlstate) {                   printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                   exit(1);
                 }
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                 prop[s[m][i]][(int)agev[m][i]] += weight[i];                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                 prop[s[m][i]][iagemax+3] += weight[i];                   prop[s[m][i]][iagemax+3] += weight[i]; 
               }                 } /* end valid statuses */ 
             }              } /* end selection of dates */
           } /* end selection of waves */            } /* end selection of waves */
         }          } /* end bool */
       }        } /* end wave */
       for(i=iagemin; i <= iagemax+3; i++){        } /* end individual */
         for(jk=1,posprop=0; jk <=nlstate ; jk++) {       for(i=iagemin; i <= iagemax+3; i++){  
           posprop += prop[jk][i];         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         }           posprop += prop[jk][i]; 
                 } 
         for(jk=1; jk <=nlstate ; jk++){             
           if( i <=  iagemax){         for(jk=1; jk <=nlstate ; jk++){       
             if(posprop>=1.e-5){           if( i <=  iagemax){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;            if(posprop>=1.e-5){ 
             } else{              probs[i][jk][j1]= prop[jk][i]/posprop;
               if(first==1){            } else{
                 first=0;              if(first==1){
                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);                first=0;
               }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
             }              }
           }             }
         }/* end jk */           } 
       }/* end i */         }/* end jk */ 
     /*} *//* end i1 */      }/* end i */ 
        /*} *//* end i1 */
   } /* end j1 */    } /* end j1 */
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin,iagemax+3);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
 }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 3147  void  concatwav(int wav[], int **dh, int Line 4361  void  concatwav(int wav[], int **dh, int
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */    */
   
   int i, mi, m;    int i=0, mi=0, m=0, mli=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/       double sum=0., jmean=0.;*/
   int first;    int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
     firstwo=0;
     firsthree=0;
     firstfour=0;
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){  
     mi=0;  /* Treating live states */
     for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
       mi=0;  /* First valid wave */
       mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){      while(s[m][i] <= nlstate){  /* a live state */
       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)        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; */
         }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;
       if(m >=lastpass)          mli=m;
         } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
         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 */
         }
         else{ /* m >= lastpass, eventual special issue with warning */
   #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
         break;          break;
       else  #else
         m++;          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
             if(firsthree == 0){
               printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
               firsthree=1;
             }
             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
             mw[++mi][i]=m;
             mli=m;
           }
           if(s[m][i]==-2){ /* Vital status is really unknown */
             nbwarn++;
             if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
               printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
               fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
             }
             break;
           }
           break;
   #endif
         }/* End m >= lastpass */
     }/* end while */      }/* end while */
     if (s[m][i] > nlstate){  
       /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
       /* After last pass */
   /* Treating death states */
       if (s[m][i] > nlstate){  /* In a death state */
         /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
         /* } */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
          /* Only death is a correct wave */        /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }      }
   #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     wav[i]=mi;      else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
         /* m++; */
         /* mi++; */
         /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
         /* mw[mi][i]=m; */
         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 */
             nbwarn++;
             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 );
               firstfiv=1;
             }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 );
             }
           }else{ /* Death occured afer last wave potential bias */
             nberr++;
             if(firstwo==0){
               printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
               firstwo=1;
             }
             fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
           }
         }else{ /* end date of interview is known */
           /* death is known but not confirmed by death status at any wave */
           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 );
             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 );
         }
       } /* end if date of death is known */
   #endif
       wav[i]=mi; /* mi should be the last effective wave (or mli) */
       /* wav[i]=mw[mi][i]; */
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
Line 3189  void  concatwav(int wav[], int **dh, int Line 4475  void  concatwav(int wav[], int **dh, int
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
     /* wav and mw are no more changed */
           
     
   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 3224  void  concatwav(int wav[], int **dh, int Line 4512  void  concatwav(int wav[], int **dh, int
         else{          else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                           
           k=k+1;            k=k+1;
           if (j >= jmax) {            if (j >= jmax) {
             jmax=j;              jmax=j;
Line 3278  void  concatwav(int wav[], int **dh, int Line 4566  void  concatwav(int wav[], int **dh, int
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }  }
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
 {  {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    * Boring subroutine which should only output nbcode[Tvar[j]][k]     * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
    * nbcode[Tvar[j]][1]=      * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
   */    */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 3296  void tricode(int *Tvar, int **nbcode, in Line 4584  void tricode(int *Tvar, int **nbcode, in
   int modmincovj=0; /* Modality min of covariates j */    int modmincovj=0; /* Modality min of covariates j */
   
   
   cptcoveff=0;     /* cptcoveff=0;  */
           /* *cptcov=0; */
     
   for (k=-1; k < maxncov; k++) Ndum[k]=0;  
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* Loop on covariates without age and products and no quantitative variable */
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the     for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
                                modality of this covariate Vj*/       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                                     * If product of Vn*Vm, still boolean *:        switch(Fixed[k]) {
                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 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*/
       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the            ij=(int)(covar[Tvar[k]][i]);
                                       modality of the nth covariate of individual i. */            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       if (ij > modmaxcovj)             * If product of Vn*Vm, still boolean *:
         modmaxcovj=ij;              * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       else if (ij < modmincovj)              * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         modmincovj=ij;             /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
       if ((ij < -1) && (ij > NCOVMAX)){               modality of the nth covariate of individual i. */
         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );            if (ij > modmaxcovj)
         exit(1);              modmaxcovj=ij; 
       }else            else if (ij < modmincovj) 
       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/              modmincovj=ij; 
       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */            if ((ij < -1) && (ij > NCOVMAX)){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       /* getting the maximum value of the modality of the covariate              exit(1);
          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and            }else
          female is 1, then modmaxcovj=1.*/              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     } /* end for loop on individuals */            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     cptcode=modmaxcovj;            /* getting the maximum value of the modality of the covariate
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
    /*for (i=0; i<=cptcode; i++) {*/               female ies 1, then modmaxcovj=1.
     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */            */
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);          } /* end for loop on individuals i */
       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */          printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */          fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
       }          cptcode=modmaxcovj;
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */          /*for (i=0; i<=cptcode; i++) {*/
     } /* Ndum[-1] number of undefined modalities */          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
             printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */            fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;              if( j != -1){
        modmincovj=3; modmaxcovj = 7;                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;                                   covariate for which somebody answered excluding 
        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;                                   undefined. Usually 2: 0 and 1. */
        defining two dummy variables: variables V1_1 and V1_2.              }
        nbcode[Tvar[j]][ij]=k;              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
        nbcode[Tvar[j]][1]=0;                                      covariate for which somebody answered including 
        nbcode[Tvar[j]][2]=1;                                      undefined. Usually 3: -1, 0 and 1. */
        nbcode[Tvar[j]][3]=2;            }
     */            /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
     ij=1; /* ij is similar to i but can jumps over null modalities */             * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */          } /* Ndum[-1] number of undefined modalities */
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */          
         /*recode from 0 */          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
           nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode.              If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
                                      k is a modality. If we have model=V1+V1*sex              modmincovj=3; modmaxcovj = 7;
                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */             There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
              which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
              defining two dummy variables: variables V1_1 and V1_2.
              nbcode[Tvar[j]][ij]=k;
              nbcode[Tvar[j]][1]=0;
              nbcode[Tvar[j]][2]=1;
              nbcode[Tvar[j]][3]=2;
              To be continued (not working yet).
           */
           ij=0; /* ij is similar to i but can jump over null modalities */
           for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
               break;
             }
           ij++;            ij++;
             nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
             cptcode = ij; /* New max modality for covar j */
           } /* end of loop on modality i=-1 to 1 or more */
           break;
         case 1: /* Testing on varying covariate, could be simple and
                  * should look at waves or product of fixed *
                  * varying. No time to test -1, assuming 0 and 1 only */
           ij=0;
           for(i=0; i<=1;i++){
             nbcode[Tvar[k]][++ij]=i;
         }          }
         if (ij > ncodemax[j]) break;           break;
       }  /* end of loop on */        default:
     } /* end of loop on modality */           break;
         } /* end switch */
       } /* end dummy test */
       
       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
       /*  /\*recode from 0 *\/ */
       /*                               k is a modality. If we have model=V1+V1*sex  */
       /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
       /*  } */
       /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
       /*  if (ij > ncodemax[j]) { */
       /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
       /*    break; */
       /*  } */
       /*   }  /\* end of loop on modality k *\/ */
   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       
  for (k=-1; k< maxncov; k++) Ndum[k]=0;     for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       /* Look at fixed dummy (single or product) covariates to check empty modalities */
   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */       ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
    Ndum[ij]++; /* Might be supersed V1 + V1*age */      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
  }       /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
     } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
  ij=1;    
  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */    ij=0;
    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
    if((Ndum[i]!=0) && (i<=ncovcol)){    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
      ij++;      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
    }else        /* If product not in single variable we don't print results */
        Tvaraff[ij]=0;        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
  }        ++ij;
  ij--;        Tvaraff[ij]=Tvar[k]; /*For printing */
  cptcoveff=ij; /*Number of total covariates*/        Tmodelind[ij]=k;
         if(Fixed[k]!=0)
           anyvaryingduminmodel=1;
       /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
       /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
       /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
       /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
       /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
       /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
       } 
     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
     /* ij--; */
     /* cptcoveff=ij; /\*Number of total covariates*\/ */
     *cptcov=ij; /*Number of total real effective covariates: effective
                  * because they can be excluded from the model and real
                  * if in the model but excluded because missing values, but how to get k from ij?*/
     for(j=ij+1; j<= cptcovt; j++){
       Tvaraff[j]=0;
       Tmodelind[j]=0;
     }
     /* To be sorted */
     ;
 }  }
   
   
Line 3504  void cvevsij(double ***eij, double x[], Line 4851  void cvevsij(double ***eij, double x[],
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .       to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
Line 3598  void cvevsij(double ***eij, double x[], Line 4945  void cvevsij(double ***eij, double x[],
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   
     /* 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 */
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   
     /* Computing  Variances of health expectancies */      /* Computing  Variances of health expectancies */
     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        decrease memory allocation */         decrease memory allocation */
Line 3615  void cvevsij(double ***eij, double x[], Line 4962  void cvevsij(double ***eij, double x[],
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                             
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
           for(h=0; h<=nhstepm-1; h++){            for(h=0; h<=nhstepm-1; h++){
Line 3624  void cvevsij(double ***eij, double x[], Line 4971  void cvevsij(double ***eij, double x[],
           }            }
         }          }
       }        }
                                
       for(ij=1; ij<= nlstate*nlstate; ij++)        for(ij=1; ij<= nlstate*nlstate; ij++)
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
Line 3637  void cvevsij(double ***eij, double x[], Line 4984  void cvevsij(double ***eij, double x[],
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
           
                   
      for(ij=1;ij<=nlstate*nlstate;ij++)      for(ij=1;ij<=nlstate*nlstate;ij++)
       for(ji=1;ji<=nlstate*nlstate;ji++)        for(ji=1;ji<=nlstate*nlstate;ji++)
         varhe[ij][ji][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
                   
      printf("%d|",(int)age);fflush(stdout);      printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      for(h=0;h<=nhstepm-1;h++){      for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
Line 3653  void cvevsij(double ***eij, double x[], Line 5000  void cvevsij(double ***eij, double x[],
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                                                     
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                           
         }          }
                   
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
Line 3678  void cvevsij(double ***eij, double x[], Line 5025  void cvevsij(double ***eij, double x[],
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                   
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
Line 3691  void cvevsij(double ***eij, double x[], Line 5038  void cvevsij(double ***eij, double x[],
           }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                      
   }    }
   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
Line 3701  void cvevsij(double ***eij, double x[], Line 5048  void cvevsij(double ***eij, double x[],
   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
           
   free_vector(xm,1,npar);    free_vector(xm,1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 }  }
   
 /************ Variance ******************/  
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])  
 {  
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   /* double **newm;*/  
   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/  
     
   int movingaverage();  
   double **dnewm,**doldm;  
   double **dnewmp,**doldmp;  
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k;  
   double *xp;  
   double **gp, **gm;  /* for var eij */  
   double ***gradg, ***trgradg; /*for var eij */  
   double **gradgp, **trgradgp; /* for var p point j */  
   double *gpp, *gmp; /* for var p point j */  
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */  
   double ***p3mat;  
   double age,agelim, hf;  
   double ***mobaverage;  
   int theta;  
   char digit[4];  
   char digitp[25];  
   
   char fileresprobmorprev[FILENAMELENGTH];  
   
   if(popbased==1){  
     if(mobilav!=0)  
       strcpy(digitp,"-populbased-mobilav-");  
     else strcpy(digitp,"-populbased-nomobil-");  
   }  
   else   
     strcpy(digitp,"-stablbased-");  
   
   if (mobilav!=0) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   strcpy(fileresprobmorprev,"prmorprev");   
   sprintf(digit,"%-d",ij);  
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/  
   strcat(fileresprobmorprev,digit); /* Tvar to be done */  
   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */  
   strcat(fileresprobmorprev,fileres);  
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);  
   }  
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  
    
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  
   pstamp(ficresprobmorprev);  
   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);  
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);  
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  
   }    
   fprintf(ficresprobmorprev,"\n");  
   fprintf(ficgp,"\n# Routine varevsij");  
   /* fprintf(fichtm, "#Local time at start: %s", strstart);*/  
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);  
 /*   } */  
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   pstamp(ficresvij);  
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");  
   if(popbased==1)  
     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);  
   else  
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");  
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);  
   fprintf(ficresvij,"\n");  
   
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);  
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);  
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
     
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  
   else  hstepm=estepm;     
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.   
      nhstepm is the number of hstepm from age to agelim   
      nstepm is the number of stepm from age to agelin.   
      Look at function hpijx to understand why (it is linked to memory size questions) */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed every two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same   
      results. So we changed our mind and took the option of the best precision.  
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */   
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  
   
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   
       if (popbased==1) {  
         if(mobilav ==0){  
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][ij];  
         }else{ /* mobilav */   
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=mobaverage[(int)age][i][ij];  
         }  
       }  
     
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  
       }  
       /* This for computing probability of death (h=1 means  
          computed over hstepm matrices product = hstepm*stepm months)   
          as a weighted average of prlim.  
       */  
       for(j=nlstate+1;j<=nlstate+ndeath;j++){  
         for(i=1,gpp[j]=0.; i<= nlstate; i++)  
           gpp[j] += prlim[i][i]*p3mat[i][j][1];  
       }      
       /* end probability of death */  
   
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
     
       if (popbased==1) {  /************ Variance ******************/
         if(mobilav ==0){   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
           for(i=1; i<=nlstate;i++)   {
             prlim[i][i]=probs[(int)age][i][ij];     /* Variance of health expectancies */
         }else{ /* mobilav */      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           for(i=1; i<=nlstate;i++)     /* double **newm;*/
             prlim[i][i]=mobaverage[(int)age][i][ij];     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
         }    
       }     /* int movingaverage(); */
      double **dnewm,**doldm;
       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */     double **dnewmp,**doldmp;
         for(h=0; h<=nhstepm; h++){     int i, j, nhstepm, hstepm, h, nstepm ;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)     int k;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     double *xp;
         }     double **gp, **gm;  /* for var eij */
       }     double ***gradg, ***trgradg; /*for var eij */
       /* This for computing probability of death (h=1 means     double **gradgp, **trgradgp; /* for var p point j */
          computed over hstepm matrices product = hstepm*stepm months)      double *gpp, *gmp; /* for var p point j */
          as a weighted average of prlim.     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       */     double ***p3mat;
       for(j=nlstate+1;j<=nlstate+ndeath;j++){     double age,agelim, hf;
         for(i=1,gmp[j]=0.; i<= nlstate; i++)     /* double ***mobaverage; */
          gmp[j] += prlim[i][i]*p3mat[i][j][1];     int theta;
       }         char digit[4];
       /* end probability of death */     char digitp[25];
   
       for(j=1; j<= nlstate; j++) /* vareij */     char fileresprobmorprev[FILENAMELENGTH];
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     if(popbased==1){
         }       if(mobilav!=0)
          strcpy(digitp,"-POPULBASED-MOBILAV_");
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */       else strcpy(digitp,"-POPULBASED-NOMOBIL_");
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];     }
       }     else 
        strcpy(digitp,"-STABLBASED_");
     } /* End theta */  
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */  
   
     for(h=0; h<=nhstepm; h++) /* veij */  
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  
   
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  
       for(theta=1; theta <=npar; theta++)  
         trgradgp[j][theta]=gradgp[theta][j];  
     
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  
   
     for(h=0;h<=nhstepm;h++){     /* if (mobilav!=0) { */
       for(k=0;k<=nhstepm;k++){     /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);     /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);     /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
         for(i=1;i<=nlstate;i++)     /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
           for(j=1;j<=nlstate;j++)     /*   } */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;     /* } */
       }  
     }     strcpy(fileresprobmorprev,"PRMORPREV-"); 
      sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileresu);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      pstamp(ficresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
      fprintf(ficresprobmorprev,"\n");
     
      fprintf(ficgp,"\n# Routine varevsij");
      fprintf(ficgp,"\nunset title \n");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      pstamp(ficresvij);
      fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
        fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
      else
        fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
      fprintf(ficresvij,"\n");
   
      xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       
     /* pptj */     if(estepm < stepm){
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       printf ("Problem %d lower than %d\n",estepm, stepm);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);     }
     for(j=nlstate+1;j<=nlstate+ndeath;j++)     else  hstepm=estepm;   
       for(i=nlstate+1;i<=nlstate+ndeath;i++)     /* For example we decided to compute the life expectancy with the smallest unit */
         varppt[j][i]=doldmp[j][i];     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* end ppptj */        nhstepm is the number of hstepm from age to agelim 
     /*  x centered again */        nstepm is the number of stepm from age to agelim. 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          Look at function hpijx to understand why because of memory size limitations, 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        we decided (b) to get a life expectancy respecting the most precise curvature of the
          survival function given by stepm (the optimization length). Unfortunately it
     if (popbased==1) {        means that if the survival funtion is printed every two years of age and if
       if(mobilav ==0){        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(i=1; i<=nlstate;i++)        results. So we changed our mind and took the option of the best precision.
           prlim[i][i]=probs[(int)age][i][ij];     */
       }else{ /* mobilav */      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(i=1; i<=nlstate;i++)     agelim = AGESUP;
           prlim[i][i]=mobaverage[(int)age][i][ij];     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* This for computing probability of death (h=1 means       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        computed over hstepm (estepm) matrices product = hstepm*stepm months)        gp=matrix(0,nhstepm,1,nlstate);
        as a weighted average of prlim.       gm=matrix(0,nhstepm,1,nlstate);
                   
                   
        for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
                           
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
                           
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
          for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* Next for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end probability of death */
                           
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
                           
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
                           
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                           
          for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
            for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
              gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end probability of death */
                           
          for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
                           
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
                           
        } /* End theta */
                   
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   
        for(h=0; h<=nhstepm; h++) /* veij */
          for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
                   
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
                   
                   
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
                   
        for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
        }
                   
        /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
        /* end ppptj */
        /*  x centered again */
                   
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
                   
        if (popbased==1) {
          if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
          }
        }
                   
        /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
        */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
        /* end probability of death */
                   
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
        } 
        fprintf(ficresprobmorprev,"\n");
                   
        fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          }
        fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
      fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
     */      */
     for(j=nlstate+1;j<=nlstate+ndeath;j++){     /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
       for(i=1,gmp[j]=0.;i<= nlstate; i++)      fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];   
     }      
     /* end probability of death */  
   
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));  
       for(i=1; i<=nlstate;i++){  
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);  
       }  
     }   
     fprintf(ficresprobmorprev,"\n");  
   
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }  
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  
   free_vector(gpp,nlstate+1,nlstate+ndeath);  
   free_vector(gmp,nlstate+1,nlstate+ndeath);  
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
   fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");  
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */  
   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");  
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));  
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));  
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);  
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);  
 */  
 /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */  
   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);  
   
   free_vector(xp,1,npar);     free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);     free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(dnewm,1,nlstate,1,npar);     free_matrix(dnewm,1,nlstate,1,npar);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fclose(ficresprobmorprev);     fclose(ficresprobmorprev);
   fflush(ficgp);     fflush(ficgp);
   fflush(fichtm);      fflush(fichtm); 
 }  /* end varevsij */   }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 4027  void varprevlim(char fileres[], double * Line 5381  void varprevlim(char fileres[], double *
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
     double **mgm, **mgp;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
       
Line 4049  void varprevlim(char fileres[], double * Line 5404  void varprevlim(char fileres[], double *
     if (stepm >= YEARM) hstepm=1;      if (stepm >= YEARM) hstepm=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     gradg=matrix(1,npar,1,nlstate);      gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
     gp=vector(1,nlstate);      gp=vector(1,nlstate);
     gm=vector(1,nlstate);      gm=vector(1,nlstate);
   
Line 4056  void varprevlim(char fileres[], double * Line 5413  void varprevlim(char fileres[], double *
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
               mgp[theta][i] = prlim[i][i];
         }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
         }
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
     } /* End theta */      } /* End theta */
   
     trgradg =matrix(1,nlstate,1,npar);      trgradg =matrix(1,nlstate,1,npar);
Line 4075  void varprevlim(char fileres[], double * Line 5441  void varprevlim(char fileres[], double *
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradg[j][theta]=gradg[theta][j];          trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       }
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
Line 4089  void varprevlim(char fileres[], double * Line 5478  void varprevlim(char fileres[], double *
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
     free_matrix(gradg,1,npar,1,nlstate);      free_matrix(gradg,1,npar,1,nlstate);
     free_matrix(trgradg,1,nlstate,1,npar);      free_matrix(trgradg,1,nlstate,1,npar);
   } /* End age */    } /* End age */
Line 4101  void varprevlim(char fileres[], double * Line 5492  void varprevlim(char fileres[], double *
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {   {
   int i, j=0,  k1, l1, tj;     int i, j=0,  k1, l1, tj;
   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;
   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;
   double *gp, *gm;     double *gp, *gm;
   double **gradg, **trgradg;     double **gradg, **trgradg;
   double **mu;     double **mu;
   double age, cov[NCOVMAX+1];     double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;     int theta;
   char fileresprob[FILENAMELENGTH];     char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];     char fileresprobcov[FILENAMELENGTH];
   char fileresprobcor[FILENAMELENGTH];     char fileresprobcor[FILENAMELENGTH];
   double ***varpij;     double ***varpij;
   
   strcpy(fileresprob,"prob");      strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);     strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);       printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }     }
   strcpy(fileresprobcov,"probcov");      strcpy(fileresprobcov,"PROBCOV_"); 
   strcat(fileresprobcov,fileres);     strcat(fileresprobcov,fileresu);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);       printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }     }
   strcpy(fileresprobcor,"probcor");      strcpy(fileresprobcor,"PROBCOR_"); 
   strcat(fileresprobcor,fileres);     strcat(fileresprobcor,fileresu);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);       printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }     }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   pstamp(ficresprob);     pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");     fprintf(ficresprob,"# Age");
   pstamp(ficresprobcov);     pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");     fprintf(ficresprobcov,"# Age");
   pstamp(ficresprobcor);     pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcor,"# Age");     fprintf(ficresprobcor,"# Age");
   
   
   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(ficresprob," p%1d-%1d (SE)",i,j);         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);         fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);         fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }         }  
  /* fprintf(ficresprob,"\n");     /* fprintf(ficresprob,"\n");
   fprintf(ficresprobcov,"\n");        fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");        fprintf(ficresprobcor,"\n");
  */     */
   xp=vector(1,npar);     xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   first=1;     first=1;
   fprintf(ficgp,"\n# Routine varprob");     fprintf(ficgp,"\n# Routine varprob");
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
   file %s<br>\n",optionfilehtmcov);     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\  
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
 It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
 standard deviations wide on each axis. <br>\  standard deviations wide on each axis. <br>\
Line 4189  standard deviations wide on each axis. < Line 5579  standard deviations wide on each axis. <
  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   cov[1]=1;     cov[1]=1;
   /* tj=cptcoveff; */     /* tj=cptcoveff; */
   tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,cptcoveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;     j1=0;
   for(j1=1; j1<=tj;j1++){     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
     /*for(i1=1; i1<=ncodemax[t];i1++){ */       if  (cptcovn>0) {
     /*j1++;*/         fprintf(ficresprob, "\n#********** Variable "); 
       if  (cptcovn>0) {         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);         fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficresprob, "**********\n#\n");         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficgp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "**********\n#\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(ficgp, "**********\n#\n");                          
                  fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);                          
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(ficresprobcor, "\n#********** Variable ");    
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "**********\n#");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);         if(invalidvarcomb[j1]){
         fprintf(ficresprobcor, "**********\n#");               fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
       }           fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                  continue;
       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));         }
       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       }
       gp=vector(1,(nlstate)*(nlstate+ndeath));       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       gm=vector(1,(nlstate)*(nlstate+ndeath));       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for (age=bage; age<=fage; age ++){        gp=vector(1,(nlstate)*(nlstate+ndeath));
         cov[2]=age;       gm=vector(1,(nlstate)*(nlstate+ndeath));
         if(nagesqr==1)       for (age=bage; age<=fage; age ++){ 
           cov[3]= age*age;         cov[2]=age;
         for (k=1; k<=cptcovn;k++) {         if(nagesqr==1)
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4           cov[3]= age*age;
                                                          * 1  1 1 1 1         for (k=1; k<=cptcovn;k++) {
                                                          * 2  2 1 1 1           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
                                                          * 3  1 2 1 1           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                          */                                                                      * 1  1 1 1 1
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/                                                                      * 2  2 1 1 1
         }                                                                      * 3  1 2 1 1
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */                                                                      */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         for (k=1; k<=cptcovprod;k++)         }
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                  for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
              for (k=1; k<=cptcovprod;k++)
         for(theta=1; theta <=npar; theta++){           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
           for(i=1; i<=npar; i++)                          
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);                          
                    for(theta=1; theta <=npar; theta++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);           for(i=1; i<=npar; i++)
                        xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           k=0;                                  
           for(i=1; i<= (nlstate); i++){           pmij(pmmij,cov,ncovmodel,xp,nlstate);
             for(j=1; j<=(nlstate+ndeath);j++){                                  
               k=k+1;           k=0;
               gp[k]=pmmij[i][j];           for(i=1; i<= (nlstate); i++){
             }             for(j=1; j<=(nlstate+ndeath);j++){
           }               k=k+1;
                          gp[k]=pmmij[i][j];
           for(i=1; i<=npar; i++)             }
             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);           }
                                       
           pmij(pmmij,cov,ncovmodel,xp,nlstate);           for(i=1; i<=npar; i++)
           k=0;             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           for(i=1; i<=(nlstate); i++){                                  
             for(j=1; j<=(nlstate+ndeath);j++){           pmij(pmmij,cov,ncovmodel,xp,nlstate);
               k=k+1;           k=0;
               gm[k]=pmmij[i][j];           for(i=1; i<=(nlstate); i++){
             }             for(j=1; j<=(nlstate+ndeath);j++){
           }               k=k+1;
                     gm[k]=pmmij[i][j];
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              }
             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];             }
         }                                  
            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           for(theta=1; theta <=npar; theta++)         }
             trgradg[j][theta]=gradg[theta][j];  
           
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);   
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
           
         k=0;  
         for(i=1; i<=(nlstate); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;  
             mu[k][(int) age]=pmmij[i][j];  
           }  
         }  
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  
             varpij[i][j][(int)age] = doldm[i][j];  
   
         /*printf("\n%d ",(int)age);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
           }*/  
   
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);  
         fprintf(ficresprobcor,"\n%d ",(int)age);  
   
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }  
         i=0;  
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){   
             i++;  
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  
             for (j=1; j<=i;j++){  
               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }  
           }  
         }/* end of loop for state */  
       } /* end of loop for age */  
       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
         
       /* Confidence intervalle of pij  */  
       /*  
         fprintf(ficgp,"\nunset parametric;unset label");  
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");  
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);  
         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  
         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);  
       */  
   
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  
       first1=1;first2=2;  
       for (k2=1; k2<=(nlstate);k2++){  
         for (l2=1; l2<=(nlstate+ndeath);l2++){   
           if(l2==k2) continue;  
           j=(k2-1)*(nlstate+ndeath)+l2;  
           for (k1=1; k1<=(nlstate);k1++){  
             for (l1=1; l1<=(nlstate+ndeath);l1++){   
               if(l1==k1) continue;  
               i=(k1-1)*(nlstate+ndeath)+l1;  
               if(i<=j) continue;  
               for (age=bage; age<=fage; age ++){   
                 if ((int)age %5==0){  
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;  
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;  
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;  
                   c12=cv12/sqrt(v1*v2);  
                   /* Computing eigen value of matrix of covariance */  
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  
                   if ((lc2 <0) || (lc1 <0) ){  
                     if(first2==1){  
                       first1=0;  
                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);  
                     }  
                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);  
                     /* lc1=fabs(lc1); */ /* If we want to have them positive */  
                     /* lc2=fabs(lc2); */  
                   }  
   
                   /* Eigen vectors */         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));           for(theta=1; theta <=npar; theta++)
                   /*v21=sqrt(1.-v11*v11); *//* error */             trgradg[j][theta]=gradg[theta][j];
                   v21=(lc1-v1)/cv12*v11;                          
                   v12=-v21;         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   v22=v11;         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                   tnalp=v21/v11;                          
                   if(first1==1){         pmij(pmmij,cov,ncovmodel,x,nlstate);
                     first1=0;                          
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);         k=0;
                   }         for(i=1; i<=(nlstate); i++){
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);           for(j=1; j<=(nlstate+ndeath);j++){
                   /*printf(fignu*/             k=k+1;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */             mu[k][(int) age]=pmmij[i][j];
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */           }
                   if(first==1){         }
                     first=0;         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                     fprintf(ficgp,"\nset parametric;unset label");           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);             varpij[i][j][(int)age] = doldm[i][j];
                     fprintf(ficgp,"\nset ter png small size 320, 240");                          
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\         /*printf("\n%d ",(int)age);
  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                             subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);           }*/
                     fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);                          
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);         fprintf(ficresprob,"\n%d ",(int)age);
                     fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);         fprintf(ficresprobcov,"\n%d ",(int)age);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);         fprintf(ficresprobcor,"\n%d ",(int)age);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                          
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   }else{           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                     first=0;           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);         }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);         i=0;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);         for (k=1; k<=(nlstate);k++){
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\           for (l=1; l<=(nlstate+ndeath);l++){ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\             i++;
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   }/* if first */             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                 } /* age mod 5 */             for (j=1; j<=i;j++){
               } /* end loop age */               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
               fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
               first=1;               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             } /*l12 */             }
           } /* k12 */           }
         } /*l1 */         }/* end of loop for state */
       }/* k1 */       } /* end of loop for age */
       /* } */ /* loop covariates */       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   }       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));      
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);       /* Confidence intervalle of pij  */
   free_vector(xp,1,npar);       /*
   fclose(ficresprob);         fprintf(ficgp,"\nunset parametric;unset label");
   fclose(ficresprobcov);         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   fclose(ficresprobcor);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   fflush(ficgp);         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   fflush(fichtmcov);         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
 }         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
        */
                   
        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
            if(l2==k2) continue;
            j=(k2-1)*(nlstate+ndeath)+l2;
            for (k1=1; k1<=(nlstate);k1++){
              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                if(l1==k1) continue;
                i=(k1-1)*(nlstate+ndeath)+l1;
                if(i<=j) continue;
                for (age=bage; age<=fage; age ++){ 
                  if ((int)age %5==0){
                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    mu1=mu[i][(int) age]/stepm*YEARM ;
                    mu2=mu[j][(int) age]/stepm*YEARM;
                    c12=cv12/sqrt(v1*v2);
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    if ((lc2 <0) || (lc1 <0) ){
                      if(first2==1){
                        first1=0;
                        printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                      }
                      fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                      /* lc1=fabs(lc1); */ /* If we want to have them positive */
                      /* lc2=fabs(lc2); */
                    }
                                                                   
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
                    v21=(lc1-v1)/cv12*v11;
                    v12=-v21;
                    v22=v11;
                    tnalp=v21/v11;
                    if(first1==1){
                      first1=0;
                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    }
                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    /*printf(fignu*/
                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                    if(first==1){
                      first=0;
                      fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                      fprintf(ficgp,"\nset ter svg size 640, 480");
                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
   %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                              subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }else{
                      first=0;
                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                    }/* if first */
                  } /* age mod 5 */
                } /* end loop age */
                fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                first=1;
              } /*l12 */
            } /* k12 */
          } /*l1 */
        }/* k1 */
      }  /* loop on combination of covariates j1 */
      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(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
      free_vector(xp,1,npar);
      fclose(ficresprob);
      fclose(ficresprobcov);
      fclose(ficresprobcor);
      fflush(ficgp);
      fflush(fichtmcov);
    }
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int estepm ,\                    int popforecast, int prevfcast, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   
    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><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");
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <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,subdirf2(fileres,"p"),subdirf2(fileres,"p"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
      fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
      fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
      fprintf(fichtm,"\
    - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
    <a href=\"%s\">%s</a> <br>\n",             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));  
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Population projections by age and states: \   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));     <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
      if(prevfcast==1){
        fprintf(fichtm,"\
    - Prevalence projections by age and states:                            \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
      }
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  m=pow(2,cptcoveff);     jj1=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     for(k1=1; k1<=m;k1++){
   
  jj1=0;       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
            printf("\nCombination (%d) ignored because no cases \n",k1); 
            continue;
          }
      }       }
        /* aij, bij */
        fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
   <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
 <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);    incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
        /* Period (stable) prevalence in each health state */  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
   <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
        /* Survival functions (period) in state j */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
        }
        /* State specific survival functions (period) */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
    Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
    <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
        }
        /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
        if(backcast==1){
          /* Period (stable) back prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \           fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
 <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
        }         }
        }
        if(prevfcast==1){
          /* Projection of prevalence up to period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
          }
        }
            
      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) : <a href=\"%s%d%d.png\">%s%d%d.png</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.svg\">%s_%d%d.svg</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }       }
    } /* end i1 */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
      fprintf(fichtm,"\
  fprintf(fichtm,"\  
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
    - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
   But because parameters are usually highly correlated (a higher incidence of disability \
   and a higher incidence of recovery can give very close observed transition) it might \
   be very useful to look not only at linear confidence intervals estimated from the \
   variances but at the covariance matrix. And instead of looking at the estimated coefficients \
   (parameters) of the logistic regression, it might be more meaningful to visualize the \
   covariance matrix of the one-step probabilities. \
   See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",     fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));             subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));             subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));             subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 4536  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 5986  fprintf(fichtm," \n<ul><li><b>Graphs</b>
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
  fflush(fichtm);     fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     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;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
            continue;
          }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
 <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences: %s%d.png<br>\   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    } /* end i1 */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
  fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
     char gplotcondition[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
     int vpopbased;
     int ioffset; /* variable offset for columns */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 4582  void printinggnuplot(char fileres[], cha Line 6042  void printinggnuplot(char fileres[], cha
   
   /*#ifdef windows */    /*#ifdef windows */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* Contribution to likelihood */
     /* Plot the probability implied in the likelihood */
     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
   /* nice for mle=4 plot by number of matrix products.
      replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
   /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {
         fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }
       fprintf(ficgp,";\nset out; unset ylabel;\n"); 
     }
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/    /* 1eme*/
   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
      fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
      fprintf(ficgp,"set xlabel \"Age\" \n\          lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
 set ylabel \"Probability\" \n\          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
 set ter png small size 320, 240\n\          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
      for (i=1; i<= nlstate ; i ++) {          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        else        fprintf(ficgp," %%*lf (%%*lf)");        }
      }        fprintf(ficgp,"\n#\n");
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        if(invalidvarcomb[k1]){
      for (i=1; i<= nlstate ; i ++) {          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          continue;
        else fprintf(ficgp," %%*lf (%%*lf)");        }
      }   
      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
      for (i=1; i<= nlstate ; i ++) {        fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");        fprintf(ficgp,"set xlabel \"Age\" \n\
        else fprintf(ficgp," %%*lf (%%*lf)");  set ylabel \"Probability\" \n   \
      }    set ter svg size 640, 480\n     \
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
    }                          
   }        for (i=1; i<= nlstate ; i ++) {
   /*2 eme*/          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");          else        fprintf(ficgp," %%*lf (%%*lf)");
   for (k1=1; k1<= m ; k1 ++) {         }
     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);        for (i=1; i<= nlstate ; i ++) {
               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," %%lf (%%lf)");  
         else fprintf(ficgp," %%*lf (%%*lf)");  
       }     
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," %%lf (%%lf)");  
         else fprintf(ficgp," %%*lf (%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           } 
       fprintf(ficgp,"\" t\"\" w l lt 0,");        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        for (i=1; i<= nlstate ; i ++) {
       for (j=1; j<= nlstate+1 ; j ++) {          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
         if (j==i) fprintf(ficgp," %%lf (%%lf)");  
         else fprintf(ficgp," %%*lf (%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }  
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
       else fprintf(ficgp,"\" t\"\" w l lt 0,");        if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
           if(cptcoveff ==0){
             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
           }else{
             kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];
               kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(k==cptcoveff){
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         4+(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
               }
             } /* end covariate */
           } /* end if no covariate */
         } /* end if backcast */
         fprintf(ficgp,"\nset out \n");
       } /* k1 */
     } /* cpt */
     /*2 eme*/
     for (k1=1; k1<= m ; k1 ++) { 
   
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }
       fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         continue;
     }      }
   }                          
         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         if(vpopbased==0)
           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
         else
           fprintf(ficgp,"\nreplot ");
         for (i=1; i<= nlstate+1 ; i ++) {
           k=2*i;
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }   
           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }   
           fprintf(ficgp,"\" t\"\" w l lt 0,");
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }   
           if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         } /* state */
       } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
     } /* k1 */
           
           
   /*3eme*/    /*3eme*/
     
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                           
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       fprintf(ficgp,"set ter png small size 320, 240\n\        fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                           
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                           
       }         } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
   /* CV preval stable (period) */    /* 4eme */
     /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
   
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
                           
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n                                                                                                                                                                                     \
   unset log y\n                                                                                                                                                                                                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;
         for (i=1; i<= nlstate ; i ++){
           if(i==1){
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           }else{
             fprintf(ficgp,", '' ");
           }
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate+ndeath ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
           
   /* 5eme */
     /* Survival functions (period) from state i in state j by final state j */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
                           
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
         
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\n                                             \
   unset log y\n                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3;        k=3;
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);          if(j==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(cpt-1) +j;
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
           /* for (i=2; i<= nlstate+ndeath ; i ++) */
           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficgp,", '' ");
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           l=(nlstate+ndeath)*(cpt-1) +j;
           if(j < nlstate)
             fprintf(ficgp,"$%d +",k+l);
           else
             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
   /* 6eme */
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
         
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter png small size 320, 240\n\  set ter svg size 640, 480\n                                             \
 unset log y\n\  unset log y\n                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1)          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else          else
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1;
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=1; j<= (nlstate-1) ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
       
     
   /* 7eme */
     if(backcast == 1){
       /* CV back preval stable (period) for each covariate */
       for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\n                                             \
   unset log y\n                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3; /* Offset */
           for (i=1; i<= nlstate ; i ++){
             if(i==1)
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
             else
               fprintf(ficgp,", '' ");
             /* l=(nlstate+ndeath)*(i-1)+1; */
             l=(nlstate+ndeath)*(cpt-1)+1;
             /* 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",k1,k+l+(cpt-1)+i-1); /* a vérifier */
             /* for (j=2; j<= nlstate ; j ++) */
             /*    fprintf(ficgp,"+$%d",k+l+j-1); */
             /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
             fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* End if backcast */
     
     /* 8eme */
     if(prevfcast==1){
       /* Projection from cross-sectional to stable (period) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           }
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\n                                             \
   unset log y\n                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
           for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             if(i==1){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
             }else{
               fprintf(ficgp,",\\\n '' ");
             }
             if(cptcoveff ==0){ /* No covariate */
               ioffset=2; /* Age is in 2 */
               /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               fprintf(ficgp," u %d:(", ioffset); 
               if(i==nlstate+1)
                 fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
               else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
             }else{ /* more than 2 covariates */
               if(cptcoveff ==1){
                 ioffset=4; /* Age is in 4 */
               }else{
                 ioffset=6; /* Age is in 6 */
                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                 /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               }   
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
               }
               strcpy(gplotcondition+strlen(gplotcondition),")");
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
               }else{
                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if prevfcast */
     
     
   /* proba elementaires */    /* proba elementaires */
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
Line 4711  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6529  plot [%.f:%.f]  ", ageminpar, agemaxpar)
         fprintf(ficgp,"\n");          fprintf(ficgp,"\n");
       }        }
     }      }
    }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
     
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
Line 4729  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6547  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
      fprintf(ficgp,"# ng=%d\n",ng);      fprintf(ficgp,"# ng=%d\n",ng);
      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {      for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"#    jk=%d\n",jk);        fprintf(ficgp,"#    jk=%d\n",jk);
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
        if (ng==2)        fprintf(ficgp,"\nset ter svg size 640, 480 ");
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        if (ng==1){
        else          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
          fprintf(ficgp,"\nset title \"Probability\"\n");          fprintf(ficgp,"\nunset log y");
        fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        }else if (ng==2){
        i=1;          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
        for(k2=1; k2<=nlstate; k2++) {          fprintf(ficgp,"\nset log y");
          k3=i;        }else if (ng==3){
          for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
            if (k != k2){          fprintf(ficgp,"\nset log y");
              if(ng==2)        }else
                if(nagesqr==0)          fprintf(ficgp,"\nunset title ");
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                else /* nagesqr =1 */        i=1;
                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);        for(k2=1; k2<=nlstate; k2++) {
              else          k3=i;
                if(nagesqr==0)          for(k=1; k<=(nlstate+ndeath); k++) {
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            if (k != k2){
                else /* nagesqr =1 */              switch( ng) {
                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);              case 1:
              ij=1;/* To be checked else nbcode[0][0] wrong */                if(nagesqr==0)
              for(j=3; j <=ncovmodel-nagesqr; j++) {                  fprintf(ficgp," p%d+p%d*x",i,i+1);
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */                else /* nagesqr =1 */
                  fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                  ij++;                break;
                }              case 2: /* ng=2 */
                else                if(nagesqr==0)
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
              }                else /* nagesqr =1 */
              fprintf(ficgp,")/(1");                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                              break;
              for(k1=1; k1 <=nlstate; k1++){               case 3:
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                   break;
                ij=1;              }
                for(j=3; j <=ncovmodel-nagesqr; j++){              ij=1;/* To be checked else nbcode[0][0] wrong */
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              for(j=3; j <=ncovmodel-nagesqr; j++) {
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                    ij++;                if(ij <=cptcovage) { /* Bug valgrind */
                  }                  if((j-2)==Tage[ij]) { /* Bug valgrind */
                  else                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                }                    ij++;
                fprintf(ficgp,")");                  }
              }                }
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                else
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
              i=i+ncovmodel;              }
            }            }else{
          } /* end k */              i=i-ncovmodel;
        } /* end k2 */              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
      } /* end jk */                fprintf(ficgp," (1.");
    } /* end ng */            }
  /* avoid: */            
    fflush(ficgp);             if(ng != 1){
               fprintf(ficgp,")/(1");
               
               for(k1=1; k1 <=nlstate; k1++){ 
                 if(nagesqr==0)
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                  
                 ij=1;
                 for(j=3; j <=ncovmodel-nagesqr; j++){
                   if(ij <=cptcovage) { /* Bug valgrind */
                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                       /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                       ij++;
                     }
                   }
                   else
                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
                 }
                 fprintf(ficgp,")");
               }
               fprintf(ficgp,")");
               if(ng ==2)
                 fprintf(ficgp," t \"p%d%d\" ", k2,k);
               else /* ng= 3 */
                 fprintf(ficgp," t \"i%d%d\" ", k2,k);
             }else{ /* end ng <> 1 */
               if( k !=k2) /* logit p11 is hard to draw */
                 fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
             }
             if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
               fprintf(ficgp,",");
             if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
               fprintf(ficgp,",");
             i=i+ncovmodel;
           } /* end k */
         } /* end k2 */
         fprintf(ficgp,"\n set out\n");
       } /* end jk */
     } /* end ng */
     /* avoid: */
     fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){  /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
    int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
   int i, cpt, cptcod;     
   int modcovmax =1;     int i, cpt, cptcod;
   int mobilavrange, mob;     int modcovmax =1;
   double age;     int mobilavrange, mob;
      int iage=0;
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose   
                            a covariate has 2 modalities */     double sum=0.;
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */     double age;
      double *sumnewp, *sumnewm;
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     if(mobilav==1) mobilavrange=5; /* default */    
     else mobilavrange=mobilav;    
     for (age=bage; age<=fage; age++)     /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
       for (i=1; i<=nlstate;i++)     /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
         for (cptcod=1;cptcod<=modcovmax;cptcod++)  
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];     sumnewp = vector(1,ncovcombmax);
     /* We keep the original values on the extreme ages bage, fage and for      sumnewm = vector(1,ncovcombmax);
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2     agemingood = vector(1,ncovcombmax);  
        we use a 5 terms etc. until the borders are no more concerned.      agemaxgood = vector(1,ncovcombmax);
     */   
     for (mob=3;mob <=mobilavrange;mob=mob+2){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){       sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){       sumnewp[cptcod]=0.;
           for (cptcod=1;cptcod<=modcovmax;cptcod++){       agemingood[cptcod]=0;
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];       agemaxgood[cptcod]=0;
               for (cpt=1;cpt<=(mob-1)/2;cpt++){     }
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];    
               }     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;       if(mobilav==1) mobilavrange=5; /* default */
           }       else mobilavrange=mobilav;
         }       for (age=bage; age<=fage; age++)
       }/* end age */         for (i=1; i<=nlstate;i++)
     }/* end mob */           for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
   }else return -1;             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   return 0;       /* We keep the original values on the extreme ages bage, fage and for 
 }/* End movingaverage */          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
        */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                }
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
            }
          }/* end age */
        }/* end mob */
      }else
        return -1;
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
        if(invalidvarcomb[cptcod]){
          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
          continue;
        }
   
        agemingood[cptcod]=fage-(mob-1)/2;
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemingood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        /* From youngest, finding the oldest wrong */
        agemaxgood[cptcod]=bage+(mob-1)/2;
        for (age=bage+(mob-1)/2; age<=fage; age++){
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
                   
        for (age=bage; age<=fage; age++){
          printf("%d %d ", cptcod, (int)age);
          sumnewp[cptcod]=0.;
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewp[cptcod]+=probs[(int)age][i][cptcod];
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
          }
          /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
        }
        /* printf("\n"); */
        /* } */
        /* brutal averaging */
        for (i=1; i<=nlstate;i++){
          for (age=1; age<=bage; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }        
          for (age=fage; age<=AGESUP; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }
        } /* end i status */
        for (i=nlstate+1; i<=nlstate+ndeath;i++){
          for (age=1; age<=AGESUP; age++){
            /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
            mobaverage[(int)age][i][cptcod]=0.;
          }
        }
      }/* end cptcod */
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
    
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
Line 4850  void prevforecast(char fileres[], double Line 6824  void prevforecast(char fileres[], double
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
     
   strcpy(fileresf,"f");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileresu);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    if((ficresf=fopen(fileresf,"w"))==NULL) {
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   }    }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   if (mobilav!=0) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){  
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
Line 4893  void prevforecast(char fileres[], double Line 6865  void prevforecast(char fileres[], double
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
   
   i1=cptcoveff;    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
     
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(k=1;k<=i1;k++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if(invalidvarcomb[k]){
       k=k+1;        printf("\nCombination (%d) projection ignored because no cases \n",k); 
       fprintf(ficresf,"\n#******");        continue;
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       }      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresf,"******\n");        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");      }
       for(j=1; j<=nlstate+ndeath;j++){       fprintf(ficresf," yearproj age");
         for(i=1; i<=nlstate;i++)                    for(j=1; j<=nlstate+ndeath;j++){ 
           fprintf(ficresf," p%d%d",i,j);        for(i=1; i<=nlstate;i++)        
         fprintf(ficresf," p.%d",j);          fprintf(ficresf," p%d%d",i,j);
       }        fprintf(ficresf," wp.%d",j);
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {       }
         fprintf(ficresf,"\n");      for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         for (agec=fage; agec>=(ageminpar-1); agec--){         for (agec=fage; agec>=(ageminpar-1); agec--){ 
           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm;           nhstepm = nhstepm/hstepm; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
                   
           for (h=0; h<=nhstepm; h++){          for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==yearp) {            if (h*hstepm/YEARM*stepm ==yearp) {
               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]][codtab[k][j]]);                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }             } 
             for(j=1; j<=nlstate+ndeath;j++) {            for(j=1; j<=nlstate+ndeath;j++) {
               ppij=0.;              ppij=0.;
               for(i=1; i<=nlstate;i++) {              for(i=1; i<=nlstate;i++) {
                 if (mobilav==1)                 if (mobilav==1) 
                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
                 else {                else {
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
                 }  
                 if (h*hstepm/YEARM*stepm== yearp) {  
                   fprintf(ficresf," %.3f", p3mat[i][j][h]);  
                 }  
               } /* end i */  
               if (h*hstepm/YEARM*stepm==yearp) {  
                 fprintf(ficresf," %.3f", ppij);  
               }                }
             }/* end j */                if (h*hstepm/YEARM*stepm== yearp) {
           } /* end h */                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                }
         } /* end agec */              } /* end i */
       } /* end yearp */              if (h*hstepm/YEARM*stepm==yearp) {
     } /* end cptcod */                fprintf(ficresf," %.3f", ppij);
   } /* end  cptcov */              }
                    }/* end j */
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end  k */
           
   fclose(ficresf);    fclose(ficresf);
 }    printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
 /************** Forecasting *****not tested NB*************/  
 void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;  
   double calagedatem, agelim, kk1, kk2;  
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;  
   double ***mobaverage;  
   char filerespop[FILENAMELENGTH];  
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   agelim=AGESUP;  
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
     
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  
     
     
   strcpy(filerespop,"pop");   
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   
   if (mobilav!=0) {  }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){  
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /* /\************** Back Forecasting ******************\/ */
   if (stepm<=12) stepsize=1;  /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
     /*   /\* back1, year, month, day of starting backection  */
   agelim=AGESUP;  /*      agemin, agemax range of age */
   /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
   /*      anback2 year of en of backection (same day and month as back1). */
   /*   *\/ */
   /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
   /*   double agec; /\* generic age *\/ */
   /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
   /*   double *popeffectif,*popcount; */
   /*   double ***p3mat; */
   /*   /\* double ***mobaverage; *\/ */
   /*   char fileresfb[FILENAMELENGTH]; */
           
   /*   agelim=AGESUP; */
   /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
   /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
   /*      We still use firstpass and lastpass as another selection. */
   /*   *\/ */
   /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
   /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
   /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
           
   /*   strcpy(fileresfb,"FB_");  */
   /*   strcat(fileresfb,fileresu); */
   /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
   /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
   /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
   /*   } */
   /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
   /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
           
   /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
           
   /*   /\* if (mobilav!=0) { *\/ */
   /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
   /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*   } *\/ */
   /*   /\* } *\/ */
           
   /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   /*   if (stepm<=12) stepsize=1; */
   /*   if(estepm < stepm){ */
   /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
   /*   } */
   /*   else  hstepm=estepm;    */
           
   /*   hstepm=hstepm/stepm;  */
   /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
   /*                                fractional in yp1 *\/ */
   /*   anprojmean=yp; */
   /*   yp2=modf((yp1*12),&yp); */
   /*   mprojmean=yp; */
   /*   yp1=modf((yp2*30.5),&yp); */
   /*   jprojmean=yp; */
   /*   if(jprojmean==0) jprojmean=1; */
   /*   if(mprojmean==0) jprojmean=1; */
           
   /*   i1=cptcoveff; */
   /*   if (cptcovn < 1){i1=1;} */
       
   hstepm=1;  /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
   hstepm=hstepm/stepm;   
       
   if (popforecast==1) {  /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);  
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  
     }   
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);  
       
     i=1;     
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
      
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }  
   
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }  
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
         
       for (cpt=0; cpt<=0;cpt++) {   
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     
                   
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){   /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
           nhstepm = nhstepm/hstepm;   /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
             /*       k=k+1; */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
           oldm=oldms;savm=savms;  /*       for(j=1;j<=cptcoveff;j++) { */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*       } */
   /*       fprintf(ficresfb," yearbproj age"); */
   /*       for(j=1; j<=nlstate+ndeath;j++){  */
   /*                              for(i=1; i<=nlstate;i++)               */
   /*           fprintf(ficresfb," p%d%d",i,j); */
   /*                              fprintf(ficresfb," p.%d",j); */
   /*       } */
   /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
   /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
   /*                              fprintf(ficresfb,"\n"); */
   /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
   /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
   /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
   /*                                      nhstepm = nhstepm/hstepm;  */
   /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*                                      oldm=oldms;savm=savms; */
   /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
   /*                                      for (h=0; h<=nhstepm; h++){ */
   /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
   /*               fprintf(ficresfb,"\n"); */
   /*               for(j=1;j<=cptcoveff;j++)  */
   /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
   /*                                              }  */
   /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
   /*                                                      ppij=0.; */
   /*                                                      for(i=1; i<=nlstate;i++) { */
   /*                                                              if (mobilav==1)  */
   /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
   /*                                                              else { */
   /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
   /*                                                              } */
   /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
   /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
   /*                                                              } */
   /*                                                      } /\* end i *\/ */
   /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
   /*                                                              fprintf(ficresfb," %.3f", ppij); */
   /*                                                      } */
   /*                                              }/\* end j *\/ */
   /*                                      } /\* end h *\/ */
   /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*                              } /\* end agec *\/ */
   /*       } /\* end yearp *\/ */
   /*     } /\* end cptcod *\/ */
   /*   } /\* end  cptcov *\/ */
                   
           for (h=0; h<=nhstepm; h++){  /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
             if (h==(int) (calagedatem+YEARM*cpt)) {          
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*   fclose(ficresfb); */
             }   /*   printf("End of Computing Back forecasting \n"); */
             for(j=1; j<=nlstate+ndeath;j++) {  /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
               kk1=0.;kk2=0;          
               for(i=1; i<=nlstate;i++) {                /* } */
                 if (mobilav==1)   
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }  
               }  
               if (h==(int)(calagedatem+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }  
             }  
             for(i=1; i<=nlstate;i++){  
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];  
             }  
   
             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)   
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }  
       }  
    
   /******/  
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {   /************** Forecasting *****not tested NB*************/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){     
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
           nhstepm = nhstepm/hstepm;   /*   int *popage; */
             /*   double calagedatem, agelim, kk1, kk2; */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   double *popeffectif,*popcount; */
           oldm=oldms;savm=savms;  /*   double ***p3mat,***tabpop,***tabpopprev; */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*   /\* double ***mobaverage; *\/ */
           for (h=0; h<=nhstepm; h++){  /*   char filerespop[FILENAMELENGTH]; */
             if (h==(int) (calagedatem+YEARM*cpt)) {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
             }   /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
             for(j=1; j<=nlstate+ndeath;j++) {  /*   agelim=AGESUP; */
               kk1=0.;kk2=0;  /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
               for(i=1; i<=nlstate;i++) {                  
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
               }    
               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);            
             }  /*   strcpy(filerespop,"POP_");  */
           }  /*   strcat(filerespop,fileresu); */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
         }  /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
       }  /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
    }   /*   } */
   }  /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
    /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
   
   if (popforecast==1) {  /*   /\* if (mobilav!=0) { *\/ */
     free_ivector(popage,0,AGESUP);  /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
     free_vector(popeffectif,0,AGESUP);  /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
     free_vector(popcount,0,AGESUP);  /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   }  /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   /\*   } *\/ */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   /\* } *\/ */
   fclose(ficrespop);  
 } /* End of popforecast */  
   
   /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   /*   if (stepm<=12) stepsize=1; */
     
   /*   agelim=AGESUP; */
     
   /*   hstepm=1; */
   /*   hstepm=hstepm/stepm;  */
           
   /*   if (popforecast==1) { */
   /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
   /*       printf("Problem with population file : %s\n",popfile);exit(0); */
   /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
   /*     }  */
   /*     popage=ivector(0,AGESUP); */
   /*     popeffectif=vector(0,AGESUP); */
   /*     popcount=vector(0,AGESUP); */
       
   /*     i=1;    */
   /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
       
   /*     imx=i; */
   /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
   /*   } */
     
   /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
   /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
   /*       k=k+1; */
   /*       fprintf(ficrespop,"\n#******"); */
   /*       for(j=1;j<=cptcoveff;j++) { */
   /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*       } */
   /*       fprintf(ficrespop,"******\n"); */
   /*       fprintf(ficrespop,"# Age"); */
   /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
   /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
         
   /*       for (cpt=0; cpt<=0;cpt++) {  */
   /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
           
   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
   /*        nhstepm = nhstepm/hstepm;  */
             
   /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*        oldm=oldms;savm=savms; */
   /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
             
   /*        for (h=0; h<=nhstepm; h++){ */
   /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
   /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
   /*          }  */
   /*          for(j=1; j<=nlstate+ndeath;j++) { */
   /*            kk1=0.;kk2=0; */
   /*            for(i=1; i<=nlstate;i++) {               */
   /*              if (mobilav==1)  */
   /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
   /*              else { */
   /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
   /*              } */
   /*            } */
   /*            if (h==(int)(calagedatem+12*cpt)){ */
   /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
   /*              /\*fprintf(ficrespop," %.3f", kk1); */
   /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
   /*            } */
   /*          } */
   /*          for(i=1; i<=nlstate;i++){ */
   /*            kk1=0.; */
   /*            for(j=1; j<=nlstate;j++){ */
   /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
   /*            } */
   /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
   /*          } */
               
   /*          if (h==(int)(calagedatem+12*cpt)) */
   /*            for(j=1; j<=nlstate;j++)  */
   /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
   /*        } */
   /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*      } */
   /*       } */
         
   /*       /\******\/ */
         
   /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
   /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
   /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
   /*        nhstepm = nhstepm/hstepm;  */
             
   /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*        oldm=oldms;savm=savms; */
   /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
   /*        for (h=0; h<=nhstepm; h++){ */
   /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
   /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
   /*          }  */
   /*          for(j=1; j<=nlstate+ndeath;j++) { */
   /*            kk1=0.;kk2=0; */
   /*            for(i=1; i<=nlstate;i++) {               */
   /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
   /*            } */
   /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
   /*          } */
   /*        } */
   /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*      } */
   /*       } */
   /*     }  */
   /*   } */
     
   /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
     
   /*   if (popforecast==1) { */
   /*     free_ivector(popage,0,AGESUP); */
   /*     free_vector(popeffectif,0,AGESUP); */
   /*     free_vector(popcount,0,AGESUP); */
   /*   } */
   /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   /*   fclose(ficrespop); */
   /* } /\* End of popforecast *\/ */
    
 int fileappend(FILE *fichier, char *optionfich)  int fileappend(FILE *fichier, char *optionfich)
 {  {
   if((fichier=fopen(optionfich,"a"))==NULL) {    if((fichier=fopen(optionfich,"a"))==NULL) {
Line 5261  double gompertz(double x[]) Line 7364  double gompertz(double x[])
   double A,B,L=0.0,sump=0.,num=0.;    double A,B,L=0.0,sump=0.,num=0.;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
   for (i=0;i<=imx-1 ; i++) {    for (i=1;i<=imx ; i++) {
     sump=sump+weight[i];      sump=sump+weight[i];
     /*    sump=sump+1;*/      /*    sump=sump+1;*/
     num=num+1;      num=num+1;
Line 5334  double gompertz_f(const gsl_vector *v, v Line 7437  double gompertz_f(const gsl_vector *v, v
 #endif  #endif
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,  double p[],double **matcov,double agemortsup){                    int imx,  double p[],double **matcov,double agemortsup){
   int i,k;    int i,k;
Line 5343  void printinghtmlmort(char fileres[], ch Line 7446  void printinghtmlmort(char fileres[], ch
   fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);    fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
   for (i=1;i<=2;i++)     for (i=1;i<=2;i++) 
     fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));      fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");    fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
   fprintf(fichtm,"</ul>");    fprintf(fichtm,"</ul>");
   
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");  fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
Line 5358  fprintf(fichtm,"<ul><li><h4>Life table</ Line 7461  fprintf(fichtm,"<ul><li><h4>Life table</
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   
Line 5372  void printinggnuplotmort(char fileres[], Line 7475  void printinggnuplotmort(char fileres[],
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   fprintf(ficgp,"set out \"graphmort.png\"\n ");     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
   fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
   fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");     fprintf(ficgp, "set ter svg size 640, 480\n set log y\n"); 
   /* fprintf(ficgp, "set size 0.65,0.65\n"); */    /* fprintf(ficgp, "set size 0.65,0.65\n"); */
   fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);    fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
Line 5386  int readdata(char datafile[], int firsto Line 7489  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0;    int i=0, j=0, n=0, iv=0;
     int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;  
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s\n", datafile);return 1;      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;    i=1;
Line 5418  int readdata(char datafile[], int firsto Line 7522  int readdata(char datafile[], int firsto
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     strcpy(line, linetmp);      strcpy(line, linetmp);
         
       /* Loops on waves */
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             lval=-1;
             cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
             if(isalpha(strb[1])) { /* .m or .d Really Missing value */
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
               return 1;
             }
           }else{
             errno=0;
             /* what_kind_of_number(strb); */
             dval=strtod(strb,&endptr); 
             /* if( strb[0]=='\0' || (*endptr != '\0')){ */
             /* if(strb != endptr && *endptr == '\0') */
             /*    dval=dlval; */
             /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
             if( strb[0]=='\0' || (*endptr != '\0')){
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
               return 1;
             }
             cotqvar[j][iv][i]=dval; 
           }
           strcpy(line,stra);
         }/* end loop ntqv */
         
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
           cutv(stra, strb, line, ' '); 
           if(strb[0]=='.') { /* Missing value */
             lval=-1;
           }else{
             errno=0;
             lval=strtol(strb,&endptr,10); 
             /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
             if( strb[0]=='\0' || (*endptr != '\0')){
               printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
               fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
               return 1;
             }
           }
           if(lval <-1 || lval >1){
             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 \
    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                 \
    build V1=0 V2=0 for the reference value (1),\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 \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);
             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 \
    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                 \
    build V1=0 V2=0 for the reference value (1),\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 \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
             return 1;
           }
           cotvar[j][iv][i]=(double)(lval);
           strcpy(line,stra);
         }/* end loop ntv */
         
         /* Statuses  at wave */
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing value */
         lval=-1;          lval=-1;
       }else{        }else{
         errno=0;          errno=0;
         lval=strtol(strb,&endptr,10);           lval=strtol(strb,&endptr,10); 
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/          /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){          if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
           return 1;            return 1;
         }          }
       }        }
         
       s[j][i]=lval;        s[j][i]=lval;
               
         /* Date of Interview */
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
Line 5451  int readdata(char datafile[], int firsto Line 7625  int readdata(char datafile[], int firsto
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month; 
       strcpy(line,stra);        strcpy(line,stra);
     } /* ENd Waves */      } /* End loop on waves */
           
       /* Date of death */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 5461  int readdata(char datafile[], int firsto Line 7636  int readdata(char datafile[], int firsto
       year=9999;        year=9999;
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;        return 1;
     }      }
     andc[i]=(double) year;       andc[i]=(double) year; 
     moisdc[i]=(double) month;       moisdc[i]=(double) month; 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Date of birth */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 5477  int readdata(char datafile[], int firsto Line 7653  int readdata(char datafile[], int firsto
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;        return 1;
     }      }
     if (year==9999) {      if (year==9999) {
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;        return 1;
         
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Sample weight */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     dval=strtod(strb,&endptr);       dval=strtod(strb,&endptr); 
Line 5501  int readdata(char datafile[], int firsto Line 7678  int readdata(char datafile[], int firsto
     weight[i]=dval;       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
           
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
           lval=-1;
         }else{
           errno=0;
           /* what_kind_of_number(strb); */
           dval=strtod(strb,&endptr);
           /* if(strb != endptr && *endptr == '\0') */
           /*   dval=dlval; */
           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
             return 1;
           }
           coqvar[iv][i]=dval; 
           covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
         }
         strcpy(line,stra);
       }/* end loop nqv */
       
       /* Covariate values */
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing covariate value */
         lval=-1;          lval=-1;
       }else{        }else{
         errno=0;          errno=0;
Line 5518  int readdata(char datafile[], int firsto Line 7718  int readdata(char datafile[], int firsto
         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 (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,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 (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,j);fflush(ficlog);
         return 1;          return 1;
       }        }
Line 5539  int readdata(char datafile[], int firsto Line 7739  int readdata(char datafile[], int firsto
       strcpy(line,stra);        strcpy(line,stra);
     }        }  
     lstra=strlen(stra);      lstra=strlen(stra);
            
     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
       stratrunc = &(stra[lstra-9]);        stratrunc = &(stra[lstra-9]);
       num[i]=atol(stratrunc);        num[i]=atol(stratrunc);
Line 5551  int readdata(char datafile[], int firsto Line 7751  int readdata(char datafile[], int firsto
           
     i=i+1;      i=i+1;
   } /* End loop reading  data */    } /* End loop reading  data */
     
   *imax=i-1; /* Number of individuals */    *imax=i-1; /* Number of individuals */
   fclose(fic);    fclose(fic);
      
   return (0);    return (0);
   /* endread: */    /* endread: */
     printf("Exiting readdata: ");    printf("Exiting readdata: ");
     fclose(fic);    fclose(fic);
     return (1);    return (1);
   
   
   
 }  }
   
 void removespace(char *str) {  void removespace(char *str) {
   char *p1 = str, *p2 = str;    char *p1 = str, *p2 = str;
   do    do
Line 5572  void removespace(char *str) { Line 7770  void removespace(char *str) {
   while (*p1++ == *p2++);    while (*p1++ == *p2++);
 }  }
   
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:  int decodemodel ( char model[], int lastobs)
    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age   /**< This routine decode the model and returns:
    * - nagesqr = 1 if age*age in the model, otherwise 0.          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age          * - nagesqr = 1 if age*age in the model, otherwise 0.
    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
    * - cptcovage number of covariates with age*products =2          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
    * - cptcovs number of simple covariates          * - cptcovage number of covariates with age*products =2
    * - 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          * - cptcovs number of simple covariates
    *     which is a new column after the 9 (ncovcol) variables.           * - 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
    * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual          *     which is a new column after the 9 (ncovcol) variables. 
    * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage          * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
    *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
    * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          *    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 .
           */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int  j1, k1, k2;    int  j1, k1, k2, k3, k4;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   char *strpt;    char *strpt;
Line 5597  int decodemodel ( char model[], int last Line 7796  int decodemodel ( char model[], int last
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
     if (strstr(model,"AGE") !=0){      if (strstr(model,"AGE") !=0){
       printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
Line 5610  int decodemodel ( char model[], int last Line 7809  int decodemodel ( char model[], int last
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
       return 1;          return 1;
     }        }
   
       nagesqr=1;        nagesqr=1;
       if (strstr(model,"+age*age") !=0)        if (strstr(model,"+age*age") !=0)
         substrchaine(modelsav, model, "+age*age");          substrchaine(modelsav, model, "+age*age");
Line 5631  int decodemodel ( char model[], int last Line 7829  int decodemodel ( char model[], int last
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){
       j=nbocc(modelsav,'+'); /**< j=Number of '+' */        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */        cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
       cptcovt= j+1; /* Number of total covariates in the model, not including        cptcovt= j+1; /* Number of total covariates in the model, not including
                    * cst, age and age*age                        * cst, age and age*age 
                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
                   /* including age products which are counted in cptcovage.        /* including age products which are counted in cptcovage.
                   * but the covariates which are products must be treated          * but the covariates which are products must be treated 
                   * separately: ncovn=4- 2=2 (V1+V3). */         * separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
         
             
       /*   Design        /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >         *  <          ncovcol=8                >
Line 5649  int decodemodel ( char model[], int last Line 7847  int decodemodel ( char model[], int last
        *   k=  1    2      3       4     5       6      7        8         *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:         *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k         *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1         *       if products, new covar are created after ncovcol with k1
Line 5675  int decodemodel ( char model[], int last Line 7873  int decodemodel ( char model[], int last
        *       {2,   1,     4,      8,    5,      6,     3,       7}         *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []         * Struct []
        */         */
         
       /* This loop fills the array Tvar from the string 'model'.*/        /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */        /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */        /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
Line 5685  int decodemodel ( char model[], int last Line 7883  int decodemodel ( char model[], int last
       /*        k=1 Tvar[1]=2 (from V2) */        /*        k=1 Tvar[1]=2 (from V2) */
       /*        k=5 Tvar[5] */        /*        k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */        /* for (k=1; k<=cptcovn;k++) { */
       /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */        /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       /*        } */        /*        } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
       /*        /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */         * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */        for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
         Tvar[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
         }
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
Line 5706  int decodemodel ( char model[], int last Line 7905  int decodemodel ( char model[], int last
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */              cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */              Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
               Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
Line 5713  int decodemodel ( char model[], int last Line 7913  int decodemodel ( char model[], int last
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strc,'V');              cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);              Tvar[k]=atoi(stre);
               Typevar[k]=1;  /* 1 for age product */
             cptcovage++;              cptcovage++;
             Tage[cptcovage]=k;              Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/            } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
Line 5720  int decodemodel ( char model[], int last Line 7921  int decodemodel ( char model[], int last
             cptcovn++;              cptcovn++;
             cptcovprodnoage++;k1++;              cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+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
                                    ncovcol + k1                                     which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
               Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;              k2=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) *\/ */
               /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
               /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
             for (i=1; i<=lastobs;i++){              for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of                /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
Line 5743  int decodemodel ( char model[], int last Line 7948  int decodemodel ( char model[], int last
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */            ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
           cptcovn++;            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
           Tvar[k]=atoi(strd);            Tvar[k]=atoi(strd);
             Typevar[k]=0;  /* 0 for simple covariates */
         }          }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/                                    scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* end if strlen(model == 0) */
       
   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
     
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);       printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);       fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
        scanf("%d ",i);*/
   scanf("%d ",i);*/  
   
   /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
      of variable (dummy vs quantitative, fixed vs time varying) is behind */
   /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
      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
      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
      Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
      Dummy[k]      1    0   0     0       3       1      1      2        3
             Tmodelind[combination of covar]=k;
   */  
   /* Dispatching between quantitative and time varying covariates */
     /* 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 */
           /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
     printf("Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     fprintf(ficlog,"Model=%s\n\
   Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
   Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   
     for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
       if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
         Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;  /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
         Fixed[k]= 1;
         Dummy[k]= 0;
         ntveff++; /* Only simple time varying dummy variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
           Fixed[k]= 1;
           Dummy[k]= 1;
           nqtveff++;/* Only simple time varying quantitative variable */
       }else if (Typevar[k] == 1) {  /* product with age */
         if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
           Fixed[k]= 2;
           Dummy[k]= 2;
           /* ncoveff++; */
         }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
           Fixed[k]= 2;
           Dummy[k]= 3;
           /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           Fixed[k]= 3;
           Dummy[k]= 2;
           /* ntveff++; /\* Only simple time varying dummy variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 3;
           Dummy[k]= 3;
           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }
       }else if (Typevar[k] == 2) {  /* product without age */
         k1=Tposprod[k];
         if(Tvard[k1][1] <=ncovcol){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0; /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else{
           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         } /* end k1 */
       }else{
         printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
         fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       }
       printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
     }
     /* Searching for doublons in the model */
     for(k1=1; k1<= cptcovt;k1++){
       for(k2=1; k2 <k1;k2++){
         if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
           if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
             if(Tvar[k1]==Tvar[k2]){
               printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }else if (Typevar[k1] ==2){
             k3=Tposprod[k1];
             k4=Tposprod[k2];
             if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
               printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
               fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
               return(1);
             }
           }
         }
       }
     }
     printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
     printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
     return (1);    return (1);
 }  }
   
 int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {
   int i, m;    int i, m;
     int firstone=0;
     
   for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
     for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
         anint[m][i]=9999;          anint[m][i]=9999;
         s[m][i]=-1;          if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
             s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         *nberr = *nberr + 1;          *nberr = *nberr + 1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);          if(firstone == 0){
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);            firstone=1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
           }
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
Line 5798  int calandcheckages(int imx, int maxwav, Line 8160  int calandcheckages(int imx, int maxwav,
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){        if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0){            if(agedc[i]>0){
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){              if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             }else {              }else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 nbwarn++;                  nbwarn++;
Line 5813  int calandcheckages(int imx, int maxwav, Line 8175  int calandcheckages(int imx, int maxwav,
               }                }
             }              }
           } /* agedc > 0 */            } /* agedc > 0 */
         }          } /* end if */
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a month */                                   years but with the precision of a month */
           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
Line 5829  int calandcheckages(int imx, int maxwav, Line 8191  int calandcheckages(int imx, int maxwav,
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
         }          } /* en if 9*/
         else { /* =9 */          else { /* =9 */
             /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
           agev[m][i]=1;            agev[m][i]=1;
           s[m][i]=-1;            s[m][i]=-1;
         }          }
       }        }
       else /*= 0 Unknown */        else if(s[m][i]==0) /*= 0 Unknown */
         agev[m][i]=1;          agev[m][i]=1;
     }        else{
               printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           agev[m][i]=0;
         }
       } /* End for lastpass */
   }    }
       
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
Line 6063  void syscompilerinfo(int logged) Line 8431  void syscompilerinfo(int logged)
 #endif  #endif
         
   
  }  }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    int i, j, k, i1 ;
   double ftolpl = 1.e-10;    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
     double tot;
   
     strcpy(filerespl,"pl");    strcpy(filerespl,"PL_");
     strcat(filerespl,fileres);    strcat(filerespl,fileresu);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     }    }
     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     pstamp(ficrespl);    pstamp(ficrespl);
     fprintf(ficrespl,"# Period (stable) prevalence \n");    fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");    fprintf(ficrespl,"\n");
       
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */    /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
     agebase=ageminpar;    agebase=ageminpar;
     agelim=agemaxpar;    agelim=agemaxpar;
   
     i1=pow(2,cptcoveff);    /* i1=pow(2,ncoveff); */
     if (cptcovn < 1){i1=1;}    i1=pow(2,cptcoveff); /* Number of dummy covariates */
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){    for(k=1; k<=i1;k++){
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */      /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;      /* k=k+1; */
         /* to clean */      /* to clean */
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);      //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"\n#******");      fprintf(ficrespl,"#******");
         printf("\n#******");      printf("#******");
         fprintf(ficlog,"\n#******");      fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff ;j++) {/* all covariates */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }      }
         fprintf(ficrespl,"******\n");      fprintf(ficrespl,"******\n");
         printf("******\n");      printf("******\n");
         fprintf(ficlog,"******\n");      fprintf(ficlog,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespl,"#Age ");        printf("\nCombination (%d) ignored because no case \n",k); 
         for(j=1;j<=cptcoveff;j++) {        fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
         }                                                  continue;
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      }
         fprintf(ficrespl,"\n");  
               fprintf(ficrespl,"#Age ");
         for (age=agebase; age<=agelim; age++){      for(j=1;j<=cptcoveff;j++) {
         /* for (age=agebase; age<=agebase; age++){ */        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
           fprintf(ficrespl,"%.0f ",age );      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
           for(j=1;j<=cptcoveff;j++)      fprintf(ficrespl,"Total Years_to_converge\n");
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
           for(i=1; i<=nlstate;i++)      for (age=agebase; age<=agelim; age++){
             fprintf(ficrespl," %.5f", prlim[i][i]);        /* for (age=agebase; age<=agebase; age++){ */
           fprintf(ficrespl,"\n");        prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
         } /* Age */        fprintf(ficrespl,"%.0f ",age );
         /* was end of cptcod */        for(j=1;j<=cptcoveff;j++)
     } /* cptcov */          fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         return 0;        tot=0.;
         for(i=1; i<=nlstate;i++){
           tot +=  prlim[i][i];
           fprintf(ficrespl," %.5f", prlim[i][i]);
         }
         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
       } /* Age */
       /* was end of cptcod */
     } /* cptcov */
     return 0;
 }  }
   
   int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
           /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
           
           /* Computes the back prevalence limit  for any combination      of covariate values 
      * at any age between ageminpar and agemaxpar
            */
     int i, j, k, i1 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
     /* double ***mobaverage; */
     /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
   
     strcpy(fileresplb,"PLB_");
     strcat(fileresplb,fileresu);
     if((ficresplb=fopen(fileresplb,"w"))==NULL) {
       printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
       fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
     }
     printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
     pstamp(ficresplb);
     fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficresplb,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
     fprintf(ficresplb,"\n");
     
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
     
     agebase=ageminpar;
     agelim=agemaxpar;
     
     
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     for(k=1; k<=i1;k++){ 
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       fprintf(ficresplb,"#******");
       printf("#******");
       fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficresplb,"******\n");
       printf("******\n");
       fprintf(ficlog,"******\n");
       if(invalidvarcomb[k]){
         printf("\nCombination (%d) ignored because no cases \n",k); 
         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       fprintf(ficresplb,"#Age ");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
       fprintf(ficresplb,"Total Years_to_converge\n");
       
       
       for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */
         if(mobilavproj > 0){
           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
         }else if (mobilavproj == 0){
           printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
           fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
           exit(1);
         }else{
           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
         }
         fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)
           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         tot=0.;
         for(i=1; i<=nlstate;i++){
           tot +=  bprlim[i][i];
           fprintf(ficresplb," %.5f", bprlim[i][i]);
         }
         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
       } /* Age */
       /* was end of cptcod */
     } /* cptcov */
     
     /* hBijx(p, bage, fage); */
     /* fclose(ficrespijb); */
     
     return 0;
   }
    
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
   
Line 6145  int hPijx(double *p, int bage, int fage) Line 8623  int hPijx(double *p, int bage, int fage)
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
   
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);      strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {      if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;        printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;        fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
Line 6159  int hPijx(double *p, int bage, int fage) Line 8637  int hPijx(double *p, int bage, int fage)
     agelim=AGESUP;      agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */      hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);      i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*   k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
       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]][codtab[k][j]]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 6200  int hPijx(double *p, int bage, int fage) Line 8678  int hPijx(double *p, int bage, int fage)
       }        }
       /*}*/        /*}*/
     }      }
         return 0;      return 0;
 }  }
    
    int hBijx(double *p, int bage, int fage, double ***prevacurrent){
       /*------------- h Bij x at various ages ------------*/
   
     int stepsize;
     /* int agelim; */
           int ageminl;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
           
     double agedeb;
     double ***p3mat;
           
     strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
     if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
       printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
       fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
     }
     printf("Computing pij back: result on file '%s' \n", filerespijb);
     fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
     
     /* agelim=AGESUP; */
     ageminl=30;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
     
     /* hstepm=1;   aff par mois*/
     pstamp(ficrespijb);
     fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
     i1= pow(2,cptcoveff);
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
     /*    k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
         
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
           fprintf(ficrespijb,"\n");
         }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       }
       /*}*/
     }
     return 0;
    } /*  hBijx */
   
   
 /***********************************************/  /***********************************************/
Line 6219  int main(int argc, char *argv[]) Line 8778  int main(int argc, char *argv[])
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
     int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
Line 6231  int main(int argc, char *argv[]) Line 8791  int main(int argc, char *argv[])
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb=0.;    double agedeb=0.;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
   double fret;    double fret;
   double dum=0.; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int c,  h , cpt;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
     int count=0;
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 6258  int main(int argc, char *argv[]) Line 8825  int main(int argc, char *argv[])
   double bage=0, fage=110., age, agelim=0., agebase=0.;    double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
     double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double  *p;
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
Line 6268  int main(int argc, char *argv[]) Line 8837  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
Line 6317  int main(int argc, char *argv[]) Line 8888  int main(int argc, char *argv[])
   getcwd(pathcd, size);    getcwd(pathcd, size);
 #endif  #endif
   syscompilerinfo(0);    syscompilerinfo(0);
   printf("\n%s\n%s",version,fullversion);    printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     fgets(pathr,FILENAMELENGTH,stdin);      if(!fgets(pathr,FILENAMELENGTH,stdin)){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]=='\n')      if(pathr[i-1]=='\n')
       pathr[i-1]='\0';        pathr[i-1]='\0';
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */      if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
       pathr[i-1]='\0';        pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){      }
       i=strlen(pathr);
       if( i==0 ){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);        printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
       printf("val= |%s| pathr=%s\n",val,pathr);        printf("val= |%s| pathr=%s\n",val,pathr);
Line 6381  int main(int argc, char *argv[]) Line 8961  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);    fprintf(ficlog,"Version %s %s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: \n");    fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\   path=%s \n\
Line 6389  int main(int argc, char *argv[]) Line 8969  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   syscompilerinfo(0);    syscompilerinfo(1);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
Line 6400  int main(int argc, char *argv[]) Line 8980  int main(int argc, char *argv[])
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
   /* Main ---------arguments file --------*/    /* Main ---------arguments file --------*/
   
Line 6415  int main(int argc, char *argv[]) Line 8997  int main(int argc, char *argv[])
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
Line 6425  int main(int argc, char *argv[]) Line 9007  int main(int argc, char *argv[])
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* First parameter line */
     fgets(line, MAXLINE, ficpar);    while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
     numlinepar++;      numlinepar++;
     fputs(line,stdout);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     fputs(line,ficparo);  
     fputs(line,ficlog);  
   }    }
   ungetc(c,ficpar);    /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      /* If line starts with a # it is a comment */
   numlinepar++;      if (line[0] == '#') {
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);        numlinepar++;
   if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */        fputs(line,stdout);
     model[strlen(model)-1]='\0';        fputs(line,ficparo);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        fputs(line,ficlog);
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 11) {
         printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
       }
       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
     }
     /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
     /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
     /* Third parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
       if (num_filled == 0)
               model[0]='\0';
       else if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
           strcpy(model,modeltemp); 
         }
       }
       /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
       printf("model=1+age+%s\n",model);fflush(stdout);
     }
     /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
Line 6457  int main(int argc, char *argv[]) Line 9101  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     numlinepar++;      numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);      fputs(line, stdout);
     //puts(line);      //puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
Line 6466  int main(int argc, char *argv[]) Line 9114  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
     cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */
     cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
Line 6495  int main(int argc, char *argv[]) Line 9146  int main(int argc, char *argv[])
     fclose (ficlog);      fclose (ficlog);
     goto end;      goto end;
     exit(0);      exit(0);
   }    }  else if(mle==-5) { /* Main Wizard */
   else if(mle==-3) { /* Main Wizard */  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   }      hess=matrix(1,npar,1,npar);
   else{    }  else{ /* Begin of mle != -1 or -5 */
     /* Read guessed parameters */      /* Read guessed parameters */
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 6517  int main(int argc, char *argv[]) Line 9167  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       j=0;                          j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;                                  if(jj==i) continue;
         j++;                                  j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);                                  fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){                                  if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \                                          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 It might be a problem of design; if ncovcol and the model are correct\n \  It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
           exit(1);                                          exit(1);
         }                                  }
         fprintf(ficparo,"%1d%1d",i1,j1);                                  fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)                                  if(mle==1)
           printf("%1d%1d",i,j);                                          printf("%1d%1d",i,jj);
         fprintf(ficlog,"%1d%1d",i,j);                                  fprintf(ficlog,"%1d%1d",i,jj);
         for(k=1; k<=ncovmodel;k++){                                  for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);                                          fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){                                          if(mle==1){
             printf(" %lf",param[i][j][k]);                                                  printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);                                                  fprintf(ficlog," %lf",param[i][j][k]);
           }                                          }
           else                                          else
             fprintf(ficlog," %lf",param[i][j][k]);                                                  fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);                                          fprintf(ficparo," %lf",param[i][j][k]);
         }                                  }
         fscanf(ficpar,"\n");                                  fscanf(ficpar,"\n");
         numlinepar++;                                  numlinepar++;
         if(mle==1)                                  if(mle==1)
           printf("\n");                                          printf("\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");                                  fprintf(ficparo,"\n");
       }        }
     }        }  
     fflush(ficlog);      fflush(ficlog);
Line 6569  run imach with mle=-1 to get a correct t Line 9219  run imach with mle=-1 to get a correct t
   
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);                                  fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ( (i1-i) * (j1-j) != 0){                                  if ( (i1-i) * (j1-j) != 0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);                                          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);                                          exit(1);
         }                                  }
         printf("%1d%1d",i,j);                                  printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);                                  fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);                                  fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){                                  for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);                                          fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);                                          printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);                                          fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);                                          fprintf(ficlog," %le",delti3[i][j][k]);
         }                                  }
         fscanf(ficpar,"\n");                                  fscanf(ficpar,"\n");
         numlinepar++;                                  numlinepar++;
         printf("\n");                                  printf("\n");
         fprintf(ficparo,"\n");                                  fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");                                  fprintf(ficlog,"\n");
       }        }
     }      }
     fflush(ficlog);      fflush(ficlog);
                   
     /* Reads covariance matrix */      /* Reads covariance matrix */
     delti=delti3[1][1];      delti=delti3[1][1];
                   
                   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
                     
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
Line 6608  run imach with mle=-1 to get a correct t Line 9258  run imach with mle=-1 to get a correct t
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
                     
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;        for(j=1; j <=npar; j++) matcov[i][j]=0.;
                         
       /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",str);        count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
       if(mle==1)        if(count != 3){
         printf("%s",str);          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
       fprintf(ficlog,"%s",str);  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
       fprintf(ficparo,"%s",str);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
           exit(1);
         }else{
           if(mle==1)
             printf("%1d%1d%d",i1,j1,jk);
         }
         fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
         fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){          if(mle==1){
Line 6630  run imach with mle=-1 to get a correct t Line 9292  run imach with mle=-1 to get a correct t
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
       numlinepar++;        numlinepar++;
       if(mle==1)        if(mle==1)
         printf("\n");                                  printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");        fprintf(ficparo,"\n");
     }      }
       /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
Line 6650  run imach with mle=-1 to get a correct t Line 9313  run imach with mle=-1 to get a correct t
     strcat(rfileres,".");    /* */      strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */      strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {      if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
     
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    n= lastobs;
Line 6664  run imach with mle=-1 to get a correct t Line 9327  run imach with mle=-1 to get a correct t
   annais=vector(1,n);    annais=vector(1,n);
   moisdc=vector(1,n);    moisdc=vector(1,n);
   andc=vector(1,n);    andc=vector(1,n);
     weight=vector(1,n);
   agedc=vector(1,n);    agedc=vector(1,n);
   cod=ivector(1,n);    cod=ivector(1,n);
   weight=vector(1,n);    for(i=1;i<=n;i++){
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                  num[i]=0;
                   moisnais[i]=0;
                   annais[i]=0;
                   moisdc[i]=0;
                   andc[i]=0;
                   agedc[i]=0;
                   cod[i]=0;
                   weight[i]=1.0; /* Equal weights, 1 by default */
           }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
   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 */
   
   /* Reads data from file datafile */    /* Reads data from file datafile */
   if (readdata(datafile, firstobs, lastobs, &imx)==1)    if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 6686  run imach with mle=-1 to get a correct t Line 9359  run imach with mle=-1 to get a correct t
         k=1 Tvar[1]=2 (from V2)          k=1 Tvar[1]=2 (from V2)
     */      */
   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 6695  run imach with mle=-1 to get a correct t Line 9371  run imach with mle=-1 to get a correct t
     ncovcol + k1      ncovcol + k1
     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
     Tvar[3=V1*V4]=4+1 etc */      Tvar[3=V1*V4]=4+1 etc */
   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */    Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
     Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
      if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)       if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
        Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
   */    */
   Tvaraff=ivector(1,NCOVMAX); /* Unclear */    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
Line 6707  run imach with mle=-1 to get a correct t Line 9385  run imach with mle=-1 to get a correct t
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
     Tmodelind=ivector(1,NCOVMAX);/** five the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 /* Main decodemodel */  /* Main decodemodel */
   
   
   if(decodemodel(model, lastobs) == 1)    if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
     goto end;      goto end;
   
   if((double)(lastobs-imx)/(double)imx > 1.10){    if((double)(lastobs-imx)/(double)imx > 1.10){
Line 6736  run imach with mle=-1 to get a correct t Line 9418  run imach with mle=-1 to get a correct t
   free_vector(annais,1,n);    free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   free_vector(moisdc,1,n);    /* free_vector(moisdc,1,n); */
   free_vector(andc,1,n);    /* free_vector(andc,1,n); */
   /* */    /* */
       
   wav=ivector(1,imx);    wav=ivector(1,imx);
   dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
   bh=imatrix(1,lastpass-firstpass+1,1,imx);    /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
   mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
     dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
     bh=imatrix(1,lastpass-firstpass+2,1,imx);
     mw=imatrix(1,lastpass-firstpass+2,1,imx);
         
   /* Concatenates waves */    /* Concatenates waves */
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     */
   
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* */    /* */
     
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */    cptcoveff=0;
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
   /* Nbcode gives the value of the lth modality of jth covariate, in      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     }
     
     ncovcombmax=pow(2,cptcoveff);
     invalidvarcomb=ivector(1, ncovcombmax); 
     for(i=1;i<ncovcombmax;i++)
       invalidvarcomb[i]=0;
     
     /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
     
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
      * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
      * (currently 0 or 1) in the data.
      * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
      * corresponding modality (h,j).
      */
   
     h=0;
   /*if (cptcovn > 0) */    /*if (cptcovn > 0) */
         
    
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */  
     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */   
       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/  
         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */   
           h++;  
           if (h>m)   
             h=1;  
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
            * For k=4 covariates, h goes from 1 to 2**k             * For k=4 covariates, h goes from 1 to m=2**k
            * codtabm(h,k)=  1 & (h-1) >> (k-1) ;             * 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
            *______________________________               *______________________________  
            *     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
Line 6791  run imach with mle=-1 to get a correct t Line 9490  run imach with mle=-1 to get a correct t
            *     6     2     1     2     1             *     6     2     1     2     1
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1
            *     8     2     2     2     1             *     8     2     2     2     1
            *     9 i=5 1 i=3 1 i=2 1     1             *     9 i=5 1 i=3 1 i=2 1     2
            *    10     2     1     1     1             *    10     2     1     1     2
            *    11 i=6 1     2     1     1             *    11 i=6 1     2     1     2
            *    12     2     2     1     1             *    12     2     2     1     2
            *    13 i=7 1 i=4 1     2     1                 *    13 i=7 1 i=4 1     2     2    
            *    14     2     1     2     1             *    14     2     1     2     2
            *    15 i=8 1     2     2     1             *    15 i=8 1     2     2     2
            *    16     2     2     2     1             *    16     2     2     2     2
            */             */
           codtab[h][k]=j;    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
           /* codtab[12][3]=1; */       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
           /*codtab[h][Tvar[k]]=j;*/       * and the value of each covariate?
           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);       * V1=1, V2=1, V3=2, V4=1 ?
         }        * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
       }       * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
     }       * In order to get the real value in the data, we use nbcode
   }        * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        * We are keeping this crazy system in order to be able (in the future?) 
      codtab[1][2]=1;codtab[2][2]=2; */       * to have more than 2 values (0 or 1) for a covariate.
   /* for(i=1; i <=m ;i++){        * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
      for(k=1; k <=cptcovn; k++){       * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);       *              bbbbbbbb
      }       *              76543210     
      printf("\n");       *   h-1        00000101 (6-1=5)
      }       *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
      scanf("%d",i);*/       *           &
        *     1        00000001 (1)
        *              00000000        = 1 & ((h-1) >> (k-1))
        *          +1= 00000001 =1 
        *
        * h=14, k=3 => h'=h-1=13, k'=k-1=2
        *          h'      1101 =2^3+2^2+0x2^1+2^0
        *    >>k'            11
        *          &   00000001
        *            = 00000001
        *      +1    = 00000010=2    =  codtabm(14,3)   
        * Reverse h=6 and m=16?
        * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
        * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
        * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
        * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
        * V3=decodtabm(14,3,2**4)=2
        *          h'=13   1101 =2^3+2^2+0x2^1+2^0
        *(h-1) >> (j-1)    0011 =13 >> 2
        *          &1 000000001
        *           = 000000001
        *         +1= 000000010 =2
        *                  2211
        *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
        *                  V3=2
                    * codtabm and decodtabm are identical
        */
   
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
Line 6825  run imach with mle=-1 to get a correct t Line 9551  run imach with mle=-1 to get a correct t
   /* Initialisation of ----------- gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-MORT_");
   strcat(optionfilegnuplot,".gp");    strcat(optionfilegnuplot,".gp");
   
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
   else{    else{
     fprintf(ficgp,"\n# %s\n", version);       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
     fprintf(ficgp,"# %s\n", optionfilegnuplot);       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
     //fprintf(ficgp,"set missing 'NaNq'\n");      //fprintf(ficgp,"set missing 'NaNq'\n");
     fprintf(ficgp,"set datafile missing 'NaNq'\n");      fprintf(ficgp,"set datafile missing 'NaNq'\n");
Line 6844  run imach with mle=-1 to get a correct t Line 9570  run imach with mle=-1 to get a correct t
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
     strcat(optionfilehtm,"-mort");      strcat(optionfilehtm,"-MORT_");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm);      printf("Problem with %s \n",optionfilehtm);
Line 6859  run imach with mle=-1 to get a correct t Line 9585  run imach with mle=-1 to get a correct t
   else{    else{
   fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %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=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
           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<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \    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\
   <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
Line 6889  Title=%s <br>Datafile=%s Firstpass=%d La Line 9617  Title=%s <br>Datafile=%s Firstpass=%d La
 #endif  #endif
                       
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                 firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 6899  Youngest age at first (selected) pass %. Line 9629  Youngest age at first (selected) pass %.
 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);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* For Powell, parameters are in a vector p[] starting at p[1]
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
Line 6913  Interval (in months) between two waves: Line 9642  Interval (in months) between two waves:
   /* For mortality only */    /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
                   for(i=1;i<=NDIM;i++)
                           for(j=1;j<=NDIM;j++)
                                   ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
     dcwave=ivector(1,n);      dcwave=ivector(1,n);
                    
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
Line 6928  Interval (in months) between two waves: Line 9660  Interval (in months) between two waves:
           break;            break;
         }          }
     }      }
       
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       if (wav[i]>0){        if (wav[i]>0){
         ageexmed[i]=agev[mw[1][i]][i];          ageexmed[i]=agev[mw[1][i]][i];
         j=wav[i];          j=wav[i];
         agecens[i]=1.;           agecens[i]=1.; 
           
         if (ageexmed[i]> 1 && wav[i] > 0){          if (ageexmed[i]> 1 && wav[i] > 0){
           agecens[i]=agev[mw[j][i]][i];            agecens[i]=agev[mw[j][i]][i];
           cens[i]= 1;            cens[i]= 1;
Line 6960  Interval (in months) between two waves: Line 9692  Interval (in months) between two waves:
 #else  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif  #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"POW-MORT_"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileresu);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
Line 7057  Interval (in months) between two waves: Line 9789  Interval (in months) between two waves:
 #endif    #endif  
     fclose(ficrespow);      fclose(ficrespow);
           
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
     for(i=1; i <=NDIM; i++)      for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)        for(j=i+1;j<=NDIM;j++)
         matcov[i][j]=matcov[j][i];                                  matcov[i][j]=matcov[j][i];
           
     printf("\nCovariance matrix\n ");      printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
     for(i=1; i <=NDIM; i++) {      for(i=1; i <=NDIM; i++) {
       for(j=1;j<=NDIM;j++){         for(j=1;j<=NDIM;j++){ 
         printf("%f ",matcov[i][j]);                                  printf("%f ",matcov[i][j]);
                                   fprintf(ficlog,"%f ",matcov[i][j]);
       }        }
       printf("\n ");        printf("\n ");  fprintf(ficlog,"\n ");
     }      }
           
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);      printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
     for (i=1;i<=NDIM;i++)       for (i=1;i<=NDIM;i++) {
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
         fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       }
     lsurv=vector(1,AGESUP);      lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);      lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);      tpop=vector(1,AGESUP);
Line 7106  Interval (in months) between two waves: Line 9841  Interval (in months) between two waves:
           
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);                  ageminpar=50;
                       agemaxpar=100;
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \      if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
           printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
           fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
   This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
   Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
       }else{
                           printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                           fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
         printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
       printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
           
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,AGESUP);
 #ifdef GSL      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(cens,1,n);
     free_vector(agecens,1,n);      free_vector(agecens,1,n);
     free_ivector(dcwave,1,n);      free_ivector(dcwave,1,n);
     free_matrix(ximort,1,NDIM,1,NDIM);  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
   /* Standard maximisation */    /* Standard  */
   else{ /* For mle >=1 */    else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
     globpr=0;/* debug */      globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
     /* Computes likelihood for initial parameters */      /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     globpr=1; /* again, to print the contributions */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
         /* mlikeli uses func not funcone */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
         globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
         /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
         likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       }
       globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximisation */  
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 7166  Interval (in months) between two waves: Line 9919  Interval (in months) between two waves:
         }          }
       }        }
     }      }
     if(mle!=0){      if(mle != 0){
       /* Computing hessian and covariance matrix */        /* 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, 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");
         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");
         for(i=1,jk=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {
               printf("%d%d ",i,k);
               fprintf(ficlog,"%d%d ",i,k);
               for(j=1; j <=ncovmodel; j++){
                 printf("%12.7f 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]));
                 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]));
                 jk++; 
               }
               printf("\n");
               fprintf(ficlog,"\n");
             }
           }
         }
       } /* end of hesscov and Wald tests */
       
       /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
Line 7194  Interval (in months) between two waves: Line 9966  Interval (in months) between two waves:
     }      }
           
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)      if(mle >= 1) /* To big for the screen */
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     /* # 121 Var(a12)\n\ */      /* # 121 Var(a12)\n\ */
Line 7257  Interval (in months) between two waves: Line 10029  Interval (in months) between two waves:
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);                          fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{                        }else{
                         if(mle>=1)                          if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]);                             printf(" %.7e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]);                           fprintf(ficlog," %.7e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]);                           fprintf(ficres," %.7e",matcov[jj][ll]); 
                       }                        }
                     }                      }
                   }                    }
Line 7278  Interval (in months) between two waves: Line 10050  Interval (in months) between two waves:
           
     fflush(ficlog);      fflush(ficlog);
     fflush(ficres);      fflush(ficres);
           while(fgets(line, MAXLINE, ficpar)) {
     while((c=getc(ficpar))=='#' && c!= EOF){        /* If line starts with a # it is a comment */
       ungetc(c,ficpar);        if (line[0] == '#') {
       fgets(line, MAXLINE, ficpar);          numlinepar++;
       fputs(line,stdout);          fputs(line,stdout);
       fputs(line,ficparo);          fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);      
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
           
     estepm=0;      estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
         
         if (num_filled != 6) {
           printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
           goto end;
         }
         printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
       }
       /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
       /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
       
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
     if (estepm==0 || estepm < stepm) estepm=stepm;      if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {      if (fage <= 2) {
       bage = ageminpar;        bage = ageminpar;
Line 7296  Interval (in months) between two waves: Line 10091  Interval (in months) between two waves:
     }      }
           
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   
     /* Other stuffs, more or less useful */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
Line 7327  Interval (in months) between two waves: Line 10122  Interval (in months) between two waves:
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);         fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);         fprintf(ficres,"pop_based=%d\n",popbased);   
           
Line 7345  Interval (in months) between two waves: Line 10141  Interval (in months) between two waves:
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);      fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
       fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
           
           
      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */                  /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
                               printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                          fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
         This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
    /*------------ free_vector  -------------*/  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
    /*  chdir(path); */      }else{
          printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
     free_ivector(wav,1,imx);      }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);                   model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                      jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
                   
       /*------------ free_vector  -------------*/
       /*  chdir(path); */
                   
       /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
       /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
       /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,1,n);
     free_vector(agedc,1,n);      free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
     fclose(ficres);      fclose(ficres);
                   
                   
     /* Other results (useful)*/      /* Other results (useful)*/
                   
                   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
     prevalence_limit(p, prlim,  ageminpar, agemaxpar);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  
 #include "freeexit2.h"  
 #endif  
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
       
   /*-------------- Variance of one-step probabilities---*/      /* ncovcombmax=  pow(2,cptcoveff); */
       /*-------------- Variance of one-step probabilities---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
       
       /* Prevalence for each covariates in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
         for(k=1;k<=NCOVMAX;k++)          for(k=1;k<=ncovcombmax;k++)
           probs[i][j][k]=0.;            probs[i][j][k]=0.;
       prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       if (mobilav!=0 ||mobilavproj !=0 ) {
         mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
         for(i=1;i<=AGESUP;i++)
           for(j=1;j<=nlstate;j++)
             for(k=1;k<=ncovcombmax;k++)
               mobaverages[i][j][k]=0.;
         mobaverage=mobaverages;
         if (mobilav!=0) {
           if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
             fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             printf(" Error in movingaverage mobilav=%d\n",mobilav);
           }
         }
         /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
         /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
         else if (mobilavproj !=0) {
           if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
             fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
             printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
           }
         }
       }/* end if moving average */
       
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/  
       /*      }  */  
       /*      else{ */  
       /*        erreur=108; */  
       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */  
       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */  
       /*      } */  
     }      }
       if(backcast==1){
         ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
   
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
         bprlim=matrix(1,nlstate,1,nlstate);
         back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
         fclose(ficresplb);
   
         hBijx(p, bage, fage, mobaverage);
         fclose(ficrespijb);
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
   
         /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
            bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       }
       
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\      free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);                  
     */                  
   
     if (mobilav!=0) {  
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
         printf(" Error in movingaverage mobilav=%d\n",mobilav);  
       }  
     }  
   
   
     /*---------- Health expectancies, no variances ------------*/      /*---------- Health expectancies, no variances ------------*/
                   
     strcpy(filerese,"e");      strcpy(filerese,"E_");
     strcat(filerese,fileres);      strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }      }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){                  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/      for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
                   fprintf(ficreseij,"\n#****** ");
     for (k=1; k <= (int) pow(2,cptcoveff); k++){        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for(j=1;j<=cptcoveff;j++) {        }
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficreseij,"******\n");
         }  
         fprintf(ficreseij,"******\n");  
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
         oldm=oldms;savm=savms;  
         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);    
               
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       /*}*/        oldm=oldms;savm=savms;
         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     }      }
     fclose(ficreseij);      fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
     /*---------- Health expectancies and variances ------------*/                  
       /*---------- State-specific expectancies and variances ------------*/
                   
     strcpy(filerest,"t");                  
     strcat(filerest,fileres);      strcpy(filerest,"T_");
       strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
                   
   
       strcpy(fileresstde,"STDE_");
     strcpy(fileresstde,"stde");      strcat(fileresstde,fileresu);
     strcat(fileresstde,fileres);  
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
     }      }
     printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"cve");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileres);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"v");      strcpy(fileresv,"V_");
     strcat(fileresv,fileres);      strcat(fileresv,fileresu);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }      }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");        printf("\n#****** ");
         for(j=1;j<=cptcoveff;j++)         fprintf(ficrest,"\n#****** ");
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog,"\n#****** ");
         fprintf(ficrest,"******\n");        for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresstdeij,"\n#****** ");          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrescveij,"\n#****** ");          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for(j=1;j<=cptcoveff;j++) {        }
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficrest,"******\n");
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog,"******\n");
         }        printf("******\n");
         fprintf(ficresstdeij,"******\n");        
         fprintf(ficrescveij,"******\n");        fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");
         fprintf(ficresvij,"\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(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");        }
         fprintf(ficresstdeij,"******\n");
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficrescveij,"******\n");
         oldm=oldms;savm=savms;        
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);          fprintf(ficresvij,"\n#****** ");
         /*        for(j=1;j<=cptcoveff;j++) 
          */          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         /* goto endfree; */        fprintf(ficresvij,"******\n");
          
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         pstamp(ficrest);        oldm=oldms;savm=savms;
         printf(" cvevsij combination#=%d, ",k);
         fprintf(ficlog, " cvevsij combination#=%d, ",k);
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
           oldm=oldms;savm=savms; /* Segmentation fault */        printf(" end cvevsij \n ");
           cptcod= 0; /* To be deleted */        fprintf(ficlog, " end cvevsij \n ");
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */        
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");        /*
           if(vpopbased==1)         */
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);        /* goto endfree; */
           else        
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           fprintf(ficrest,"# Age e.. (std) ");        pstamp(ficrest);
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        
           fprintf(ficrest,"\n");        
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           epj=vector(1,nlstate+1);          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           for(age=bage; age <=fage ;age++){          cptcod= 0; /* To be deleted */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          printf("varevsij vpopbased=%d \n",vpopbased);
             if (vpopbased==1) {          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
               if(mobilav ==0){          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
                 for(i=1; i<=nlstate;i++)          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
                   prlim[i][i]=probs[(int)age][i][k];          if(vpopbased==1)
               }else{ /* mobilav */             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
                 for(i=1; i<=nlstate;i++)          else
                   prlim[i][i]=mobaverage[(int)age][i][k];            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
               }          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
             }          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   fprintf(ficrest,"\n");
             fprintf(ficrest," %4.0f",age);          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          epj=vector(1,nlstate+1);
               for(i=1, epj[j]=0.;i <=nlstate;i++) {          printf("Computing age specific period (stable) prevalences in each health state \n");
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/          for(age=bage; age <=fage ;age++){
               }            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
               epj[nlstate+1] +=epj[j];            if (vpopbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
             }              }
             }
             for(i=1, vepp=0.;i <=nlstate;i++)            
               for(j=1;j <=nlstate;j++)            fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
                 vepp += vareij[i][j][(int)age];            /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            /* printf(" age %4.0f ",age); */
             for(j=1;j <=nlstate;j++){            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
             }              }
             fprintf(ficrest,"\n");              epj[nlstate+1] +=epj[j];
             }
             /* printf(" age %4.0f \n",age); */
             
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }            }
             fprintf(ficrest,"\n");
         }          }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        } /* End vpopbased */
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
         printf("done \n");fflush(stdout);
         fprintf(ficlog,"done\n");fflush(ficlog);
         
         /*}*/
       } /* End k */
   
       printf("done State-specific expectancies\n");fflush(stdout);
       fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
       /*------- Variance of period (stable) prevalence------*/   
       
       strcpy(fileresvpl,"VPL_");
       strcat(fileresvpl,fileresu);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
       
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");
         printf("\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
       
       fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
       
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,1,n);
Line 7599  Interval (in months) between two waves: Line 10504  Interval (in months) between two waves:
     fclose(ficresvij);      fclose(ficresvij);
     fclose(ficrest);      fclose(ficrest);
     fclose(ficpar);      fclose(ficpar);
         
     /*------- Variance of period (stable) prevalence------*/         
   
     strcpy(fileresvpl,"vpl");  
     strcat(fileresvpl,fileres);  
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);  
       exit(0);  
     }  
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);  
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
             
     for (k=1; k <= (int) pow(2,cptcoveff); k++){  
         fprintf(ficresvpl,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)   
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficresvpl,"******\n");  
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);  
         oldm=oldms;savm=savms;  
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);  
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
       /*}*/  
     }  
   
     fclose(ficresvpl);  
   
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0 ||mobilavproj !=0)
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
   }  /* mle==-3 arrives here for freeing */      free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
  /* endfree:*/  
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    }  /* mle==-3 arrives here for freeing */
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* endfree:*/
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(matcov,1,npar,1,npar);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     /*free_vector(delti,1,npar);*/    free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
     free_matrix(agev,1,maxwav,1,imx);    free_matrix(coqvar,1,maxwav,1,n);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_ivector(ncodemax,1,NCOVMAX);    free_matrix(hess,1,npar,1,npar);
     free_ivector(Tvar,1,NCOVMAX);    /*free_vector(delti,1,npar);*/
     free_ivector(Tprod,1,NCOVMAX);    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_ivector(Tvaraff,1,NCOVMAX);    free_matrix(agev,1,maxwav,1,imx);
     free_ivector(Tage,1,NCOVMAX);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_ivector(ncodemax,1,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);    free_ivector(ncodemaxwundef,1,NCOVMAX);
     free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
     
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);      printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
   }else{    }else{
     printf("End of Imach\n");      printf("End of Imach\n");
     fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"End of Imach\n");
Line 7674  Interval (in months) between two waves: Line 10564  Interval (in months) between two waves:
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     
   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
Line 7687  Interval (in months) between two waves: Line 10577  Interval (in months) between two waves:
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
     
     
    printf("Before Current directory %s!\n",pathcd);    printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
    if (_chdir(pathcd) != 0)    if (_chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n",path);      printf("Can't move to directory %s!\n",path);
    if(_getcwd(pathcd,MAXLINE) > 0)    if(_getcwd(pathcd,MAXLINE) > 0)
 #else  #else
    if(chdir(pathcd) != 0)      if(chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n", path);        printf("Can't move to directory %s!\n", path);
    if (getcwd(pathcd, MAXLINE) > 0)    if (getcwd(pathcd, MAXLINE) > 0)
 #endif   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
Line 7723  Interval (in months) between two waves: Line 10613  Interval (in months) between two waves:
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
Line 7751  Interval (in months) between two waves: Line 10641  Interval (in months) between two waves:
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   end:  end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: ");      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }

Removed from v.1.191  
changed lines
  Added in v.1.227


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