Diff for /imach/src/imach.c between versions 1.2 and 1.230

version 1.2, 2001/03/13 18:10:26 version 1.230, 2016/08/22 06:55:53
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.230  2016/08/22 06:55:53  brouard
   individuals from different ages are interviewed on their health status    Summary: Not working
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.229  2016/07/23 09:45:53  brouard
   Health expectancies are computed from the transistions observed between    Summary: Completing for func too
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.228  2016/07/22 17:45:30  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    Summary: Fixing some arrays, still debugging
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.226  2016/07/12 18:42:34  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: temp
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.225  2016/07/12 08:40:03  brouard
   age", you should modify the program where the markup    Summary: saving but not running
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.224  2016/07/01 13:16:01  brouard
     Summary: Fixes
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.223  2016/02/19 09:23:35  brouard
   individual missed an interview, the information is not rounded or lost, but    Summary: temporary
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.222  2016/02/17 08:14:50  brouard
   observed in state i at age x+h conditional to the observed state i at age    Summary: Probably last 0.98 stable version 0.98r6
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.221  2016/02/15 23:35:36  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    Summary: minor bug
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.219  2016/02/15 00:48:12  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.218  2016/02/12 11:29:23  brouard
      Summary: 0.99 Back projections
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.217  2015/12/23 17:18:31  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Experimental backcast
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.216  2015/12/18 17:32:11  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: 0.98r4 Warning and status=-2
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Version 0.98r4 is now:
       - displaying an error when status is -1, date of interview unknown and date of death known;
 #include <math.h>     - permitting a status -2 when the vital status is unknown at a known date of right truncation.
 #include <stdio.h>    Older changes concerning s=-2, dating from 2005 have been supersed.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.215  2015/12/16 08:52:24  brouard
     Summary: 0.98r4 working
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Revision 1.214  2015/12/16 06:57:54  brouard
 /*#define DEBUG*/    Summary: temporary not working
 #define windows  
     Revision 1.213  2015/12/11 18:22:17  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: 0.98r4
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.212  2015/11/21 12:47:24  brouard
 #define NINTERVMAX 8    Summary: minor typo
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.211  2015/11/21 12:41:11  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: 0.98r3 with some graph of projected cross-sectional
 #define MAXN 80000  
 #define YEARM 12. /* Number of months per year */    Author: Nicolas Brouard
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
 int nvar;    Revision 1.209  2015/11/17 22:12:03  brouard
 static int cptcov;    Summary: Adding ftolpl parameter
 int cptcovn;    Author: N Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    We had difficulties to get smoothed confidence intervals. It was due
 int ndeath=1; /* Number of dead states */    to the period prevalence which wasn't computed accurately. The inner
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
 int *wav; /* Number of waves for this individuual 0 is possible */    computation are long.
 int maxwav; /* Maxim number of waves */  
 int mle, weightopt;    Revision 1.208  2015/11/17 14:31:57  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: temporary
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.207  2015/10/27 17:36:57  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    *** empty log message ***
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.206  2015/10/24 07:14:11  brouard
 FILE *ficreseij;    *** empty log message ***
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.205  2015/10/23 15:50:53  brouard
   char fileresv[FILENAMELENGTH];    Summary: 0.98r3 some clarification for graphs on likelihood contributions
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    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
 #define NR_END 1  
 #define FREE_ARG char*    Also a better criteria for convergence to the period prevalence And
 #define FTOL 1.0e-10    therefore adding the number of years needed to converge. (The
     prevalence in any alive state shold sum to one
 #define NRANSI  
 #define ITMAX 200    Revision 1.202  2015/09/22 19:45:16  brouard
     Summary: Adding some overall graph on contribution to likelihood. Might change
 #define TOL 2.0e-4  
     Revision 1.201  2015/09/15 17:34:58  brouard
 #define CGOLD 0.3819660    Summary: 0.98r0
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    - Some new graphs like suvival functions
     - Some bugs fixed like model=1+age+V2.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.200  2015/09/09 16:53:55  brouard
 #define TINY 1.0e-20    Summary: Big bug thanks to Flavia
   
 static double maxarg1,maxarg2;    Even model=1+age+V2. did not work anymore
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.199  2015/09/07 14:09:23  brouard
      Summary: 0.98q6 changing default small png format for graph to vectorized svg.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.197  2015/09/01 18:24:39  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.196  2015/08/18 23:17:52  brouard
 int stepm;    Summary: 0.98q5
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.195  2015/08/18 16:28:39  brouard
 int m,nb;    Summary: Adding a hack for testing purpose
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    After reading the title, ftol and model lines, if the comment line has
 double **pmmij;    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
 double *weight;    $ echo q | imach foo.imach
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.194  2015/08/18 13:32:00  brouard
 int **nbcode, *Tcode, *Tvar, **codtab;    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.193  2015/08/04 07:17:42  brouard
 double ftolhess; /* Tolerance for computing hessian */    Summary: 0.98q4
   
     Revision 1.192  2015/07/16 16:49:02  brouard
 /******************************************/    Summary: Fixing some outputs
   
 void replace(char *s, char*t)    Revision 1.191  2015/07/14 10:00:33  brouard
 {    Summary: Some fixes
   int i;  
   int lg=20;    Revision 1.190  2015/05/05 08:51:13  brouard
   i=0;    Summary: Adding digits in output parameters (7 digits instead of 6)
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Fix 1+age+.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.189  2015/04/30 14:45:16  brouard
   }    Summary: 0.98q2
 }  
     Revision 1.188  2015/04/30 08:27:53  brouard
 int nbocc(char *s, char occ)    *** empty log message ***
 {  
   int i,j=0;    Revision 1.187  2015/04/29 09:11:15  brouard
   int lg=20;    *** empty log message ***
   i=0;  
   lg=strlen(s);    Revision 1.186  2015/04/23 12:01:52  brouard
   for(i=0; i<= lg; i++) {    Summary: V1*age is working now, version 0.98q1
   if  (s[i] == occ ) j++;  
   }    Some codes had been disabled in order to simplify and Vn*age was
   return j;    working in the optimization phase, ie, giving correct MLE parameters,
 }    but, as usual, outputs were not correct and program core dumped.
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.185  2015/03/11 13:26:42  brouard
 {    Summary: Inclusion of compile and links command line for Intel Compiler
   int i,lg,j,p;  
   i=0;    Revision 1.184  2015/03/11 11:52:39  brouard
   if (t[0]== occ) p=0;    Summary: Back from Windows 8. Intel Compiler
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]==occ)) p=j+1;    Revision 1.183  2015/03/10 20:34:32  brouard
   }    Summary: 0.98q0, trying with directest, mnbrak fixed
   
   lg=strlen(t);    We use directest instead of original Powell test; probably no
   for(j=0; j<p; j++) {    incidence on the results, but better justifications;
     (u[j] = t[j]);    We fixed Numerical Recipes mnbrak routine which was wrong and gave
     u[p]='\0';    wrong results.
   }  
     Revision 1.182  2015/02/12 08:19:57  brouard
    for(j=0; j<= lg; j++) {    Summary: Trying to keep directest which seems simpler and more general
     if (j>=(p+1))(v[j-p-1] = t[j]);    Author: Nicolas Brouard
   }  
 }    Revision 1.181  2015/02/11 23:22:24  brouard
     Summary: Comments on Powell added
   
 /********************** nrerror ********************/    Author:
   
 void nrerror(char error_text[])    Revision 1.180  2015/02/11 17:33:45  brouard
 {    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.179  2015/01/04 09:57:06  brouard
   exit(1);    Summary: back to OS/X
 }  
 /*********************** vector *******************/    Revision 1.178  2015/01/04 09:35:48  brouard
 double *vector(int nl, int nh)    *** empty log message ***
 {  
   double *v;    Revision 1.177  2015/01/03 18:40:56  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Summary: Still testing ilc32 on OSX
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.176  2015/01/03 16:45:04  brouard
 }    *** empty log message ***
   
 /************************ free vector ******************/    Revision 1.175  2015/01/03 16:33:42  brouard
 void free_vector(double*v, int nl, int nh)    *** empty log message ***
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.174  2015/01/03 16:15:49  brouard
 }    Summary: Still in cross-compilation
   
 /************************ivector *******************************/    Revision 1.173  2015/01/03 12:06:26  brouard
 int *ivector(long nl,long nh)    Summary: trying to detect cross-compilation
 {  
   int *v;    Revision 1.172  2014/12/27 12:07:47  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.171  2014/12/23 13:26:59  brouard
 }    Summary: Back from Visual C
   
 /******************free ivector **************************/    Still problem with utsname.h on Windows
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.170  2014/12/23 11:17:12  brouard
   free((FREE_ARG)(v+nl-NR_END));    Summary: Cleaning some \%% back to %%
 }  
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.169  2014/12/22 23:08:31  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Summary: 0.98p
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   int **m;  
      Revision 1.168  2014/12/22 15:17:42  brouard
   /* allocate pointers to rows */    Summary: update
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.167  2014/12/22 13:50:56  brouard
   m += NR_END;    Summary: Testing uname and compiler version and if compiled 32 or 64
   m -= nrl;  
      Testing on Linux 64
    
   /* allocate rows and set pointers to them */    Revision 1.166  2014/12/22 11:40:47  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    *** empty log message ***
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.165  2014/12/16 11:20:36  brouard
   m[nrl] -= ncl;    Summary: After compiling on Visual C
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    * imach.c (Module): Merging 1.61 to 1.162
    
   /* return pointer to array of pointers to rows */    Revision 1.164  2014/12/16 10:52:11  brouard
   return m;    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 }  
     * imach.c (Module): Merging 1.61 to 1.162
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.163  2014/12/16 10:30:11  brouard
       int **m;    * imach.c (Module): Merging 1.61 to 1.162
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.162  2014/09/25 11:43:39  brouard
 {    Summary: temporary backup 0.99!
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.1  2014/09/16 11:06:58  brouard
 }    Summary: With some code (wrong) for nlopt
   
 /******************* matrix *******************************/    Author:
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.161  2014/09/15 20:41:41  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Summary: Problem with macro SQR on Intel compiler
   double **m;  
     Revision 1.160  2014/09/02 09:24:05  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    *** empty log message ***
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.159  2014/09/01 10:34:10  brouard
   m -= nrl;    Summary: WIN32
     Author: Brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.158  2014/08/27 17:11:51  brouard
   m[nrl] += NR_END;    *** empty log message ***
   m[nrl] -= ncl;  
     Revision 1.157  2014/08/27 16:26:55  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Summary: Preparing windows Visual studio version
   return m;    Author: Brouard
 }  
     In order to compile on Visual studio, time.h is now correct and time_t
 /*************************free matrix ************************/    and tm struct should be used. difftime should be used but sometimes I
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    just make the differences in raw time format (time(&now).
 {    Trying to suppress #ifdef LINUX
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Add xdg-open for __linux in order to open default browser.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.155  2014/08/25 18:32:34  brouard
 {    Summary: New compile, minor changes
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Author: Brouard
   double ***m;  
     Revision 1.154  2014/06/20 17:32:08  brouard
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Summary: Outputs now all graphs of convergence to period prevalence
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.153  2014/06/20 16:45:46  brouard
   m -= nrl;    Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.152  2014/06/18 17:54:09  brouard
   m[nrl] += NR_END;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   m[nrl] -= ncl;  
     Revision 1.151  2014/06/18 16:43:30  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    *** empty log message ***
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.150  2014/06/18 16:42:35  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   m[nrl][ncl] += NR_END;    Author: brouard
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.149  2014/06/18 15:51:14  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    Summary: Some fixes in parameter files errors
      Author: Nicolas Brouard
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.148  2014/06/17 17:38:48  brouard
     for (j=ncl+1; j<=nch; j++)    Summary: Nothing new
       m[i][j]=m[i][j-1]+nlay;    Author: Brouard
   }  
   return m;    Just a new packaging for OS/X version 0.98nS
 }  
     Revision 1.147  2014/06/16 10:33:11  brouard
 /*************************free ma3x ************************/    *** empty log message ***
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.146  2014/06/16 10:20:28  brouard
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Summary: Merge
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Author: Brouard
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Merge, before building revised version.
   
 /***************** f1dim *************************/    Revision 1.145  2014/06/10 21:23:15  brouard
 extern int ncom;    Summary: Debugging with valgrind
 extern double *pcom,*xicom;    Author: Nicolas Brouard
 extern double (*nrfunc)(double []);  
      Lot of changes in order to output the results with some covariates
 double f1dim(double x)    After the Edimburgh REVES conference 2014, it seems mandatory to
 {    improve the code.
   int j;    No more memory valgrind error but a lot has to be done in order to
   double f;    continue the work of splitting the code into subroutines.
   double *xt;    Also, decodemodel has been improved. Tricode is still not
      optimal. nbcode should be improved. Documentation has been added in
   xt=vector(1,ncom);    the source code.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.143  2014/01/26 09:45:38  brouard
   free_vector(xt,1,ncom);    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   return f;  
 }    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.142  2014/01/26 03:57:36  brouard
 {    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   int iter;  
   double a,b,d,etemp;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.141  2014/01/26 02:42:01  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   double e=0.0;  
      Revision 1.140  2011/09/02 10:37:54  brouard
   a=(ax < cx ? ax : cx);    Summary: times.h is ok with mingw32 now.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.139  2010/06/14 07:50:17  brouard
   fw=fv=fx=(*f)(x);    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   for (iter=1;iter<=ITMAX;iter++) {    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Revision 1.138  2010/04/30 18:19:40  brouard
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    *** empty log message ***
     printf(".");fflush(stdout);  
 #ifdef DEBUG    Revision 1.137  2010/04/29 18:11:38  brouard
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    (Module): Checking covariates for more complex models
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    than V1+V2. A lot of change to be done. Unstable.
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.136  2010/04/26 20:30:53  brouard
       *xmin=x;    (Module): merging some libgsl code. Fixing computation
       return fx;    of likelione (using inter/intrapolation if mle = 0) in order to
     }    get same likelihood as if mle=1.
     ftemp=fu;    Some cleaning of code and comments added.
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Revision 1.135  2009/10/29 15:33:14  brouard
       q=(x-v)*(fx-fw);    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);    Revision 1.134  2009/10/29 13:18:53  brouard
       if (q > 0.0) p = -p;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       q=fabs(q);  
       etemp=e;    Revision 1.133  2009/07/06 10:21:25  brouard
       e=d;    just nforces
       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));    Revision 1.132  2009/07/06 08:22:05  brouard
       else {    Many tings
         d=p/q;  
         u=x+d;    Revision 1.131  2009/06/20 16:22:47  brouard
         if (u-a < tol2 || b-u < tol2)    Some dimensions resccaled
           d=SIGN(tol1,xm-x);  
       }    Revision 1.130  2009/05/26 06:44:34  brouard
     } else {    (Module): Max Covariate is now set to 20 instead of 8. A
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    lot of cleaning with variables initialized to 0. Trying to make
     }    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Revision 1.129  2007/08/31 13:49:27  lievre
     if (fu <= fx) {    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    Revision 1.128  2006/06/30 13:02:05  brouard
         SHFT(fv,fw,fx,fu)    (Module): Clarifications on computing e.j
         } else {  
           if (u < x) a=u; else b=u;    Revision 1.127  2006/04/28 18:11:50  brouard
           if (fu <= fw || w == x) {    (Module): Yes the sum of survivors was wrong since
             v=w;    imach-114 because nhstepm was no more computed in the age
             w=u;    loop. Now we define nhstepma in the age loop.
             fv=fw;    (Module): In order to speed up (in case of numerous covariates) we
             fw=fu;    compute health expectancies (without variances) in a first step
           } else if (fu <= fv || v == x || v == w) {    and then all the health expectancies with variances or standard
             v=u;    deviation (needs data from the Hessian matrices) which slows the
             fv=fu;    computation.
           }    In the future we should be able to stop the program is only health
         }    expectancies and graph are needed without standard deviations.
   }  
   nrerror("Too many iterations in brent");    Revision 1.126  2006/04/28 17:23:28  brouard
   *xmin=x;    (Module): Yes the sum of survivors was wrong since
   return fx;    imach-114 because nhstepm was no more computed in the age
 }    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 /****************** mnbrak ***********************/  
     Revision 1.125  2006/04/04 15:20:31  lievre
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    Errors in calculation of health expectancies. Age was not initialized.
             double (*func)(double))    Forecasting file added.
 {  
   double ulim,u,r,q, dum;    Revision 1.124  2006/03/22 17:13:53  lievre
   double fu;    Parameters are printed with %lf instead of %f (more numbers after the comma).
      The log-likelihood is printed in the log file
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    Revision 1.123  2006/03/20 10:52:43  brouard
   if (*fb > *fa) {    * imach.c (Module): <title> changed, corresponds to .htm file
     SHFT(dum,*ax,*bx,dum)    name. <head> headers where missing.
       SHFT(dum,*fb,*fa,dum)  
       }    * imach.c (Module): Weights can have a decimal point as for
   *cx=(*bx)+GOLD*(*bx-*ax);    English (a comma might work with a correct LC_NUMERIC environment,
   *fc=(*func)(*cx);    otherwise the weight is truncated).
   while (*fb > *fc) {    Modification of warning when the covariates values are not 0 or
     r=(*bx-*ax)*(*fb-*fc);    1.
     q=(*bx-*cx)*(*fb-*fa);    Version 0.98g
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Revision 1.122  2006/03/20 09:45:41  brouard
     ulim=(*bx)+GLIMIT*(*cx-*bx);    (Module): Weights can have a decimal point as for
     if ((*bx-u)*(u-*cx) > 0.0) {    English (a comma might work with a correct LC_NUMERIC environment,
       fu=(*func)(u);    otherwise the weight is truncated).
     } else if ((*cx-u)*(u-ulim) > 0.0) {    Modification of warning when the covariates values are not 0 or
       fu=(*func)(u);    1.
       if (fu < *fc) {    Version 0.98g
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    Revision 1.121  2006/03/16 17:45:01  lievre
           }    * imach.c (Module): Comments concerning covariates added
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    * imach.c (Module): refinements in the computation of lli if
       fu=(*func)(u);    status=-2 in order to have more reliable computation if stepm is
     } else {    not 1 month. Version 0.98f
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    Revision 1.120  2006/03/16 15:10:38  lievre
     }    (Module): refinements in the computation of lli if
     SHFT(*ax,*bx,*cx,u)    status=-2 in order to have more reliable computation if stepm is
       SHFT(*fa,*fb,*fc,fu)    not 1 month. Version 0.98f
       }  
 }    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 /*************** linmin ************************/    computed as likelihood omitting the logarithm. Version O.98e
   
 int ncom;    Revision 1.118  2006/03/14 18:20:07  brouard
 double *pcom,*xicom;    (Module): varevsij Comments added explaining the second
 double (*nrfunc)(double []);    table of variances if popbased=1 .
      (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    (Module): Function pstamp added
 {    (Module): Version 0.98d
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    Revision 1.117  2006/03/14 17:16:22  brouard
   double f1dim(double x);    (Module): varevsij Comments added explaining the second
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    table of variances if popbased=1 .
               double *fc, double (*func)(double));    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   int j;    (Module): Function pstamp added
   double xx,xmin,bx,ax;    (Module): Version 0.98d
   double fx,fb,fa;  
      Revision 1.116  2006/03/06 10:29:27  brouard
   ncom=n;    (Module): Variance-covariance wrong links and
   pcom=vector(1,n);    varian-covariance of ej. is needed (Saito).
   xicom=vector(1,n);  
   nrfunc=func;    Revision 1.115  2006/02/27 12:17:45  brouard
   for (j=1;j<=n;j++) {    (Module): One freematrix added in mlikeli! 0.98c
     pcom[j]=p[j];  
     xicom[j]=xi[j];    Revision 1.114  2006/02/26 12:57:58  brouard
   }    (Module): Some improvements in processing parameter
   ax=0.0;    filename with strsep.
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    Revision 1.113  2006/02/24 14:20:24  brouard
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    (Module): Memory leaks checks with valgrind and:
 #ifdef DEBUG    datafile was not closed, some imatrix were not freed and on matrix
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    allocation too.
 #endif  
   for (j=1;j<=n;j++) {    Revision 1.112  2006/01/30 09:55:26  brouard
     xi[j] *= xmin;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
     p[j] += xi[j];  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
   free_vector(xicom,1,n);    (Module): Lots of cleaning and bugs added (Gompertz)
   free_vector(pcom,1,n);    (Module): Comments can be added in data file. Missing date values
 }    can be a simple dot '.'.
   
 /*************** powell ************************/    Revision 1.110  2006/01/25 00:51:50  brouard
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    (Module): Lots of cleaning and bugs added (Gompertz)
             double (*func)(double []))  
 {    Revision 1.109  2006/01/24 19:37:15  brouard
   void linmin(double p[], double xi[], int n, double *fret,    (Module): Comments (lines starting with a #) are allowed in data.
               double (*func)(double []));  
   int i,ibig,j;    Revision 1.108  2006/01/19 18:05:42  lievre
   double del,t,*pt,*ptt,*xit;    Gnuplot problem appeared...
   double fp,fptt;    To be fixed
   double *xits;  
   pt=vector(1,n);    Revision 1.107  2006/01/19 16:20:37  brouard
   ptt=vector(1,n);    Test existence of gnuplot in imach path
   xit=vector(1,n);  
   xits=vector(1,n);    Revision 1.106  2006/01/19 13:24:36  brouard
   *fret=(*func)(p);    Some cleaning and links added in html output
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {    Revision 1.105  2006/01/05 20:23:19  lievre
     fp=(*fret);    *** empty log message ***
     ibig=0;  
     del=0.0;    Revision 1.104  2005/09/30 16:11:43  lievre
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    (Module): sump fixed, loop imx fixed, and simplifications.
     for (i=1;i<=n;i++)    (Module): If the status is missing at the last wave but we know
       printf(" %d %.12f",i, p[i]);    that the person is alive, then we can code his/her status as -2
     printf("\n");    (instead of missing=-1 in earlier versions) and his/her
     for (i=1;i<=n;i++) {    contributions to the likelihood is 1 - Prob of dying from last
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    health status (= 1-p13= p11+p12 in the easiest case of somebody in
       fptt=(*fret);    the healthy state at last known wave). Version is 0.98
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);    Revision 1.103  2005/09/30 15:54:49  lievre
 #endif    (Module): sump fixed, loop imx fixed, and simplifications.
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);    Revision 1.102  2004/09/15 17:31:30  brouard
       if (fabs(fptt-(*fret)) > del) {    Add the possibility to read data file including tab characters.
         del=fabs(fptt-(*fret));  
         ibig=i;    Revision 1.101  2004/09/15 10:38:38  brouard
       }    Fix on curr_time
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));    Revision 1.100  2004/07/12 18:29:06  brouard
       for (j=1;j<=n;j++) {    Add version for Mac OS X. Just define UNIX in Makefile
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);    Revision 1.99  2004/06/05 08:57:40  brouard
       }    *** empty log message ***
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);    Revision 1.98  2004/05/16 15:05:56  brouard
       printf("\n");    New version 0.97 . First attempt to estimate force of mortality
 #endif    directly from the data i.e. without the need of knowing the health
     }    state at each age, but using a Gompertz model: log u =a + b*age .
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    This is the basic analysis of mortality and should be done before any
 #ifdef DEBUG    other analysis, in order to test if the mortality estimated from the
       int k[2],l;    cross-longitudinal survey is different from the mortality estimated
       k[0]=1;    from other sources like vital statistic data.
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));    The same imach parameter file can be used but the option for mle should be -3.
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);    Agnès, who wrote this part of the code, tried to keep most of the
       printf("\n");    former routines in order to include the new code within the former code.
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {    The output is very simple: only an estimate of the intercept and of
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    the slope with 95% confident intervals.
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }    Current limitations:
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    A) Even if you enter covariates, i.e. with the
       }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #endif    B) There is no computation of Life Expectancy nor Life Table.
   
     Revision 1.97  2004/02/20 13:25:42  lievre
       free_vector(xit,1,n);    Version 0.96d. Population forecasting command line is (temporarily)
       free_vector(xits,1,n);    suppressed.
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);    Revision 1.96  2003/07/15 15:38:55  brouard
       return;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     }    rewritten within the same printf. Workaround: many printfs.
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    Revision 1.95  2003/07/08 07:54:34  brouard
       ptt[j]=2.0*p[j]-pt[j];    * imach.c (Repository):
       xit[j]=p[j]-pt[j];    (Repository): Using imachwizard code to output a more meaningful covariance
       pt[j]=p[j];    matrix (cov(a12,c31) instead of numbers.
     }  
     fptt=(*func)(ptt);    Revision 1.94  2003/06/27 13:00:02  brouard
     if (fptt < fp) {    Just cleaning
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    Revision 1.93  2003/06/25 16:33:55  brouard
         linmin(p,xit,n,fret,func);    (Module): On windows (cygwin) function asctime_r doesn't
         for (j=1;j<=n;j++) {    exist so I changed back to asctime which exists.
           xi[j][ibig]=xi[j][n];    (Module): Version 0.96b
           xi[j][n]=xit[j];  
         }    Revision 1.92  2003/06/25 16:30:45  brouard
 #ifdef DEBUG    (Module): On windows (cygwin) function asctime_r doesn't
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    exist so I changed back to asctime which exists.
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);    Revision 1.91  2003/06/25 15:30:29  brouard
         printf("\n");    * imach.c (Repository): Duplicated warning errors corrected.
 #endif    (Repository): Elapsed time after each iteration is now output. It
       }    helps to forecast when convergence will be reached. Elapsed time
     }    is stamped in powell.  We created a new html file for the graphs
   }    concerning matrix of covariance. It has extension -cov.htm.
 }  
     Revision 1.90  2003/06/24 12:34:15  brouard
 /**** Prevalence limit ****************/    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    of the covariance matrix to be input.
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    Revision 1.89  2003/06/24 12:30:52  brouard
      matrix by transitions matrix until convergence is reached */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   int i, ii,j,k;    of the covariance matrix to be input.
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();    Revision 1.88  2003/06/23 17:54:56  brouard
   double **out, cov[NCOVMAX], **pmij();    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){    Revision 1.86  2003/06/17 20:04:08  brouard
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    (Module): Change position of html and gnuplot routines and added
     }    routine fileappend.
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    Revision 1.85  2003/06/17 13:12:43  brouard
     newm=savm;    * imach.c (Repository): Check when date of death was earlier that
     /* Covariates have to be included here again */    current date of interview. It may happen when the death was just
     cov[1]=1.;    prior to the death. In this case, dh was negative and likelihood
     cov[2]=agefin;    was wrong (infinity). We still send an "Error" but patch by
     if (cptcovn>0){    assuming that the date of death was just one stepm after the
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}    interview.
     }    (Repository): Because some people have very long ID (first column)
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
     savm=oldm;    truncation)
     oldm=newm;    (Repository): No more line truncation errors.
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){    Revision 1.84  2003/06/13 21:44:43  brouard
       min=1.;    * imach.c (Repository): Replace "freqsummary" at a correct
       max=0.;    place. It differs from routine "prevalence" which may be called
       for(i=1; i<=nlstate; i++) {    many times. Probs is memory consuming and must be used with
         sumnew=0;    parcimony.
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);    Revision 1.83  2003/06/10 13:39:11  lievre
         min=FMIN(min,prlim[i][j]);    *** empty log message ***
       }  
       maxmin=max-min;    Revision 1.82  2003/06/05 15:57:20  brouard
       maxmax=FMAX(maxmax,maxmin);    Add log in  imach.c and  fullversion number is now printed.
     }  
     if(maxmax < ftolpl){  */
       return prlim;  /*
     }     Interpolated Markov Chain
   }  
 }    Short summary of the programme:
     
 /*************** transition probabilities **********/    This program computes Healthy Life Expectancies or State-specific
     (if states aren't health statuses) Expectancies from
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    cross-longitudinal data. Cross-longitudinal data consist in: 
 {  
   double s1, s2;    -1- a first survey ("cross") where individuals from different ages
   /*double t34;*/    are interviewed on their health status or degree of disability (in
   int i,j,j1, nc, ii, jj;    the case of a health survey which is our main interest)
   
     for(i=1; i<= nlstate; i++){    -2- at least a second wave of interviews ("longitudinal") which
     for(j=1; j<i;j++){    measure each change (if any) in individual health status.  Health
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    expectancies are computed from the time spent in each health state
         /*s2 += param[i][j][nc]*cov[nc];*/    according to a model. More health states you consider, more time is
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    necessary to reach the Maximum Likelihood of the parameters involved
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    in the model.  The simplest model is the multinomial logistic model
       }    where pij is the probability to be observed in state j at the second
       ps[i][j]=s2;    wave conditional to be observed in state i at the first
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
     }    etc , where 'age' is age and 'sex' is a covariate. If you want to
     for(j=i+1; j<=nlstate+ndeath;j++){    have a more complex model than "constant and age", you should modify
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    the program where the markup *Covariates have to be included here
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    again* invites you to do it.  More covariates you add, slower the
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    convergence.
       }  
       ps[i][j]=s2;    The advantage of this computer programme, compared to a simple
     }    multinomial logistic model, is clear when the delay between waves is not
   }    identical for each individual. Also, if a individual missed an
   for(i=1; i<= nlstate; i++){    intermediate interview, the information is lost, but taken into
      s1=0;    account using an interpolation or extrapolation.  
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    hPijx is the probability to be observed in state i at age x+h
     for(j=i+1; j<=nlstate+ndeath; j++)    conditional to the observed state i at age x. The delay 'h' can be
       s1+=exp(ps[i][j]);    split into an exact number (nh*stepm) of unobserved intermediate
     ps[i][i]=1./(s1+1.);    states. This elementary transition (by month, quarter,
     for(j=1; j<i; j++)    semester or year) is modelled as a multinomial logistic.  The hPx
       ps[i][j]= exp(ps[i][j])*ps[i][i];    matrix is simply the matrix product of nh*stepm elementary matrices
     for(j=i+1; j<=nlstate+ndeath; j++)    and the contribution of each individual to the likelihood is simply
       ps[i][j]= exp(ps[i][j])*ps[i][i];    hPijx.
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence.
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  Back prevalence and projections:
       ps[ii][jj]=0;  
       ps[ii][ii]=1;   - 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)
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){      Computes the back prevalence limit for any combination of
      printf("%lf ",ps[ii][jj]);      covariate values k at any age between ageminpar and agemaxpar and
    }      returns it in **bprlim. In the loops,
     printf("\n ");  
     }     - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
     printf("\n ");printf("%lf ",cov[2]);*/         **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);     - hBijx Back Probability to be in state i at age x-h being in j at x
   goto end;*/     Computes for any combination of covariates k and any age between bage and fage 
     return ps;     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }                          oldm=oldms;savm=savms;
   
 /**************** Product of 2 matrices ******************/     - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
        Computes the transition matrix starting at age 'age' over
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)       'nhstepm*hstepm*stepm' months (i.e. until
 {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times       nhstepm*hstepm matrices. 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized       Returns p3mat[i][j][h] after calling
      before: only the contents of out is modified. The function returns       p3mat[i][j][h]=matprod2(newm,
      a pointer to pointers identical to out */       bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
   long i, j, k;       dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=nrl; i<= nrh; i++)       oldm);
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  Important routines
         out[i][k] +=in[i][j]*b[j][k];  
   - func (or funcone), computes logit (pij) distinguishing
   return out;    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:
 /************* Higher Matrix Product ***************/         % fixed dummy (treated) or quantitative (not done because time-consuming);
          % varying dummy (not done) or quantitative (not done);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  - 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.
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
      duration (i.e. until    o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
      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).  
      Model is determined by parameters x and covariates have to be    
      included manually here.    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
      */    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   int i, j, d, h, k;    It is copyrighted identically to a GNU software product, ie programme and
   double **out, cov[NCOVMAX];    software can be distributed freely for non commercial use. Latest version
   double **newm;    can be accessed at http://euroreves.ined.fr/imach .
   
   /* Hstepm could be zero and should return the unit matrix */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for (i=1;i<=nlstate+ndeath;i++)    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     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);  /*
     }    main
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    read parameterfile
   for(h=1; h <=nhstepm; h++){    read datafile
     for(d=1; d <=hstepm; d++){    concatwav
       newm=savm;    freqsummary
       /* Covariates have to be included here again */    if (mle >= 1)
       cov[1]=1.;      mlikeli
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    print results files
       if (cptcovn>0){    if mle==1 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];       computes hessian
     }    read end of parameter file: agemin, agemax, bage, fage, estepm
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        begin-prev-date,...
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    open gnuplot file
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    open html file
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       savm=oldm;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       oldm=newm;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     }      freexexit2 possible for memory heap.
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {    h Pij x                         | pij_nom  ficrestpij
         po[i][j][h]=newm[i][j];     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
          */         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       }  
   } /* end h */         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   return po;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 }    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
      Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
      Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 /*************** log-likelihood *************/  
 double func( double *x)    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   int i, ii, j, k, mi, d;    Variance-covariance of DFLE
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    prevalence()
   double **out;     movingaverage()
   double sw; /* Sum of weights */    varevsij() 
   double lli; /* Individual log likelihood */    if popbased==1 varevsij(,popbased)
   long ipmx;    total life expectancies
   /*extern weight */    Variance of period (stable) prevalence
   /* We are differentiating ll according to initial status */   end
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  */
   /*for(i=1;i<imx;i++)  
 printf(" %d\n",s[4][i]);  /* #define DEBUG */
   */  /* #define DEBUGBRENT */
   /* #define DEBUGLINMIN */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /* #define DEBUGHESS */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #define DEBUGHESSIJ
        for(mi=1; mi<= wav[i]-1; mi++){  /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
       for (ii=1;ii<=nlstate+ndeath;ii++)  #define POWELL /* Instead of NLOPT */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define POWELLNOF3INFF1TEST /* Skip test */
             for(d=0; d<dh[mi][i]; d++){  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
         newm=savm;  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
           cov[1]=1.;  
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #include <math.h>
           if (cptcovn>0){  #include <stdio.h>
             for (k=1; k<=cptcovn;k++) {  #include <stdlib.h>
               cov[2+k]=covar[Tvar[k]][i];  #include <string.h>
               /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][i]);*/  #include <ctype.h>
             }  
             }  #ifdef _WIN32
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #include <io.h>
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #include <windows.h>
           savm=oldm;  #include <tchar.h>
           oldm=newm;  #else
       } /* end mult */  #include <unistd.h>
      #endif
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  #include <limits.h>
       ipmx +=1;  #include <sys/types.h>
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #if defined(__GNUC__)
     } /* end of wave */  #include <sys/utsname.h> /* Doesn't work on Windows */
   } /* end of individual */  #endif
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  #include <sys/stat.h>
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #include <errno.h>
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /* extern int errno; */
   
   return -l;  /* #ifdef LINUX */
 }  /* #include <time.h> */
   /* #include "timeval.h" */
   /* #else */
 /*********** Maximum Likelihood Estimation ***************/  /* #include <sys/time.h> */
   /* #endif */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  #include <time.h>
   int i,j, iter;  
   double **xi,*delti;  #ifdef GSL
   double fret;  #include <gsl/gsl_errno.h>
   xi=matrix(1,npar,1,npar);  #include <gsl/gsl_multimin.h>
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  #ifdef NLOPT
   powell(p,xi,npar,ftol,&iter,&fret,func);  #include <nlopt.h>
   typedef struct {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double (* function)(double [] );
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  } myfunc_data ;
   #endif
 }  
   /* #include <libintl.h> */
 /**** Computes Hessian and covariance matrix ***/  /* #define _(String) gettext (String) */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   double  **a,**y,*x,pd;  
   double **hess;  #define GNUPLOTPROGRAM "gnuplot"
   int i, j,jk;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   int *indx;  #define FILENAMELENGTH 132
   
   double hessii(double p[], double delta, int theta, double delti[]);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double hessij(double p[], double delti[], int i, int j);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
   hess=matrix(1,npar,1,npar);  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   printf("\nCalculation of the hessian matrix. Wait...\n");  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   for (i=1;i<=npar;i++){  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     printf("%d",i);fflush(stdout);  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
     /*printf(" %f ",p[i]);*/  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
   }  #define MAXN 20000
   #define YEARM 12. /**< Number of months per year */
   for (i=1;i<=npar;i++) {  /* #define AGESUP 130 */
     for (j=1;j<=npar;j++)  {  #define AGESUP 150
       if (j>i) {  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
         printf(".%d%d",i,j);fflush(stdout);  #define AGEBASE 40
         hess[i][j]=hessij(p,delti,i,j);  #define AGEOVERFLOW 1.e20
         hess[j][i]=hess[i][j];  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       }  #ifdef _WIN32
     }  #define DIRSEPARATOR '\\'
   }  #define CHARSEPARATOR "\\"
   printf("\n");  #define ODIRSEPARATOR '/'
   #else
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   a=matrix(1,npar,1,npar);  #define ODIRSEPARATOR '\\'
   y=matrix(1,npar,1,npar);  #endif
   x=vector(1,npar);  
   indx=ivector(1,npar);  /* $Id$ */
   for (i=1;i<=npar;i++)  /* $State$ */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  #include "version.h"
   ludcmp(a,npar,indx,&pd);  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";
   for (j=1;j<=npar;j++) {  char fullversion[]="$Revision$ $Date$"; 
     for (i=1;i<=npar;i++) x[i]=0;  char strstart[80];
     x[j]=1;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     lubksb(a,npar,indx,x);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     for (i=1;i<=npar;i++){  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
       matcov[i][j]=x[i];  /* 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 cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
   printf("\n#Hessian matrix#\n");  int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
   for (i=1;i<=npar;i++) {  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     for (j=1;j<=npar;j++) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       printf("%.3e ",hess[i][j]);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     }  int ncoveff=0; /* Total number of effective covariates in the model */
     printf("\n");  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 */
   /* Recompute Inverse */  int cptcov=0; /* Working variable */
   for (i=1;i<=npar;i++)  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  int npar=NPARMAX;
   ludcmp(a,npar,indx,&pd);  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   /*  printf("\n#Hessian matrix recomputed#\n");  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 */ 
   for (j=1;j<=npar;j++) {  int popbased=0;
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  int *wav; /* Number of waves for this individuual 0 is possible */
     lubksb(a,npar,indx,x);  int maxwav=0; /* Maxim number of waves */
     for (i=1;i<=npar;i++){  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       y[i][j]=x[i];  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       printf("%.3e ",y[i][j]);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     }                     to the likelihood and the sum of weights (done by funcone)*/
     printf("\n");  int mle=1, weightopt=0;
   }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   free_matrix(a,1,npar,1,npar);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free_matrix(y,1,npar,1,npar);  int countcallfunc=0;  /* Count the number of calls to func */
   free_vector(x,1,npar);  int selected(int kvar); /* Is covariate kvar selected for printing results */
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /*FILE *fic ; */ /* Used in readdata only */
 {  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
   int i;  FILE *ficlog, *ficrespow;
   int l=1, lmax=20;  int globpr=0; /* Global variable for printing or not */
   double k1,k2;  double fretone; /* Only one call to likelihood */
   double p2[NPARMAX+1];  long ipmx=0; /* Number of contributions */
   double res;  double sw; /* Sum of weights */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  char filerespow[FILENAMELENGTH];
   double fx;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   int k=0,kmax=10;  FILE *ficresilk;
   double l1;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   fx=func(x);  FILE *fichtm, *fichtmcov; /* Html File */
   for (i=1;i<=npar;i++) p2[i]=x[i];  FILE *ficreseij;
   for(l=0 ; l <=lmax; l++){  char filerese[FILENAMELENGTH];
     l1=pow(10,l);  FILE *ficresstdeij;
     delts=delt;  char fileresstde[FILENAMELENGTH];
     for(k=1 ; k <kmax; k=k+1){  FILE *ficrescveij;
       delt = delta*(l1*k);  char filerescve[FILENAMELENGTH];
       p2[theta]=x[theta] +delt;  FILE  *ficresvij;
       k1=func(p2)-fx;  char fileresv[FILENAMELENGTH];
       p2[theta]=x[theta]-delt;  FILE  *ficresvpl;
       k2=func(p2)-fx;  char fileresvpl[FILENAMELENGTH];
       /*res= (k1-2.0*fx+k2)/delt/delt; */  char title[MAXLINE];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
        char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 #ifdef DEBUG  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       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);  char command[FILENAMELENGTH];
 #endif  int  outcmd=0;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         k=kmax;  char fileresu[FILENAMELENGTH]; /* fileres without r in front */
       }  char filelog[FILENAMELENGTH]; /* Log file */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  char filerest[FILENAMELENGTH];
         k=kmax; l=lmax*10.;  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       }  
     }  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
   }  /* struct timezone tzp; */
   delti[theta]=delts;  /* extern int gettimeofday(); */
   return res;    struct tm tml, *gmtime(), *localtime();
 }  
   extern time_t time();
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   int i;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   int l=1, l1, lmax=20;  struct tm tm;
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];  char strcurr[80], strfor[80];
   int k;  
   char *endptr;
   fx=func(x);  long lval;
   for (k=1; k<=2; k++) {  double dval;
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  #define NR_END 1
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #define FREE_ARG char*
     k1=func(p2)-fx;  #define FTOL 1.0e-10
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  #define NRANSI 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #define ITMAX 200 
     k2=func(p2)-fx;  
    #define TOL 2.0e-4 
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #define CGOLD 0.3819660 
     k3=func(p2)-fx;  #define ZEPS 1.0e-10 
    #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #define GOLD 1.618034 
     k4=func(p2)-fx;  #define GLIMIT 100.0 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #define TINY 1.0e-20 
 #ifdef DEBUG  
     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);  static double maxarg1,maxarg2;
 #endif  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   return res;    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /************** Inverse of matrix **************/  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
 void ludcmp(double **a, int n, int *indx, double *d)  #define mytinydouble 1.0e-16
 {  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   int i,imax,j,k;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   double big,dum,sum,temp;  /* static double dsqrarg; */
   double *vv;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
    static double sqrarg;
   vv=vector(1,n);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   *d=1.0;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for (i=1;i<=n;i++) {  int agegomp= AGEGOMP;
     big=0.0;  
     for (j=1;j<=n;j++)  int imx; 
       if ((temp=fabs(a[i][j])) > big) big=temp;  int stepm=1;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /* Stepm, step in month: minimum step interpolation*/
     vv[i]=1.0/big;  
   }  int estepm;
   for (j=1;j<=n;j++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     for (i=1;i<j;i++) {  
       sum=a[i][j];  int m,nb;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  long *num;
       a[i][j]=sum;  int firstpass=0, lastpass=4,*cod, *cens;
     }  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
     big=0.0;                     covariate for which somebody answered excluding 
     for (i=j;i<=n;i++) {                     undefined. Usually 2: 0 and 1. */
       sum=a[i][j];  int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
       for (k=1;k<j;k++)                               covariate for which somebody answered including 
         sum -= a[i][k]*a[k][j];                               undefined. Usually 3: -1, 0 and 1. */
       a[i][j]=sum;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if ( (dum=vv[i]*fabs(sum)) >= big) {  double **pmmij, ***probs; /* Global pointer */
         big=dum;  double ***mobaverage, ***mobaverages; /* New global variable */
         imax=i;  double *ageexmed,*agecens;
       }  double dateintmean=0;
     }  
     if (j != imax) {  double *weight;
       for (k=1;k<=n;k++) {  int **s; /* Status */
         dum=a[imax][k];  double *agedc;
         a[imax][k]=a[j][k];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         a[j][k]=dum;                    * covar=matrix(0,NCOVMAX,1,n); 
       }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
       *d = -(*d);  double **coqvar; /* Fixed quantitative covariate iqv */
       vv[imax]=vv[j];  double ***cotvar; /* Time varying covariate itv */
     }  double ***cotqvar; /* Time varying quantitative covariate itqv */
     indx[j]=imax;  double  idx; 
     if (a[j][j] == 0.0) a[j][j]=TINY;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     if (j != n) {  int *Tvarsel; /**< Selected covariates for output */
       dum=1.0/(a[j][j]);  double *Tvalsel; /**< Selected modality value of covariate for output */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  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 */ 
   free_vector(vv,1,n);  /* Doesn't work */  int *Tage;
 ;  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
 }  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/ 
 void lubksb(double **a, int n, int *indx, double b[])  int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
 {  int *Ndum; /** Freq of modality (tricode */
   int i,ii=0,ip,j;  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
   double sum;  int **Tvard;
    int *Tprod;/**< Gives the k position of the k1 product */
   for (i=1;i<=n;i++) {  int *Tposprod; /**< Gives the k1 product from the k position */
     ip=indx[i];  /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
     sum=b[ip];     if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     b[ip]=b[i];     Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
     if (ii)  */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  int cptcovprod, *Tvaraff, *invalidvarcomb;
     else if (sum) ii=i;  double *lsurv, *lpop, *tpop;
     b[i]=sum;  
   }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for (i=n;i>=1;i--) {  double ftolhess; /**< Tolerance for computing hessian */
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /**************** split *************************/
     b[i]=sum/a[i][i];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   }  {
 }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /************ Frequencies ********************/    */ 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)    char  *ss;                            /* pointer */
 {  /* Some frequencies */    int   l1=0, l2=0;                             /* length counters */
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    l1 = strlen(path );                   /* length of path */
   double ***freq; /* Frequencies */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double *pp;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double pos;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   FILE *ficresp;      strcpy( name, path );               /* we got the fullname name because no directory */
   char fileresp[FILENAMELENGTH];      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   pp=vector(1,nlstate);      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
   strcpy(fileresp,"p");  #ifdef WIN32
   strcat(fileresp,fileres);      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if((ficresp=fopen(fileresp,"w"))==NULL) {  #else
     printf("Problem with prevalence resultfile: %s\n", fileresp);          if (getcwd(dirc, FILENAME_MAX) == NULL) {
     exit(0);  #endif
   }        return( GLOCK_ERROR_GETCWD );
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
   j=cptcovn;    } else {                              /* strip directory from path */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
   for(k1=1; k1<=j;k1++){      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
    for(i1=1; i1<=ncodemax[k1];i1++){      strcpy( name, ss );         /* save file name */
        j1++;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = '\0';                 /* add zero */
         for (i=-1; i<=nlstate+ndeath; i++)        printf(" DIRC2 = %s \n",dirc);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      }
            for(m=agemin; m <= agemax+3; m++)    /* We add a separator at the end of dirc if not exists */
              freq[i][jk][m]=0;    l1 = strlen( dirc );                  /* length of directory */
            if( dirc[l1-1] != DIRSEPARATOR ){
        for (i=1; i<=imx; i++) {      dirc[l1] =  DIRSEPARATOR;
          bool=1;      dirc[l1+1] = 0; 
          if  (cptcovn>0) {      printf(" DIRC3 = %s \n",dirc);
            for (z1=1; z1<=cptcovn; z1++)    }
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;    ss = strrchr( name, '.' );            /* find last / */
          }    if (ss >0){
           if (bool==1) {      ss++;
            for(m=firstpass; m<=lastpass-1; m++){      strcpy(ext,ss);                     /* save extension */
              if(agev[m][i]==0) agev[m][i]=agemax+1;      l1= strlen( name);
              if(agev[m][i]==1) agev[m][i]=agemax+2;      l2= strlen(ss)+1;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      strncpy( finame, name, l1-l2);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      finame[l1-l2]= 0;
            }    }
          }  
        }    return( 0 );                          /* we're done */
         if  (cptcovn>0) {  }
          fprintf(ficresp, "\n#Variable");  
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);  
        }  /******************************************/
        fprintf(ficresp, "\n#");  
        for(i=1; i<=nlstate;i++)  void replace_back_to_slash(char *s, char*t)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
        fprintf(ficresp, "\n");    int i;
            int lg=0;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    i=0;
     if(i==(int)agemax+3)    lg=strlen(t);
       printf("Total");    for(i=0; i<= lg; i++) {
     else      (s[i] = t[i]);
       printf("Age %d", i);      if (t[i]== '\\') s[i]='/';
     for(jk=1; jk <=nlstate ; jk++){    }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  char *trimbb(char *out, char *in)
     for(jk=1; jk <=nlstate ; jk++){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       for(m=-1, pos=0; m <=0 ; m++)    char *s;
         pos += freq[jk][m][i];    s=out;
       if(pp[jk]>=1.e-10)    while (*in != '\0'){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       else        in++;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      }
     }      *out++ = *in++;
     for(jk=1; jk <=nlstate ; jk++){    }
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    *out='\0';
         pp[jk] += freq[jk][m][i];    return s;
     }  }
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];  /* char *substrchaine(char *out, char *in, char *chain) */
     for(jk=1; jk <=nlstate ; jk++){  /* { */
       if(pos>=1.e-5)  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*   char *s, *t; */
       else  /*   t=in;s=out; */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*   while ((*in != *chain) && (*in != '\0')){ */
       if( i <= (int) agemax){  /*     *out++ = *in++; */
         if(pos>=1.e-5)  /*   } */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
       else  /*   /\* *in matches *chain *\/ */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /*   while ((*in++ == *chain++) && (*in != '\0')){ */
       }  /*     printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     }  /*   } */
     for(jk=-1; jk <=nlstate+ndeath; jk++)  /*   in--; chain--; */
       for(m=-1; m <=nlstate+ndeath; m++)  /*   while ( (*in != '\0')){ */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*     printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     if(i <= (int) agemax)  /*     *out++ = *in++; */
       fprintf(ficresp,"\n");  /*     printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain);  */
     printf("\n");  /*   } */
     }  /*   *out='\0'; */
     }  /*   out=s; */
  }  /*   return out; */
    /* } */
   fclose(ficresp);  char *substrchaine(char *out, char *in, char *chain)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  {
   free_vector(pp,1,nlstate);    /* Substract chain 'chain' from 'in', return and output 'out' */
     /* in="V1+V1*age+age*age+V2", chain="age*age" */
 }  /* End of Freq */  
     char *strloc;
 /************* Waves Concatenation ***************/  
     strcpy (out, in); 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
 {    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    if(strloc != NULL){ 
      Death is a valid wave (if date is known).      /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      /* strcpy (strloc, strloc +strlen(chain));*/
      and mw[mi+1][i]. dh depends on stepm.    }
      */    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
     return out;
   int i, mi, m;  }
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
 float sum=0.;  
   char *cutl(char *blocc, char *alocc, char *in, char occ)
   for(i=1; i<=imx; i++){  {
     mi=0;    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
     m=firstpass;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     while(s[m][i] <= nlstate){       gives blocc="abcdef" and alocc="ghi2j".
       if(s[m][i]>=1)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         mw[++mi][i]=m;    */
       if(m >=lastpass)    char *s, *t;
         break;    t=in;s=in;
       else    while ((*in != occ) && (*in != '\0')){
         m++;      *alocc++ = *in++;
     }/* end while */    }
     if (s[m][i] > nlstate){    if( *in == occ){
       mi++;     /* Death is another wave */      *(alocc)='\0';
       /* if(mi==0)  never been interviewed correctly before death */      s=++in;
          /* Only death is a correct wave */    }
       mw[mi][i]=m;   
     }    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
     wav[i]=mi;      in=s;
     if(mi==0)    }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    while ( *in != '\0'){
   }      *blocc++ = *in++;
     }
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    *blocc='\0';
       if (stepm <=0)    return t;
         dh[mi][i]=1;  }
       else{  char *cutv(char *blocc, char *alocc, char *in, char occ)
         if (s[mw[mi+1][i]][i] > nlstate) {  {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ' 
           if(j=0) j=1;  /* Survives at least one month after exam */       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         }       gives blocc="abcdef2ghi" and alocc="j".
         else{       If occ is not found blocc is null and alocc is equal to in. Returns alocc
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    */
           /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/    char *s, *t;
     t=in;s=in;
           k=k+1;    while (*in != '\0'){
           if (j >= jmax) jmax=j;      while( *in == occ){
           else if (j <= jmin)jmin=j;        *blocc++ = *in++;
           sum=sum+j;        s=in;
         }      }
         jk= j/stepm;      *blocc++ = *in++;
         jl= j -jk*stepm;    }
         ju= j -(jk+1)*stepm;    if (s == t) /* occ not found */
         if(jl <= -ju)      *(blocc-(in-s))='\0';
           dh[mi][i]=jk;    else
         else      *(blocc-(in-s)-1)='\0';
           dh[mi][i]=jk+1;    in=s;
         if(dh[mi][i]==0)    while ( *in != '\0'){
           dh[mi][i]=1; /* At least one step */      *alocc++ = *in++;
       }    }
     }  
   }    *alocc='\0';
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    return s;
 }  }
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  int nbocc(char *s, char occ)
 {  {
   int Ndum[80],ij, k, j, i;    int i,j=0;
   int cptcode=0;    int lg=20;
   for (k=0; k<79; k++) Ndum[k]=0;    i=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
   for (j=1; j<=cptcovn; j++) {    if  (s[i] == occ ) j++;
     for (i=1; i<=imx; i++) {    }
       ij=(int)(covar[Tvar[j]][i]);    return j;
       Ndum[ij]++;  }
       if (ij > cptcode) cptcode=ij;  
     }  /* void cutv(char *u,char *v, char*t, char occ) */
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/  /* { */
     for (i=0; i<=cptcode; i++) {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       if(Ndum[i]!=0) ncodemax[j]++;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
    /*   int i,lg,j,p=0; */
     ij=1;  /*   i=0; */
     for (i=1; i<=ncodemax[j]; i++) {  /*   lg=strlen(t); */
       for (k=0; k<=79; k++) {  /*   for(j=0; j<=lg-1; j++) { */
         if (Ndum[k] != 0) {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
           nbcode[Tvar[j]][ij]=k;  /*   } */
           ij++;  
         }  /*   for(j=0; j<p; j++) { */
         if (ij > ncodemax[j]) break;  /*     (u[j] = t[j]); */
       }    /*   } */
     }  /*      u[p]='\0'; */
   }    
   /*    for(j=0; j<= lg; j++) { */
   }  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
 /*********** Health Expectancies ****************/  /* } */
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  #ifdef _WIN32
 {  char * strsep(char **pp, const char *delim)
   /* Health expectancies */  {
   int i, j, nhstepm, hstepm, h;    char *p, *q;
   double age, agelim,hf;           
   double ***p3mat;    if ((p = *pp) == NULL)
        return 0;
   fprintf(ficreseij,"# Health expectancies\n");    if ((q = strpbrk (p, delim)) != NULL)
   fprintf(ficreseij,"# Age");    {
   for(i=1; i<=nlstate;i++)      *pp = q + 1;
     for(j=1; j<=nlstate;j++)      *q = '\0';
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");    else
       *pp = 0;
   hstepm=1*YEARM; /*  Every j years of age (in month) */    return p;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  }
   #endif
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /********************** nrerror ********************/
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  void nrerror(char error_text[])
     /* Typically if 20 years = 20*12/6=40 stepm */  {
     if (stepm >= YEARM) hstepm=1;    fprintf(stderr,"ERREUR ...\n");
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    fprintf(stderr,"%s\n",error_text);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    exit(EXIT_FAILURE);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  /*********************** vector *******************/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    double *vector(int nl, int nh)
   {
     double *v;
     for(i=1; i<=nlstate;i++)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       for(j=1; j<=nlstate;j++)    if (!v) nrerror("allocation failure in vector");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    return v-nl+NR_END;
           eij[i][j][(int)age] +=p3mat[i][j][h];  }
         }  
      /************************ free vector ******************/
     hf=1;  void free_vector(double*v, int nl, int nh)
     if (stepm >= YEARM) hf=stepm/YEARM;  {
     fprintf(ficreseij,"%.0f",age );    free((FREE_ARG)(v+nl-NR_END));
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  /************************ivector *******************************/
       }  int *ivector(long nl,long nh)
     fprintf(ficreseij,"\n");  {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int *v;
   }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /************ Variance ******************/  }
 void varevsij(char fileres[], 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)  
 {  /******************free ivector **************************/
   /* Variance of health expectancies */  void free_ivector(int *v, long nl, long nh)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  {
   double **newm;    free((FREE_ARG)(v+nl-NR_END));
   double **dnewm,**doldm;  }
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;  /************************lvector *******************************/
    double *xp;  long *lvector(long nl,long nh)
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    long *v;
   double ***p3mat;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double age,agelim;    if (!v) nrerror("allocation failure in ivector");
   int theta;    return v-nl+NR_END;
   }
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");  /******************free lvector **************************/
   for(i=1; i<=nlstate;i++)  void free_lvector(long *v, long nl, long nh)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    free((FREE_ARG)(v+nl-NR_END));
   fprintf(ficresvij,"\n");  }
   
   xp=vector(1,npar);  /******************* imatrix *******************************/
   dnewm=matrix(1,nlstate,1,npar);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   doldm=matrix(1,nlstate,1,nlstate);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   hstepm=1*YEARM; /* Every year of age */    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int **m; 
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* allocate pointers to rows */ 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (stepm >= YEARM) hstepm=1;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    m += NR_END; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    m -= nrl; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for(theta=1; theta <=npar; theta++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for(i=1; i<=npar; i++){ /* Computes gradient */    m[nrl] += NR_END; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    m[nrl] -= ncl; 
       }    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       for(j=1; j<= nlstate; j++){    /* return pointer to array of pointers to rows */ 
         for(h=0; h<=nhstepm; h++){    return m; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  } 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /****************** free_imatrix *************************/
       }  void free_imatrix(m,nrl,nrh,ncl,nch)
            int **m;
       for(i=1; i<=npar; i++) /* Computes gradient */        long nch,ncl,nrh,nrl; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       /* free an int matrix allocated by imatrix() */ 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for(j=1; j<= nlstate; j++){    free((FREE_ARG) (m+nrl-NR_END)); 
         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];  /******************* matrix *******************************/
         }  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
       for(j=1; j<= nlstate; j++)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         for(h=0; h<=nhstepm; h++){    double **m;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } /* End theta */    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    m -= nrl;
   
     for(h=0; h<=nhstepm; h++)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for(j=1; j<=nlstate;j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         for(theta=1; theta <=npar; theta++)    m[nrl] += NR_END;
           trgradg[h][j][theta]=gradg[h][theta][j];    m[nrl] -= ncl;
   
     for(i=1;i<=nlstate;i++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for(j=1;j<=nlstate;j++)    return m;
         vareij[i][j][(int)age] =0.;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     for(h=0;h<=nhstepm;h++){  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       for(k=0;k<=nhstepm;k++){  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
         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++)  /*************************free matrix ************************/
             vareij[i][j][(int)age] += doldm[i][j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     h=1;    free((FREE_ARG)(m+nrl-NR_END));
     if (stepm >= YEARM) h=stepm/YEARM;  }
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /******************* ma3x *******************************/
       for(j=1; j<=nlstate;j++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     fprintf(ficresvij,"\n");    double ***m;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    if (!m) nrerror("allocation failure 1 in matrix()");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    m += NR_END;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    m -= nrl;
   } /* End age */  
      m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free_vector(xp,1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_matrix(doldm,1,nlstate,1,npar);    m[nrl] += NR_END;
   free_matrix(dnewm,1,nlstate,1,nlstate);    m[nrl] -= ncl;
   
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 /************ Variance of prevlim ******************/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 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)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   /* Variance of prevalence limit */    m[nrl][ncl] -= nll;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (j=ncl+1; j<=nch; j++) 
   double **newm;      m[nrl][j]=m[nrl][j-1]+nlay;
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;    for (i=nrl+1; i<=nrh; i++) {
   int k, cptcode;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double *xp;      for (j=ncl+1; j<=nch; j++) 
   double *gp, *gm;        m[i][j]=m[i][j-1]+nlay;
   double **gradg, **trgradg;    }
   double age,agelim;    return m; 
   int theta;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                 &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    */
   fprintf(ficresvpl,"# Age");  }
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  /*************************free ma3x ************************/
   fprintf(ficresvpl,"\n");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
   xp=vector(1,npar);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   dnewm=matrix(1,nlstate,1,npar);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   doldm=matrix(1,nlstate,1,nlstate);    free((FREE_ARG)(m+nrl-NR_END));
    }
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /*************** function subdirf ***********/
   agelim = AGESUP;  char *subdirf(char fileres[])
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* Caution optionfilefiname is hidden */
     if (stepm >= YEARM) hstepm=1;    strcpy(tmpout,optionfilefiname);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    strcat(tmpout,"/"); /* Add to the right */
     gradg=matrix(1,npar,1,nlstate);    strcat(tmpout,fileres);
     gp=vector(1,nlstate);    return tmpout;
     gm=vector(1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /*************** function subdirf2 ***********/
       for(i=1; i<=npar; i++){ /* Computes gradient */  char *subdirf2(char fileres[], char *preop)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Caution optionfilefiname is hidden */
       for(i=1;i<=nlstate;i++)    strcpy(tmpout,optionfilefiname);
         gp[i] = prlim[i][i];    strcat(tmpout,"/");
        strcat(tmpout,preop);
       for(i=1; i<=npar; i++) /* Computes gradient */    strcat(tmpout,fileres);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return tmpout;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
       for(i=1;i<=nlstate;i++)  {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    
     } /* End theta */    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     trgradg =matrix(1,nlstate,1,npar);    strcat(tmpout,"/");
     strcat(tmpout,preop);
     for(j=1; j<=nlstate;j++)    strcat(tmpout,preop2);
       for(theta=1; theta <=npar; theta++)    strcat(tmpout,fileres);
         trgradg[j][theta]=gradg[theta][j];    return tmpout;
   }
     for(i=1;i<=nlstate;i++)   
       varpl[i][(int)age] =0.;  /*************** function subdirfext ***********/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  char *subdirfext(char fileres[], char *preop, char *postop)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  {
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    strcpy(tmpout,preop);
     strcat(tmpout,fileres);
     fprintf(ficresvpl,"%.0f ",age );    strcat(tmpout,postop);
     for(i=1; i<=nlstate;i++)    return tmpout;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);  /*************** function subdirfext3 ***********/
     free_vector(gm,1,nlstate);  char *subdirfext3(char fileres[], char *preop, char *postop)
     free_matrix(gradg,1,npar,1,nlstate);  {
     free_matrix(trgradg,1,nlstate,1,npar);    
   } /* End age */    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   free_vector(xp,1,npar);    strcat(tmpout,"/");
   free_matrix(doldm,1,nlstate,1,npar);    strcat(tmpout,preop);
   free_matrix(dnewm,1,nlstate,1,nlstate);    strcat(tmpout,fileres);
     strcat(tmpout,postop);
 }    return tmpout;
   }
    
   char *asc_diff_time(long time_sec, char ascdiff[])
 /***********************************************/  {
 /**************** Main Program *****************/    long sec_left, days, hours, minutes;
 /***********************************************/    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 /*int main(int argc, char *argv[])*/    hours = (sec_left) / (60*60) ;
 int main()    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   double agedeb, agefin,hf;    return ascdiff;
   double agemin=1.e20, agemax=-1.e20;  }
   
   double fret;  /***************** f1dim *************************/
   double **xi,tmp,delta;  extern int ncom; 
   extern double *pcom,*xicom;
   double dum; /* Dummy variable */  extern double (*nrfunc)(double []); 
   double ***p3mat;   
   int *indx;  double f1dim(double x) 
   char line[MAXLINE], linepar[MAXLINE];  { 
   char title[MAXLINE];    int j; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    double f;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    double *xt; 
   char filerest[FILENAMELENGTH];   
   char fileregp[FILENAMELENGTH];    xt=vector(1,ncom); 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int firstobs=1, lastobs=10;    f=(*nrfunc)(xt); 
   int sdeb, sfin; /* Status at beginning and end */    free_vector(xt,1,ncom); 
   int c,  h , cpt,l;    return f; 
   int ju,jl, mi;  } 
   int i1,j1, k1,jk,aa,bb, stepsize;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   int hstepm, nhstepm;  {
   double bage, fage, age, agelim, agebase;    /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
   double ftolpl=FTOL;     * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
   double **prlim;     * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
   double *severity;     * the minimum is returned as xmin, and the minimum function value is returned as brent , the
   double ***param; /* Matrix of parameters */     * returned function value. 
   double  *p;    */
   double **matcov; /* Matrix of covariance */    int iter; 
   double ***delti3; /* Scale */    double a,b,d,etemp;
   double *delti; /* Scale */    double fu=0,fv,fw,fx;
   double ***eij, ***vareij;    double ftemp=0.;
   double **varpl; /* Variances of prevalence limits by age */    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double *epj, vepp;    double e=0.0; 
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    a=(ax < cx ? ax : cx); 
   char z[1]="c", occ;    b=(ax > cx ? ax : cx); 
 #include <sys/time.h>    x=w=v=bx; 
 #include <time.h>    fw=fv=fx=(*f)(x); 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    for (iter=1;iter<=ITMAX;iter++) { 
   /* long total_usecs;      xm=0.5*(a+b); 
   struct timeval start_time, end_time;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUGBRENT
   printf("\nIMACH, Version 0.63");      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   printf("\nEnter the parameter file name: ");      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #ifdef windows  #endif
   scanf("%s",pathtot);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   getcwd(pathcd, size);        *xmin=x; 
   cutv(path,optionfile,pathtot,'\\');        return fx; 
   chdir(path);      } 
   replace(pathc,path);      ftemp=fu;
 #endif      if (fabs(e) > tol1) { 
 #ifdef unix        r=(x-w)*(fx-fv); 
   scanf("%s",optionfile);        q=(x-v)*(fx-fw); 
 #endif        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /*-------- arguments in the command line --------*/        if (q > 0.0) p = -p; 
         q=fabs(q); 
   strcpy(fileres,"r");        etemp=e; 
   strcat(fileres, optionfile);        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   /*---------arguments file --------*/                                  d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                                  d=p/q; 
     printf("Problem with optionfile %s\n",optionfile);                                  u=x+d; 
     goto end;                                  if (u-a < tol2 || b-u < tol2) 
   }                                          d=SIGN(tol1,xm-x); 
         } 
   strcpy(filereso,"o");      } else { 
   strcat(filereso,fileres);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   if((ficparo=fopen(filereso,"w"))==NULL) {      } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   }      fu=(*f)(u); 
       if (fu <= fx) { 
   /* Reads comments: lines beginning with '#' */        if (u >= x) a=x; else b=x; 
   while((c=getc(ficpar))=='#' && c!= EOF){        SHFT(v,w,x,u) 
     ungetc(c,ficpar);        SHFT(fv,fw,fx,fu) 
     fgets(line, MAXLINE, ficpar);      } else { 
     puts(line);        if (u < x) a=u; else b=u; 
     fputs(line,ficparo);        if (fu <= fw || w == x) { 
   }                                  v=w; 
   ungetc(c,ficpar);                                  w=u; 
                                   fv=fw; 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                                  fw=fu; 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        } else if (fu <= fv || v == x || v == w) { 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);                                  v=u; 
                                   fv=fu; 
   covar=matrix(1,NCOVMAX,1,n);            } 
   if (strlen(model)<=1) cptcovn=0;      } 
   else {    } 
     j=0;    nrerror("Too many iterations in brent"); 
     j=nbocc(model,'+');    *xmin=x; 
     cptcovn=j+1;    return fx; 
   }  } 
   
   ncovmodel=2+cptcovn;  /****************** mnbrak ***********************/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   /* Read guess parameters */              double (*func)(double)) 
   /* Reads comments: lines beginning with '#' */  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
   while((c=getc(ficpar))=='#' && c!= EOF){  the downhill direction (defined by the function as evaluated at the initial points) and returns
     ungetc(c,ficpar);  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
     fgets(line, MAXLINE, ficpar);  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
     puts(line);     */
     fputs(line,ficparo);    double ulim,u,r,q, dum;
   }    double fu; 
   ungetc(c,ficpar);  
      double scale=10.;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    int iterscale=0;
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    *fa=(*func)(*ax); /*  xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    *fb=(*func)(*bx); /*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
         fscanf(ficpar," %lf",&param[i][j][k]);    /*   printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
         printf(" %lf",param[i][j][k]);    /*   *bx = *ax - (*ax - *bx)/scale; */
         fprintf(ficparo," %lf",param[i][j][k]);    /*   *fb=(*func)(*bx);  /\*  xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
       }    /* } */
       fscanf(ficpar,"\n");  
       printf("\n");    if (*fb > *fa) { 
       fprintf(ficparo,"\n");      SHFT(dum,*ax,*bx,dum) 
     }      SHFT(dum,*fb,*fa,dum) 
      } 
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    *cx=(*bx)+GOLD*(*bx-*ax); 
   p=param[1][1];    *fc=(*func)(*cx); 
    #ifdef DEBUG
   /* Reads comments: lines beginning with '#' */    printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
     ungetc(c,ficpar);  #endif
     fgets(line, MAXLINE, ficpar);    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
     puts(line);      r=(*bx-*ax)*(*fb-*fc); 
     fputs(line,ficparo);      q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
   }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   ungetc(c,ficpar);        (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 */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        fu=(*func)(u); 
   for(i=1; i <=nlstate; i++){  #ifdef DEBUG
     for(j=1; j <=nlstate+ndeath-1; j++){        /* f(x)=A(x-u)**2+f(u) */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        double A, fparabu; 
       printf("%1d%1d",i,j);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       fprintf(ficparo,"%1d%1d",i1,j1);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       for(k=1; k<=ncovmodel;k++){        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);
         fscanf(ficpar,"%le",&delti3[i][j][k]);        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);
         printf(" %le",delti3[i][j][k]);        /* And thus,it can be that fu > *fc even if fparabu < *fc */
         fprintf(ficparo," %le",delti3[i][j][k]);        /* 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) */
       fscanf(ficpar,"\n");        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
       printf("\n");  #endif 
       fprintf(ficparo,"\n");  #ifdef MNBRAKORIGINAL
     }  #else
   }  /*       if (fu > *fc) { */
   delti=delti3[1][1];  /* #ifdef DEBUG */
    /*       printf("mnbrak4  fu > fc \n"); */
   /* Reads comments: lines beginning with '#' */  /*       fprintf(ficlog, "mnbrak4 fu > fc\n"); */
   while((c=getc(ficpar))=='#' && c!= EOF){  /* #endif */
     ungetc(c,ficpar);  /*      /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/  *\/ */
     fgets(line, MAXLINE, ficpar);  /*      /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\\/ *\/ */
     puts(line);  /*      dum=u; /\* Shifting c and u *\/ */
     fputs(line,ficparo);  /*      u = *cx; */
   }  /*      *cx = dum; */
   ungetc(c,ficpar);  /*      dum = fu; */
    /*      fu = *fc; */
   matcov=matrix(1,npar,1,npar);  /*      *fc =dum; */
   for(i=1; i <=npar; i++){  /*       } else { /\* end *\/ */
     fscanf(ficpar,"%s",&str);  /* #ifdef DEBUG */
     printf("%s",str);  /*       printf("mnbrak3  fu < fc \n"); */
     fprintf(ficparo,"%s",str);  /*       fprintf(ficlog, "mnbrak3 fu < fc\n"); */
     for(j=1; j <=i; j++){  /* #endif */
       fscanf(ficpar," %le",&matcov[i][j]);  /*      dum=u; /\* Shifting c and u *\/ */
       printf(" %.5le",matcov[i][j]);  /*      u = *cx; */
       fprintf(ficparo," %.5le",matcov[i][j]);  /*      *cx = dum; */
     }  /*      dum = fu; */
     fscanf(ficpar,"\n");  /*      fu = *fc; */
     printf("\n");  /*      *fc =dum; */
     fprintf(ficparo,"\n");  /*       } */
   }  #ifdef DEBUGMNBRAK
   for(i=1; i <=npar; i++)                   double A, fparabu; 
     for(j=i+1;j<=npar;j++)       A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
       matcov[i][j]=matcov[j][i];       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);
   printf("\n");       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
         dum=u; /* Shifting c and u */
    if(mle==1){        u = *cx;
     /*-------- data file ----------*/        *cx = dum;
     if((ficres =fopen(fileres,"w"))==NULL) {        dum = fu;
       printf("Problem with resultfile: %s\n", fileres);goto end;        fu = *fc;
     }        *fc =dum;
     fprintf(ficres,"#%s\n",version);  #endif
          } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
     if((fic=fopen(datafile,"r"))==NULL)    {  #ifdef DEBUG
       printf("Problem with datafile: %s\n", datafile);goto end;        printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
     }        fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
   #endif
     n= lastobs;        fu=(*func)(u); 
     severity = vector(1,maxwav);        if (fu < *fc) { 
     outcome=imatrix(1,maxwav+1,1,n);  #ifdef DEBUG
     num=ivector(1,n);                                  printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
     moisnais=vector(1,n);                            fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
     annais=vector(1,n);  #endif
     moisdc=vector(1,n);                            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     andc=vector(1,n);                                  SHFT(*fb,*fc,fu,(*func)(u)) 
     agedc=vector(1,n);  #ifdef DEBUG
     cod=ivector(1,n);                                          printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
     weight=vector(1,n);  #endif
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        } 
     mint=matrix(1,maxwav,1,n);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
     anint=matrix(1,maxwav,1,n);  #ifdef DEBUG
     s=imatrix(1,maxwav+1,1,n);        printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
     tab=ivector(1,NCOVMAX);  #endif
     ncodemax=ivector(1,NCOVMAX);        u=ulim; 
         fu=(*func)(u); 
     i=1;      } else { /* u could be left to b (if r > q parabola has a maximum) */
     while (fgets(line, MAXLINE, fic) != NULL)    {  #ifdef DEBUG
       if ((i >= firstobs) && (i <=lastobs)) {        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,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
         for (j=maxwav;j>=1;j--){  #endif
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        u=(*cx)+GOLD*(*cx-*bx); 
           strcpy(line,stra);        fu=(*func)(u); 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  #ifdef DEBUG
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        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
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* end tests */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      SHFT(*ax,*bx,*cx,u) 
       SHFT(*fa,*fb,*fc,fu) 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  #ifdef DEBUG
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
         fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  #endif
         for (j=ncov;j>=1;j--){    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  } 
         }  
         num[i]=atol(stra);  /*************** linmin ************************/
   /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         /* printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         /*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]));*/  the value of func at the returned location p . This is actually all accomplished by calling the
   routines mnbrak and brent .*/
         i=i+1;  int ncom; 
       }  double *pcom,*xicom;
     }  double (*nrfunc)(double []); 
     /*scanf("%d",i);*/   
   #ifdef LINMINORIGINAL
   imx=i-1; /* Number of individuals */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
    #else
   /* Calculation of the number of parameter from char model*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat) 
   Tvar=ivector(1,8);      #endif
      { 
   if (strlen(model) >1){    double brent(double ax, double bx, double cx, 
     j=0;                 double (*f)(double), double tol, double *xmin); 
     j=nbocc(model,'+');    double f1dim(double x); 
     cptcovn=j+1;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                  double *fc, double (*func)(double)); 
     strcpy(modelsav,model);    int j; 
     if (j==0) {    double xx,xmin,bx,ax; 
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    double fx,fb,fa;
     }  
     else {  #ifdef LINMINORIGINAL
       for(i=j; i>=1;i--){  #else
         cutv(stra,strb,modelsav,'+');    double scale=10., axs, xxs; /* Scale added for infinity */
         if (strchr(strb,'*')) {  #endif
           cutv(strd,strc,strb,'*');    
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;    ncom=n; 
           cutv(strb,strc,strd,'V');    pcom=vector(1,n); 
           for (k=1; k<=lastobs;k++)    xicom=vector(1,n); 
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    nrfunc=func; 
         }    for (j=1;j<=n;j++) { 
         else {      pcom[j]=p[j]; 
           cutv(strd,strc,strb,'V');      xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
           Tvar[i+1]=atoi(strc);    } 
         }  
         strcpy(modelsav,stra);    #ifdef LINMINORIGINAL
       }    xx=1.;
       /*cutv(strd,strc,stra,'V');*/  #else
       Tvar[1]=atoi(strc);    axs=0.0;
     }    xxs=1.;
   }    do{
   /*printf("tvar=%d ",Tvar[1]);*/      xx= xxs;
   /*scanf("%d ",i);*/  #endif
     fclose(fic);      ax=0.;
       mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
     if (weightopt != 1) { /* Maximisation without weights*/      /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
       for(i=1;i<=n;i++) weight[i]=1.0;      /* 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))   */
     }      /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
     /*-calculation of age at interview from date of interview and age at death -*/      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
     agev=matrix(1,maxwav,1,imx);      /* 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]]*/
     for (i=1; i<=imx; i++)  {  #ifdef LINMINORIGINAL
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  #else
       for(m=1; (m<= maxwav); m++){      if (fx != fx){
         if (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1;                            xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
         if(s[m][i] >0){                          printf("|");
           if (s[m][i] == nlstate+1) {                          fprintf(ficlog,"|");
             if(agedc[i]>0)  #ifdef DEBUGLINMIN
               if(moisdc[i]!=99 && andc[i]!=9999)                          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);
               agev[m][i]=agedc[i];  #endif
             else{      }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    }while(fx != fx && xxs > 1.e-5);
               agev[m][i]=-1;  #endif
             }    
           }  #ifdef DEBUGLINMIN
           else if(s[m][i] !=9){ /* Should no more exist */    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);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    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);
             if(mint[m][i]==99 || anint[m][i]==9999){  #endif
               agev[m][i]=1;  #ifdef LINMINORIGINAL
               /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]);    */  #else
             }          if(fb == fx){ /* Flat function in the direction */
             else if(agev[m][i] <agemin){                  xmin=xx;
               agemin=agev[m][i];      *flat=1;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          }else{
             }      *flat=0;
             else if(agev[m][i] >agemax){  #endif
               agemax=agev[m][i];                  /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    *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]) */
             /*agev[m][i]=anint[m][i]-annais[i];*/    /* fmin = f(p[j] + xmin * xi[j]) */
             /*   agev[m][i] = age[i]+2*m;*/    /* 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]; */
           else { /* =9 */  #ifdef DEBUG
             agev[m][i]=1;    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);
             s[m][i]=-1;    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 /*= 0 Unknown */  #else
           agev[m][i]=1;                          }
       }  #endif
      #ifdef DEBUGLINMIN
     }    printf("linmin end ");
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"linmin end ");
       for(m=1; (m<= maxwav); m++){  #endif
         if (s[m][i] > (nlstate+ndeath)) {    for (j=1;j<=n;j++) { 
           printf("Error: Wrong value in nlstate or ndeath\n");    #ifdef LINMINORIGINAL
           goto end;      xi[j] *= xmin; 
         }  #else
       }  #ifdef DEBUGLINMIN
     }      if(xxs <1.0)
         printf(" before xi[%d]=%12.8f", j,xi[j]);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  #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) */
     free_vector(severity,1,maxwav);  #ifdef DEBUGLINMIN
     free_imatrix(outcome,1,maxwav+1,1,n);      if(xxs <1.0)
     free_vector(moisnais,1,n);        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 );
     free_vector(annais,1,n);  #endif
     free_matrix(mint,1,maxwav,1,n);  #endif
     free_matrix(anint,1,maxwav,1,n);      p[j] += xi[j]; /* Parameters values are updated accordingly */
     free_vector(moisdc,1,n);    } 
     free_vector(andc,1,n);  #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));
     wav=ivector(1,imx);    fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    for (j=1;j<=n;j++) { 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
          fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
     /* Concatenates waves */      if(j % ncovmodel == 0){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        printf("\n");
         fprintf(ficlog,"\n");
       }
 Tcode=ivector(1,100);    }
    nbcode=imatrix(1,nvar,1,8);    #else
    ncodemax[1]=1;  #endif
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
    codtab=imatrix(1,100,1,10);  } 
    h=0;  
    m=pow(2,cptcovn);  
    /*************** powell ************************/
    for(k=1;k<=cptcovn; k++){  /*
      for(i=1; i <=(m/pow(2,k));i++){  Minimization of a function func of n variables. Input consists of an initial starting point
        for(j=1; j <= ncodemax[k]; j++){  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
            h++;  such that failure to decrease by more than this amount on one iteration signals doneness. On
            if (h>m) h=1;codtab[h][k]=j;  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.
        }   */
      }  #ifdef LINMINORIGINAL
    }  #else
           int *flatdir; /* Function is vanishing in that direction */
    /*for(i=1; i <=m ;i++){          int flat=0, flatd=0; /* Function is vanishing in that direction */
      for(k=1; k <=cptcovn; k++){  #endif
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
      }              double (*func)(double [])) 
      printf("\n");  { 
    }  #ifdef LINMINORIGINAL
   scanf("%d",i);*/   void linmin(double p[], double xi[], int n, double *fret, 
                    double (*func)(double [])); 
    /* Calculates basic frequencies. Computes observed prevalence at single age  #else 
        and prints on file fileres'p'. */   void linmin(double p[], double xi[], int n, double *fret, 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                                                   double (*func)(double []),int *flat); 
   #endif
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i,ibig,j; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double del,t,*pt,*ptt,*xit;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double directest;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double fp,fptt;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double *xits;
        int niterf, itmp;
     /* For Powell, parameters are in a vector p[] starting at p[1]  #ifdef LINMINORIGINAL
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  #else
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
     /*scanf("%d",i);*/    flatdir=ivector(1,n); 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    for (j=1;j<=n;j++) flatdir[j]=0; 
   #endif
      
     /*--------- results files --------------*/    pt=vector(1,n); 
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    ptt=vector(1,n); 
        xit=vector(1,n); 
    jk=1;    xits=vector(1,n); 
    fprintf(ficres,"# Parameters\n");    *fret=(*func)(p); 
    printf("# Parameters\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
    for(i=1,jk=1; i <=nlstate; i++){    rcurr_time = time(NULL);  
      for(k=1; k <=(nlstate+ndeath); k++){    for (*iter=1;;++(*iter)) { 
        if (k != i)      fp=(*fret); /* From former iteration or initial value */
          {      ibig=0; 
            printf("%d%d ",i,k);      del=0.0; 
            fprintf(ficres,"%1d%1d ",i,k);      rlast_time=rcurr_time;
            for(j=1; j <=ncovmodel; j++){      /* (void) gettimeofday(&curr_time,&tzp); */
              printf("%f ",p[jk]);      rcurr_time = time(NULL);  
              fprintf(ficres,"%f ",p[jk]);      curr_time = *localtime(&rcurr_time);
              jk++;      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);
            printf("\n");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
            fprintf(ficres,"\n");      for (i=1;i<=n;i++) {
          }        printf(" %d %.12f",i, p[i]);
      }        fprintf(ficlog," %d %.12lf",i, p[i]);
    }        fprintf(ficrespow," %.12lf", p[i]);
       }
     /* Computing hessian and covariance matrix */      printf("\n");
     ftolhess=ftol; /* Usually correct */      fprintf(ficlog,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);      fprintf(ficrespow,"\n");fflush(ficrespow);
     fprintf(ficres,"# Scales\n");      if(*iter <=3){
     printf("# Scales\n");        tml = *localtime(&rcurr_time);
      for(i=1,jk=1; i <=nlstate; i++){        strcpy(strcurr,asctime(&tml));
       for(j=1; j <=nlstate+ndeath; j++){        rforecast_time=rcurr_time; 
         if (j!=i) {        itmp = strlen(strcurr);
           fprintf(ficres,"%1d%1d",i,j);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           printf("%1d%1d",i,j);                                  strcurr[itmp-1]='\0';
           for(k=1; k<=ncovmodel;k++){        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             printf(" %.5e",delti[jk]);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             fprintf(ficres," %.5e",delti[jk]);        for(niterf=10;niterf<=30;niterf+=10){
             jk++;                                  rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
           }                                  forecast_time = *localtime(&rforecast_time);
           printf("\n");                                  strcpy(strfor,asctime(&forecast_time));
           fprintf(ficres,"\n");                                  itmp = strlen(strfor);
         }                                  if(strfor[itmp-1]=='\n')
       }                                          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);
                                      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);
     k=1;        }
     fprintf(ficres,"# Covariance\n");      }
     printf("# Covariance\n");      for (i=1;i<=n;i++) { /* For each direction i */
     for(i=1;i<=npar;i++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
       /*  if (k>nlstate) k=1;        fptt=(*fret); 
       i1=(i-1)/(ncovmodel*nlstate)+1;  #ifdef DEBUG
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficres,"%3d",i);  #endif
       printf("%3d",i);        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       for(j=1; j<=i;j++){        fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficres," %.5e",matcov[i][j]);  #ifdef LINMINORIGINAL
         printf(" %.5e",matcov[i][j]);        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
       }  #else
       fprintf(ficres,"\n");        linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
       printf("\n");                          flatdir[i]=flat; /* Function is vanishing in that direction i */
       k++;  #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 */
     while((c=getc(ficpar))=='#' && c!= EOF){                                  /* because that direction will be replaced unless the gain del is small */
       ungetc(c,ficpar);                                  /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
       fgets(line, MAXLINE, ficpar);                                  /* Unless the n directions are conjugate some gain in the determinant may be obtained */
       puts(line);                                  /* with the new direction. */
       fputs(line,ficparo);                                  del=fabs(fptt-(*fret)); 
     }                                  ibig=i; 
     ungetc(c,ficpar);        } 
    #ifdef DEBUG
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        printf("%d %.12e",i,(*fret));
            fprintf(ficlog,"%d %.12e",i,(*fret));
     if (fage <= 2) {        for (j=1;j<=n;j++) {
       bage = agemin;                                  xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       fage = agemax;                                  printf(" x(%d)=%.12e",j,xit[j]);
     }                                  fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        for(j=1;j<=n;j++) {
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                                  printf(" p(%d)=%.12e",j,p[j]);
 /*------------ gnuplot -------------*/                                  fprintf(ficlog," p(%d)=%.12e",j,p[j]);
 chdir(pathcd);        }
   if((ficgp=fopen("graph.plt","w"))==NULL) {        printf("\n");
     printf("Problem with file graph.gp");goto end;        fprintf(ficlog,"\n");
   }  #endif
 #ifdef windows      } /* end loop on each direction i */
   fprintf(ficgp,"cd \"%s\" \n",pathc);      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ 
 #endif      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
 m=pow(2,cptcovn);      /* New value of last point Pn is not computed, P(n-1) */
          for(j=1;j<=n;j++) {
  /* 1eme*/                                  if(flatdir[j] >0){
   for (cpt=1; cpt<= nlstate ; cpt ++) {                                          printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
    for (k1=1; k1<= m ; k1 ++) {                                          fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
                                   }
 #ifdef windows                                  /* printf("\n"); */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);                                  /* fprintf(ficlog,"\n"); */
 #endif                          }
 #ifdef unix      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
 #endif        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
         /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
 for (i=1; i<= nlstate ; i ++) {        /* decreased of more than 3.84  */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /* 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 */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                          
     for (i=1; i<= nlstate ; i ++) {        /* Starting the program with initial values given by a former maximization will simply change */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* the scales of the directions and the directions, because the are reset to canonical directions */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
 }        /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long.  */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  #ifdef DEBUG
      for (i=1; i<= nlstate ; i ++) {        int k[2],l;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        k[0]=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        k[1]=-1;
 }          printf("Max: %.12e",(*func)(p));
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        fprintf(ficlog,"Max: %.12e",(*func)(p));
 #ifdef unix        for (j=1;j<=n;j++) {
 fprintf(ficgp,"\nset ter gif small size 400,300");          printf(" %.12e",p[j]);
 #endif          fprintf(ficlog," %.12e",p[j]);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
    }        printf("\n");
   }        fprintf(ficlog,"\n");
   /*2 eme*/        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   for (k1=1; k1<= m ; k1 ++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for (i=1; i<= nlstate+1 ; i ++) {          }
       k=2*i;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  #endif
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    #ifdef LINMINORIGINAL
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  #else
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        free_ivector(flatdir,1,n); 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  #endif
       for (j=1; j<= nlstate+1 ; j ++) {        free_vector(xit,1,n); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        free_vector(xits,1,n); 
         else fprintf(ficgp," \%%*lf (\%%*lf)");        free_vector(ptt,1,n); 
 }          free_vector(pt,1,n); 
       fprintf(ficgp,"\" t\"\" w l 0,");        return; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      } /* enough precision */ 
       for (j=1; j<= nlstate+1 ; j ++) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        ptt[j]=2.0*p[j]-pt[j]; 
 }          xit[j]=p[j]-pt[j]; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        pt[j]=p[j]; 
       else fprintf(ficgp,"\" t\"\" w l 0,");      } 
     }      fptt=(*func)(ptt); /* f_3 */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
   }                  if (*iter <=4) {
    #else
   /*3eme*/  #endif
   #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
   for (k1=1; k1<= m ; k1 ++) {  #else
     for (cpt=1; cpt<= nlstate ; cpt ++) {      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       k=2+nlstate*(cpt-1);  #endif
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       for (i=1; i< nlstate ; i ++) {        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       }        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        /* 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 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 */
   /* CV preval stat */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   for (k1=1; k1<= m ; k1 ++) {        /*  Even if f3 <f1, directest can be negative and t >0 */
     for (cpt=1; cpt<nlstate ; cpt ++) {        /* mu² and del² are equal when f3=f1 */
       k=3;                          /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                          /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
       for (i=1; i< nlstate ; i ++)                          /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
         fprintf(ficgp,"+$%d",k+i+1);                          /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  #ifdef NRCORIGINAL
              t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
       l=3+(nlstate+ndeath)*cpt;  #else
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       for (i=1; i< nlstate ; i ++) {        t= t- del*SQR(fp-fptt);
         l=3+(nlstate+ndeath)*cpt;  #endif
         fprintf(ficgp,"+$%d",l+i+1);        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
       }  #ifdef DEBUG
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          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(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        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);
     }        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   }               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   /* proba elementaires */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   for(i=1,jk=1; i <=nlstate; i++){        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
     for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
       if (k != i) {  #endif
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/  #ifdef POWELLORIGINAL
         for(j=1; j <=ncovmodel; j++){        if (t < 0.0) { /* Then we use it for new direction */
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);  #else
           jk++;        if (directest*t < 0.0) { /* Contradiction between both tests */
           fprintf(ficgp,"\n");                                  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);
       }          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);
   }        } 
   for(jk=1; jk <=m; jk++) {        if (directest < 0.0) { /* Then we use it for new direction */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  #endif
   for(i=1; i <=nlstate; i++) {  #ifdef DEBUGLINMIN
     for(k=1; k <=(nlstate+ndeath); k++){                                  printf("Before linmin in direction P%d-P0\n",n);
       if (k != i) {                                  for (j=1;j<=n;j++) {
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);                                          printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
         for(j=3; j <=ncovmodel; j++)                                          fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                                          if(j % ncovmodel == 0){
         fprintf(ficgp,")/(1");                                                  printf("\n");
         for(k1=1; k1 <=(nlstate+ndeath); k1++)                                                  fprintf(ficlog,"\n");
           if (k1 != i) {                                          }
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);                                  }
             for(j=3; j <=ncovmodel; j++)  #endif
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  #ifdef LINMINORIGINAL
             fprintf(ficgp,")");                                  linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
           }  #else
         fprintf(ficgp,") t \"p%d%d\" ", i,k);                                  linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                                  flatdir[i]=flat; /* Function is vanishing in that direction i */
       }  #endif
     }  
   }  #ifdef DEBUGLINMIN
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                                    for (j=1;j<=n;j++) { 
   }                                          printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
   fclose(ficgp);                                          fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                              if(j % ncovmodel == 0){
 chdir(path);                                                  printf("\n");
     free_matrix(agev,1,maxwav,1,imx);                                                  fprintf(ficlog,"\n");
     free_ivector(wav,1,imx);                                          }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                                  }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  #endif
                                      for (j=1;j<=n;j++) { 
     free_imatrix(s,1,maxwav+1,1,n);                                          xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                              xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                      }
     free_ivector(num,1,n);  #ifdef LINMINORIGINAL
     free_vector(agedc,1,n);  #else
     free_vector(weight,1,n);                                  for (j=1, flatd=0;j<=n;j++) {
     /*free_matrix(covar,1,NCOVMAX,1,n);*/                                          if(flatdir[j]>0)
     fclose(ficparo);                                                  flatd++;
     fclose(ficres);                                  }
    }                                  if(flatd >0){
                                              printf("%d flat directions\n",flatd);
    /*________fin mle=1_________*/                                          fprintf(ficlog,"%d flat directions\n",flatd);
                                              for (j=1;j<=n;j++) { 
                                                   if(flatdir[j]>0){
                                                            printf("%d ",j);
     /* No more information from the sample is required now */                                                          fprintf(ficlog,"%d ",j);
   /* Reads comments: lines beginning with '#' */                                                  }
   while((c=getc(ficpar))=='#' && c!= EOF){                                          }
     ungetc(c,ficpar);                                          printf("\n");
     fgets(line, MAXLINE, ficpar);                                          fprintf(ficlog,"\n");
     puts(line);                                  }
     fputs(line,ficparo);  #endif
   }                                  printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   ungetc(c,ficpar);                                  fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                    
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  #ifdef DEBUG
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                                  printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                                  fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /*--------- index.htm --------*/                                  for(j=1;j<=n;j++){
                                           printf(" %lf",xit[j]);
   if((fichtm=fopen("index.htm","w"))==NULL)    {                                          fprintf(ficlog," %lf",xit[j]);
     printf("Problem with index.htm \n");goto end;                                  }
   }                                  printf("\n");
                                   fprintf(ficlog,"\n");
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n  #endif
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        } /* end of t or directest negative */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  #ifdef POWELLNOF3INFF1TEST
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  #else
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      } /* end if (fptt < fp)  */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  #endif
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                  } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  #else
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  #endif
     } /* loop iteration */ 
  fprintf(fichtm," <li>Graphs</li>\n<p>");  } 
   
  m=cptcovn;  /**** Prevalence limit (stable or period prevalence)  ****************/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
  j1=0;  {
  for(k1=1; k1<=m;k1++){    /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
    for(i1=1; i1<=ncodemax[k1];i1++){       matrix by transitions matrix until convergence is reached with precision ftolpl */
        j1++;    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
        if (cptcovn > 0) {    /* Wx is row vector: population in state 1, population in state 2, population dead */
          fprintf(fichtm,"<hr>************ Results for covariates");    /* or prevalence in state 1, prevalence in state 2, 0 */
          for (cpt=1; cpt<=cptcovn;cpt++)    /* newm is the matrix after multiplications, its rows are identical at a factor */
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);    /* Initial matrix pimij */
          fprintf(fichtm," ************\n<hr>");    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
        }    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /*  0,                   0                  , 1} */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /*
        for(cpt=1; cpt<nlstate;cpt++){     * and after some iteration: */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
        }    /*  0,                   0                  , 1} */
     for(cpt=1; cpt<=nlstate;cpt++) {    /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    /* {0.51571254859325999, 0.4842874514067399, */
 interval) in state (%d): v%s%d%d.gif <br>    /*  0.51326036147820708, 0.48673963852179264} */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /* If we start from prlim again, prlim tends to a constant matrix */
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    int i, ii,j,k;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    double *min, *max, *meandiff, maxmax,sumnew=0.;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /* double **matprod2(); */ /* test */
      }    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double **newm;
 health expectancies in states (1) and (2): e%s%d.gif<br>    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    int ncvloop=0;
 fprintf(fichtm,"\n</body>");    
    }    min=vector(1,nlstate);
  }    max=vector(1,nlstate);
 fclose(fichtm);    meandiff=vector(1,nlstate);
   
   /*--------------- Prevalence limit --------------*/          /* Starting with matrix unity */
      for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(filerespl,"pl");      for (j=1;j<=nlstate+ndeath;j++){
   strcat(filerespl,fileres);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    
   }    cov[1]=1.;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    
   fprintf(ficrespl,"#Prevalence limit\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficrespl,"#Age ");    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   fprintf(ficrespl,"\n");      ncvloop++;
        newm=savm;
   prlim=matrix(1,nlstate,1,nlstate);      /* Covariates have to be included here again */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      cov[2]=agefin;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if(nagesqr==1)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        cov[3]= agefin*agefin;;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (k=1; k<=cptcovn;k++) {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
   k=0;                          /* Here comes the value of the covariate 'ij' */
   agebase=agemin;        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
   agelim=agemax;        /* 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])]); */
   ftolpl=1.e-10;      }
   i1=cptcovn;      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   if (cptcovn < 1){i1=1;}      /* 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(cptcov=1;cptcov<=i1;cptcov++){      for (k=1; k<=cptcovprod;k++) /* Useless */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         k=k+1;        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      
         fprintf(ficrespl,"\n#****** ");      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for(j=1;j<=cptcovn;j++)      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         fprintf(ficrespl,"******\n");      /* 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 *\/ */
         for (age=agebase; age<=agelim; age++){                  /* age and covariate values of ij are in 'cov' */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           fprintf(ficrespl,"%.0f",age );      
           for(i=1; i<=nlstate;i++)      savm=oldm;
           fprintf(ficrespl," %.5f", prlim[i][i]);      oldm=newm;
           fprintf(ficrespl,"\n");  
         }      for(j=1; j<=nlstate; j++){
       }        max[j]=0.;
     }        min[j]=1.;
   fclose(ficrespl);      }
   /*------------- h Pij x at various ages ------------*/      for(i=1;i<=nlstate;i++){
          sumnew=0;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(j=1; j<=nlstate; j++){ 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          prlim[i][j]= newm[i][j]/(1-sumnew);
   }          max[j]=FMAX(max[j],prlim[i][j]);
   printf("Computing pij: result on file '%s' \n", filerespij);          min[j]=FMIN(min[j],prlim[i][j]);
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=24) stepsize=2;  
       maxmax=0.;
   agelim=AGESUP;      for(j=1; j<=nlstate; j++){
   hstepm=stepsize*YEARM; /* Every year of age */        meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        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); */
   k=0;      } /* j loop */
   for(cptcov=1;cptcov<=i1;cptcov++){      *ncvyear= (int)age- (int)agefin;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
       k=k+1;      if(maxmax < ftolpl){
         fprintf(ficrespij,"\n#****** ");        /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         for(j=1;j<=cptcovn;j++)        free_vector(min,1,nlstate);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        free_vector(max,1,nlstate);
         fprintf(ficrespij,"******\n");        free_vector(meandiff,1,nlstate);
                return prlim;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    } /* age loop */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* After some age loop it doesn't converge */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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\
           oldm=oldms;savm=savms;  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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* 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); */
           fprintf(ficrespij,"# Age");    free_vector(min,1,nlstate);
           for(i=1; i<=nlstate;i++)    free_vector(max,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++)    free_vector(meandiff,1,nlstate);
               fprintf(ficrespij," %1d-%1d",i,j);    
           fprintf(ficrespij,"\n");    return prlim; /* should not reach here */
           for (h=0; h<=nhstepm; h++){  }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)   /**** Back Prevalence limit (stable or period prevalence)  ****************/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");   /* 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) */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
           fprintf(ficrespij,"\n");  {
         }    /* 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 */
   fclose(ficrespij);    /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
   /*---------- Health expectancies and variances ------------*/    /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   strcpy(filerest,"t");    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   strcat(filerest,fileres);    /*  0,                   0                  , 1} */
   if((ficrest=fopen(filerest,"w"))==NULL) {    /*
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     * and after some iteration: */
   }    /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
   strcpy(filerese,"e");    /* {0.51571254859325999, 0.4842874514067399, */
   strcat(filerese,fileres);    /*  0.51326036147820708, 0.48673963852179264} */
   if((ficreseij=fopen(filerese,"w"))==NULL) {    /* If we start from prlim again, prlim tends to a constant matrix */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    int i, ii,j,k;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double *min, *max, *meandiff, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
  strcpy(fileresv,"v");    double **out, cov[NCOVMAX+1], **bmij();
   strcat(fileresv,fileres);    double **newm;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double         **dnewm, **doldm, **dsavm;  /* for use */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double         **oldm, **savm;  /* for use */
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    min=vector(1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    max=vector(1,nlstate);
       k=k+1;    meandiff=vector(1,nlstate);
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcovn;j++)          dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          oldm=oldms; savm=savms;
       fprintf(ficrest,"******\n");  
           /* Starting with matrix unity */
       fprintf(ficreseij,"\n#****** ");          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1;j<=cptcovn;j++)                  for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficreseij,"******\n");      }
     
       fprintf(ficresvij,"\n#****** ");    cov[1]=1.;
       for(j=1;j<=cptcovn;j++)    
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       fprintf(ficresvij,"******\n");    /* 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 *\/ */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
       oldm=oldms;savm=savms;      ncvloop++;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        newm=savm; /* oldm should be kept from previous iteration or unity at start */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
       oldm=oldms;savm=savms;      /* Covariates have to be included here again */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      cov[2]=agefin;
            if(nagesqr==1)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        cov[3]= agefin*agefin;;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for (k=1; k<=cptcovn;k++) {
       fprintf(ficrest,"\n");        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
                cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
       hf=1;        /* 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])]); */
       if (stepm >= YEARM) hf=stepm/YEARM;      }
       epj=vector(1,nlstate+1);      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(age=bage; age <=fage ;age++){      /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
         fprintf(ficrest," %.0f",age);      for (k=1; k<=cptcovprod;k++) /* Useless */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      
           }      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
           epj[nlstate+1] +=epj[j];      /*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]);*/
         for(i=1, vepp=0.;i <=nlstate;i++)      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           for(j=1;j <=nlstate;j++)      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
             vepp += vareij[i][j][(int)age];                  /* ij should be linked to the correct index of cov */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                  /* age and covariate values ij are in 'cov', but we need to pass
         for(j=1;j <=nlstate;j++){                   * ij for the observed prevalence at age and status and covariate
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                   * number:  prevacurrent[(int)agefin][ii][ij]
         }                   */
         fprintf(ficrest,"\n");      /* 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;
  fclose(ficreseij);      for(j=1; j<=nlstate; j++){
  fclose(ficresvij);        max[j]=0.;
   fclose(ficrest);        min[j]=1.;
   fclose(ficpar);      }
   free_vector(epj,1,nlstate+1);      for(j=1; j<=nlstate; j++){ 
   /*  scanf("%d ",i); */        for(i=1;i<=nlstate;i++){
                                   /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
   /*------- Variance limit prevalence------*/                                    bprlim[i][j]= newm[i][j];
                                   max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
 strcpy(fileresvpl,"vpl");                                  min[i]=FMIN(min[i],bprlim[i][j]);
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                  
     exit(0);      maxmax=0.;
   }      for(i=1; i<=nlstate; i++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[i]);
  k=0;        /* 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); */
  for(cptcov=1;cptcov<=i1;cptcov++){      } /* j loop */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      *ncvyear= -( (int)age- (int)agefin);
      k=k+1;      /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
      fprintf(ficresvpl,"\n#****** ");      if(maxmax < ftolpl){
      for(j=1;j<=cptcovn;j++)        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        free_vector(min,1,nlstate);
      fprintf(ficresvpl,"******\n");        free_vector(max,1,nlstate);
              free_vector(meandiff,1,nlstate);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        return bprlim;
      oldm=oldms;savm=savms;      }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    } /* 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);
   fclose(ficresvpl);    /* 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);
   /*---------- End : free ----------------*/    free_vector(max,1,nlstate);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    free_vector(meandiff,1,nlstate);
      
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    return bprlim; /* should not reach here */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  }
    
    /*************** transition probabilities ***************/ 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* According to parameters values stored in x and the covariate's values stored in cov,
         computes the probability to be observed in state j being in state i by appying the
   free_matrix(matcov,1,npar,1,npar);       model to the ncovmodel covariates (including constant and age).
   free_vector(delti,1,npar);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   printf("End of Imach\n");       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       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.
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       Outputs ps[i][j] the probability to be observed in j being in j according to
   /*printf("Total time was %d uSec.\n", total_usecs);*/       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   /*------ End -----------*/    */
     double s1, lnpijopii;
  end:    /*double t34;*/
 #ifdef windows    int i,j, nc, ii, jj;
  chdir(pathcd);  
 #endif    for(i=1; i<= nlstate; i++){
  system("wgnuplot ../gp37mgw/graph.plt");      for(j=1; j<i;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 #ifdef windows          /*lnpijopii += param[i][j][nc]*cov[nc];*/
   while (z[0] != 'q') {          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     chdir(pathcd);          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        }
     scanf("%s",z);        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     if (z[0] == 'c') system("./imach");        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     else if (z[0] == 'e') {      }
       chdir(path);      for(j=i+1; j<=nlstate+ndeath;j++){
       system("index.htm");        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];*/
     else if (z[0] == 'q') exit(0);          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); */
 #endif        }
 }        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;
       }
     }
     
     
     /* 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;
   }
   
   /*************** backward transition probabilities ***************/ 
   
    /* 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 backward probability at age agefin and covariate ij
      * and returns in **ps as well as **bmij.
      */
     int i, ii, j,k;
     
     double **out, **pmij();
     double sumnew=0.;
     double agefin;
     
     double **dnewm, **dsavm, **doldm;
     double **bbmij;
     
     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 )
   {
     /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
        lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        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]
     */
     double s1, lnpijopii;
     /*double t34;*/
     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 */
     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 */
         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]);*/
                           /* right multiplication of oldm by the current matrix */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      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;
         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;
   }
   
   
   #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
     double *xt;
     int j;
     myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
    free_vector(xt,1,n);
     return fret;
   }
   #endif
   
   /*************** log-likelihood *************/
   double func( double *x)
   {
     int i, ii, j, k, mi, d, kk;
     int ioffset=0;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
     double lli; /* Individual log likelihood */
     int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
     double bbh, survp;
     long ipmx;
     double agexact;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
   
     ++countcallfunc;
   
     cov[1]=1.;
   
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
     if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
         */
         ioffset=2+nagesqr+cptcovage;
         /* 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[Tvar[iqv]][i];
         }
   
         /* 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] 
            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(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
             /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
             cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[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]][TmodelInvQind[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 (j=1;j<=nlstate+ndeath;j++){
               oldm[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++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;  /* Should be changed here */
             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 */
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
                                   
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
            */
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
            */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
                as if date of death was unknown. Death was treated as any other
                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
                to consider that at each interview the state was recorded
                (healthy, disable or death) and IMaCh was corrected; but when we
                introduced the exact date of death then we should have modified
                the contribution of an exact death to the likelihood. This new
                contribution is smaller and very dependent of the step unit
                stepm. It is no more the probability to die between last interview
                and month of death but the probability to survive from last
                interview up to one month before death multiplied by the
                probability to die within a month. Thanks to Chris
                Jackson for correcting this bug.  Former versions increased
                mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
                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.
             */
   /* #ifdef INFINITYORIGINAL */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
   /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   /*          lli=log(mytinydouble); */
   /*        else */
   /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #endif */
             lli=log(out[s1][s2] - savm[s1][s2]);
             
           } else if  ( s2==-1 ) { /* alive */
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
             lli= log(survp);
           }
           else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
           else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
           else{
             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=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*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); */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /* if (lli < log(mytinydouble)){ */
           /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
           /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
           /* } */
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[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++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[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++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[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++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
             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{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
           ipmx +=1;
           sw += weight[i];
           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]); */
         } /* end of wave */
       } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[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++){
             newm=savm;
             agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
             cov[2]=agexact;
             if(nagesqr==1)
               cov[3]= agexact*agexact;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
           sw += weight[i];
           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]);*/
         } /* end of wave */
       } /* end of individual */
     } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   }
   
   /*************** log-likelihood *************/
   double funcone( double *x)
   {
     /* Same as func but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     int ioffset=0;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
     double lli; /* Individual log likelihood */
     double llt;
     int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   
     double bbh, survp;
     double agexact;
     double agebegin, ageend;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
     cov[1]=1.;
   
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     ioffset=0;
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       ioffset=2+nagesqr+cptcovage;
       /* 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 Dummy covariates without age* products */
         cov[++ioffset]=covar[TvarFD[k]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
       }
       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
         cov[++ioffset]=coqvar[Tvar[iqv]][i]; /* Only V1 k=9 */
       }
       
       for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
           /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
           /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
           k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
           cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
           /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
         }
         for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
           iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */
           /* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); */
           cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
         }
         for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
         
         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){  /* 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;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;
           if(nagesqr==1)
             cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {
             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); */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
           oldm=newm;
         } /* end mult */
         
         s1=s[mw[mi][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; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
         }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
           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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
         ipmx +=1;
         sw += weight[i];
         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]); */
         if(globpr){
           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 ", \
                   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]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
           fprintf(ficresilk," %10.6f\n", -llt);
         }
       } /* end of wave */
     } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
       gsw=sw;
     }
     return -l;
   }
   
   
   /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     /* This routine should help understanding what is done with 
        the selection of individuals/waves and
        to check the exact contribution to the likelihood.
        Plotting could be done.
      */
     int k;
   
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ILK_"); 
       strcat(fileresilk,fileresu);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       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 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]); */
       for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   
     *fretone=(*funcone)(p);
     if(*globpri !=0){
       fclose(ficresilk);
       if (mle ==0)
         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;
   }
   
   
   /*********** Maximum Likelihood Estimation ***************/
   
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     int i,j, iter=0;
     double **xi;
     double fret;
     double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
     xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"POW_"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
     free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     printf("\n#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));
   
   }
   
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     double  **a,**y,*x,pd;
     /* double **hess; */
     int i, j;
     int *indx;
   
     double hessii(double p[], double delta, int theta, double delti[],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 ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     /* hess=matrix(1,npar,1,npar); */
   
     printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
       printf("%d-",i);fflush(stdout);
       fprintf(ficlog,"%d-",i);fflush(ficlog);
      
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     
     for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
         if (j>i) { 
           printf(".%d-%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
           
           hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
         }
       }
     }
     printf("\n");
     fprintf(ficlog,"\n");
   
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   
     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++){ 
         matcov[i][j]=x[i];
       }
     }
   
     printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
         printf("%.6e ",hess[i][j]);
         fprintf(ficlog,"%.6e ",hess[i][j]);
       }
       printf("\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 */
     /* for (i=1;i<=npar;i++) */
     /*   for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
     /* 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#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 (i=1;i<=npar;i++){ 
         printf("%.2f ",y[i][j]);
         fprintf(ficlog,"%.2f ",y[i][j]);
       }
       printf("\n");
       fprintf(ficlog,"\n");
     }
   #endif
   
     free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     /* free_matrix(hess,1,npar,1,npar); */
   
   
   }
   
   /*************** hessian matrix ****************/
   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 l=1, lmax=20;
     double k1,k2, res, fx;
     double p2[MAXPARM+1]; /* identical to x */
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     int k=0,kmax=10;
     double l1;
   
     fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     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 = delta*(l1*k);
         p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
         
   #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);
         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
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
         }
         else if((k1 >khi/nkhif) || (k2 >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; 
     
   }
   
   double hessij( double x[], double **hess, 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];
     int k, kmax=1;
     double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
     
     fx=func(x);
     for (k=1; k<=kmax; k=k+10) {
       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 */
       if(k1*k2*k3*k4 <0.){
         firstime=1;
         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
     }
     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 **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
    
     vv=vector(1,n); 
     *d=1.0; 
     for (i=1;i<=n;i++) { 
       big=0.0; 
       for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     } 
     for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
         sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       } 
       big=0.0; 
       for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
         } 
       } 
       if (j != imax) { 
         for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         } 
         *d = -(*d); 
         vv[imax]=vv[j]; 
       } 
       indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
         dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
   } 
   
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     int i,ii=0,ip,j; 
     double sum; 
    
     for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
       if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
       b[i]=sum; 
     } 
     for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
     } 
   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
   }
   
   /************ Frequencies ********************/
   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 */
     
     int i, m, jk, j1, bool, z1,j, k, iv;
     int iind=0, iage=0;
     int mi; /* Effective wave */
     int first;
     double ***freq; /* Frequencies */
     double *meanq;
     double **meanqt;
     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);
     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
     posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
     /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
     meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     meanqt=matrix(1,lastpass,1,nqtveff);
     strcpy(fileresp,"P_");
     strcat(fileresp,fileresu);
     /*strcat(fileresphtm,fileresu);*/
     if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
     }
   
     strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
     if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
       printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
       fflush(ficlog);
       exit(70); 
     }
     else{
       fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
               fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
     fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
       
     strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
     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;
     
     /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
     j=cptcoveff;  /* Only dummy covariates of the model */
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     first=1;
   
     /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
        reference=low_education V1=0,V2=0
        med_educ                V1=1 V2=0, 
        high_educ               V1=0 V2=1
        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
     */
   
     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
       posproptt=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/
       for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-5; jk<=nlstate+ndeath; jk++)  
           for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;
         
       for (i=1; i<=nlstate; i++)  {
         for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
         posprop[i]=0;
         pospropt[i]=0;
       }
       /* for (z1=1; z1<= nqfveff; z1++) {   */
       /*   meanq[z1]+=0.; */
       /*   for(m=1;m<=lastpass;m++){ */
       /*  meanqt[m][z1]=0.; */
       /*   } */
       /* } */
         
       dateintsum=0;
       k2cpt=0;
       /* For that combination of covariate j1, we count and print the frequencies in one pass */
       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
         bool=1;
         if(anyvaryingduminmodel==0){ /* If All fixed covariates */
           if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             /* for (z1=1; z1<= nqfveff; z1++) {   */
             /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
             /* } */
             for (z1=1; z1<=cptcoveff; z1++) {  
               /* if(Tvaraff[z1] ==-20){ */
               /*   /\* 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;
                   }
                 }
               }
             }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
             if(bool==1){
               /* 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;
                 k2cpt++;
                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
               }
             } /* end bool 2 */
           } /* end m */
         } /* end bool */
       } /* end iind = 1 to imx */
       /* prop[s][age] is feeded for any initial and valid live state as well as
          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
   
   
       /*      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++){ 
           /* posprop[jk]=0; */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
             pp[jk] += freq[jk][m][iage];
         } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
   
         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);
           }
           if( iage <= iagemax){
             if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               /*probs[iage][jk][j1]= pp[jk]/pos;*/
               /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
             }
             else{
               fprintf(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);
             }
           }
           pospropt[jk] +=posprop[jk];
         } /* end loop jk */
         /* pospropt=0.; */
         for(jk=-1; jk <=nlstate+ndeath; jk++){
           for(m=-1; m <=nlstate+ndeath; m++){
             if(freq[jk][m][iage] !=0 ) { /* minimizing output */
               if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
               }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
             }
             if(jk!=0 && m!=0)
               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
           }
         } /* 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");
         fprintf(ficlog,"\n");
       } /* end loop age iage */
       fprintf(ficresphtm,"<tr><th>Tot</th>");
       for(jk=1; jk <=nlstate ; jk++){
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);   
         }else{
           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);    
         }
       }
       fprintf(ficresphtm,"</tr>\n");
       fprintf(ficresphtm,"</table>\n");
       fprintf(ficresphtmfr,"</table>\n");
       if(posproptt < 1.e-5){
         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
         invalidvarcomb[j1]=1;
       }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
         invalidvarcomb[j1]=0;
       }
       fprintf(ficresphtmfr,"</table>\n");
     } /* end selected combination of covariate j1 */
     dateintmean=dateintsum/k2cpt; 
                    
     fclose(ficresp);
     fclose(ficresphtm);
     fclose(ficresphtmfr);
     free_vector(meanq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
     free_vector(pp,1,nlstate);
     /* End of freqsummary */
   }
   
   /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
    
     int i, m, jk, j1, bool, z1,j, iv;
     int mi; /* Effective wave */
     int iage;
     double agebegin, ageend;
   
     double **prop;
     double posprop; 
     double  y2; /* in fractional years */
     int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
   
     iagemin= (int) agemin;
     iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     
     /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
     first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
       for (i=1; i<=nlstate; i++)  
         for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
           prop[i][iage]=0.0;
       printf("Prevalence combination of varying and fixed dummies %d\n",j1);
       /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
       fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
       
       for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;
         /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
         for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
           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;
             }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                 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 */
               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]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
                   printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                   exit(1);
                 }
                 if (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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                 } /* end valid statuses */ 
               } /* end selection of dates */
             } /* end selection of waves */
           } /* end bool */
         } /* end wave */
       } /* end individual */
       for(i=iagemin; i <= iagemax+3; i++){  
         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           posprop += prop[jk][i]; 
         } 
         
         for(jk=1; jk <=nlstate ; jk++){       
           if( i <=  iagemax){ 
             if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;
             } else{
               if(first==1){
                 first=0;
                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
               }
             }
           } 
         }/* end jk */ 
       }/* end i */ 
        /*} *//* end i1 */
     } /* end j1 */
     
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
   }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
   
   void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
     /* 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 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]
        and mw[mi+1][i]. dh depends on stepm.
     */
   
     int i=0, mi=0, m=0, mli=0;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
     int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
     firstwo=0;
     firsthree=0;
     firstfour=0;
     jmin=100000;
     jmax=-1;
     jmean=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;
       while(s[m][i] <= nlstate){  /* a live state */
         if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
           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;
           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;
   #else
           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 */
   
       /* 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 */
         /* if(mi==0)  never been interviewed correctly before death */
         /* Only death is a correct wave */
         mw[mi][i]=m;
       }
   #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
       else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
         /* 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){
         nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
         }
         if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     } /* End individuals */
     /* wav and mw are no more changed */
           
     
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax){
                 jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
           }
           else{
             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]); */
                                           
             k=k+1;
             if (j >= jmax) {
               jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               jmin=j;
               ijmin=i;
             }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
             sum=sum+j;
           }
           jk= j/stepm;
           jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
           } /* end if mle */
         }
       } /* end wave */
     }
     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);
     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 ****************************/
    void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
   {
     /**< 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 
      * Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
      * 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 modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   
   
     /* cptcoveff=0;  */
           /* *cptcov=0; */
    
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     /* Loop on covariates without age and products and no quantitative variable */
     /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
     for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
       if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
         switch(Fixed[k]) {
         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
             ij=(int)(covar[Tvar[k]][i]);
             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
              * If product of Vn*Vm, still boolean *:
              * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
              * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
             /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                modality of the nth covariate of individual i. */
             if (ij > modmaxcovj)
               modmaxcovj=ij; 
             else if (ij < modmincovj) 
               modmincovj=ij; 
             if ((ij < -1) && (ij > NCOVMAX)){
               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
               exit(1);
             }else
               Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
             /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
             /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             /* getting the maximum value of the modality of the covariate
                (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                female ies 1, then modmaxcovj=1.
             */
           } /* end for loop on individuals i */
           printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
           fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
           cptcode=modmaxcovj;
           /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           /*for (i=0; i<=cptcode; i++) {*/
           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]);
             fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
               if( j != -1){
                 ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                                    covariate for which somebody answered excluding 
                                    undefined. Usually 2: 0 and 1. */
               }
               ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                                       covariate for which somebody answered including 
                                       undefined. Usually 3: -1, 0 and 1. */
             }
             /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
              * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           } /* Ndum[-1] number of undefined modalities */
           
           /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
              If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
              modmincovj=3; modmaxcovj = 7;
              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++;
             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;
           }
           break;
         default:
           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*/  
     
     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 */ 
       /* 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 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]++; /* 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=0;
     /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
     for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
       if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
         /* If product not in single variable we don't print results */
         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
         ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
         Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
         Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
         TmodelInvind[k]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
         if(Fixed[k]!=0)
           anyvaryingduminmodel=1;
         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
       } 
     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
     /* ij--; */
     /* cptcoveff=ij; /\*Number of total covariates*\/ */
     *cptcov=ij; /*Number of total real effective covariates: effective
                  * because they can be excluded from the model and real
                  * if in the model but excluded because missing values, but how to get k from ij?*/
     for(j=ij+1; j<= cptcovt; j++){
       Tvaraff[j]=0;
       Tmodelind[j]=0;
     }
     for(j=ntveff+1; j<= cptcovt; j++){
       TmodelInvind[j]=0;
     }
     /* To be sorted */
     ;
   }
   
   
   /*********** Health Expectancies ****************/
   
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* 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 hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* 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 only each 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;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[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]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
        to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* 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 hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* 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 only each 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 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                           
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
                           
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
                   
       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
                   
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           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]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
                   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           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;
                                           
             /* 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 );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
                   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
                   
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
           
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     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 *ncvyearp, 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,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*/
     
      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 agelim. 
         Look at function hpijx to understand why because of memory size limitations, 
         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);
          }
                           
          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);
       */
      /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
      fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
   
      free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
      fclose(ficresprobmorprev);
      fflush(ficgp);
      fflush(fichtm); 
    }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
    void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
   {
     /* 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 **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mgm, **mgp;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
           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];
           mgp[theta][i] = prlim[i][i];
         }
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
           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];
           mgm[theta][i] = prlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           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++)
         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(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++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,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(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ 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[])
    {
      int i, j=0,  k1, l1, tj;
      int k2, l2, j1,  z1;
      int k=0, l;
      int first=1, first1, first2;
      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
      double *xp;
      double *gp, *gm;
      double **gradg, **trgradg;
      double **mu;
      double age, cov[NCOVMAX+1];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
      int theta;
      char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
      double ***varpij;
   
      strcpy(fileresprob,"PROB_"); 
      strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
      strcpy(fileresprobcov,"PROBCOV_"); 
      strcat(fileresprobcov,fileresu);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
      strcpy(fileresprobcor,"PROBCOR_"); 
      strcat(fileresprobcor,fileresu);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("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);
      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);
      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);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
      pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
      pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcor,"# Age");
   
   
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      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");
   
      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,"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);
      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.\
    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. \
   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 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    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");
   
      cov[1]=1;
      /* tj=cptcoveff; */
      tj = (int) pow(2,cptcoveff);
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
      for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
        if  (cptcovn>0) {
          fprintf(ficresprob, "\n#********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprob, "**********\n#\n");
          fprintf(ficresprobcov, "\n#********** Variable "); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(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#\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\">");
                           
          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#");    
          if(invalidvarcomb[j1]){
            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));
        gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){ 
          cov[2]=age;
          if(nagesqr==1)
            cov[3]= age*age;
          for (k=1; k<=cptcovn;k++) {
            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
            /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                       * 1  1 1 1 1
                                                                       * 2  2 1 1 1
                                                                       * 3  1 2 1 1
                                                                       */
            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
          /* 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++)
            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                           
                           
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                   
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                   
            k=0;
            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);
            k=0;
            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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            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 */
                    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 ***********/
   void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int prevfcast, int backcast, int estepm , \
                     double jprev1, double mprev1,double anprev1, double dateprev1, \
                     double jprev2, double mprev2,double anprev2, double dateprev2){
     int jj1, k1, i1, cpt;
   
      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 \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
      fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
              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,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              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,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
      fprintf(fichtm,"\
    - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
      fprintf(fichtm,"\
    - (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",
              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>");
   
      m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      jj1=0;
      for(k1=1; k1<=m;k1++){
   
        /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;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);
          }
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          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 */
        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-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
    incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
   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++){
            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.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++) {
          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.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
        }
        /* } /\* end i1 *\/ */
      }/* End k1 */
      fprintf(fichtm,"</ul>");
   
      fprintf(fichtm,"\
   \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> \
    - 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," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
      fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
      fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
      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): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
      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 href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
      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",
              estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
      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",
              estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
      fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
              subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  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); */
      fflush(fichtm);
      fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
      m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      jj1=0;
      for(k1=1; k1<=m;k1++){
        /* for(i1=1; i1<=ncodemax[k1];i1++){ */
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
          fprintf(fichtm," ************\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++) {
          fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
   <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 \
   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\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
   <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
        /* } /\* end i1 *\/ */
      }/* End k1 */
      fprintf(fichtm,"</ul>");
      fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   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 gplotcondition[132];
     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 vpopbased;
     int ioffset; /* variable offset for columns */
   
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */
     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(optfileres,"vpl");
     /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
       for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
           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,"V_"),cpt,k1);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n   \
   set ter svg size 640, 480\n     \
   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 ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else        fprintf(ficgp," %%*lf (%%*lf)");
         }
         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
         for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         } 
         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
         for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }  
         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
         if(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*/
     for (k1=1; k1<= m ; k1 ++) { 
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           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+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
         fprintf(ficgp,"set ter svg size 640, 480\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
         /*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) ");
           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);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                   
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                   
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* 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 (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;
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           if(j==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(cpt-1) +j;
           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
           /* for (i=2; i<= nlstate+ndeath ; i ++) */
           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         } /* nlstate */
         fprintf(ficgp,", '' ");
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
           l=(nlstate+ndeath)*(cpt-1) +j;
           if(j < nlstate)
             fprintf(ficgp,"$%d +",k+l);
           else
             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
   /* 6eme */
     /* CV preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }
         fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;
         }
         
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter svg size 640, 480\n                                             \
   unset log y\n                                                           \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=2; j<= nlstate ; j ++)
             fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     
   /* 7eme */
     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 */
     fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
     for(i=1,jk=1; i <=nlstate; i++){
       fprintf(ficgp,"# initial state %d\n",i);
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           fprintf(ficgp,"#   current state %d\n",k);
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
             jk++; 
           }
           fprintf(ficgp,"\n");
         }
       }
     }
     fprintf(ficgp,"##############\n#\n");
     
     /*goto avoid;*/
     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)=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)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
     fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
     fprintf(ficgp,"#                      +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
     fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
     fprintf(ficgp,"#     (1+exp(a12+b12*age+c12age*age+d12*V1+e12*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,"#\n");
     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,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
       for(jk=1; jk <=m; jk++) {
         fprintf(ficgp,"#    jk=%d\n",jk);
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
         fprintf(ficgp,"\nset ter svg size 640, 480 ");
         if (ng==1){
           fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
           fprintf(ficgp,"\nunset log y");
         }else if (ng==2){
           fprintf(ficgp,"\nset ylabel \"Probability\"\n");
           fprintf(ficgp,"\nset log y");
         }else if (ng==3){
           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           fprintf(ficgp,"\nset log y");
         }else
           fprintf(ficgp,"\nunset title ");
         fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
         i=1;
         for(k2=1; k2<=nlstate; k2++) {
           k3=i;
           for(k=1; k<=(nlstate+ndeath); k++) {
             if (k != k2){
               switch( ng) {
               case 1:
                 if(nagesqr==0)
                   fprintf(ficgp," p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 2: /* ng=2 */
                 if(nagesqr==0)
                   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                 break;
               case 3:
                 if(nagesqr==0)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else /* nagesqr =1 */
                   fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                 break;
               }
               ij=1;/* To be checked else nbcode[0][0] wrong */
               for(j=3; j <=ncovmodel-nagesqr; j++) {
                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                 if(ij <=cptcovage) { /* Bug valgrind */
                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                     ij++;
                   }
                 }
                 else
                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
               }
             }else{
               i=i-ncovmodel;
               if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                 fprintf(ficgp," (1.");
             }
             
             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 */
   
   
   /*************** Moving average **************/
   /* 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 mobilavrange, mob;
      int iage=0;
   
      double sum=0.;
      double age;
      double *sumnewp, *sumnewm;
      double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     
     
      /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
      /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
   
      sumnewp = vector(1,ncovcombmax);
      sumnewm = vector(1,ncovcombmax);
      agemingood = vector(1,ncovcombmax);  
      agemaxgood = vector(1,ncovcombmax);
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        sumnewm[cptcod]=0.;
        sumnewp[cptcod]=0.;
        agemingood[cptcod]=0;
        agemaxgood[cptcod]=0;
      }
      if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
     
      if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        if(mobilav==1) mobilavrange=5; /* default */
        else mobilavrange=mobilav;
        for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
           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 ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     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 fileresf[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); */
    
     strcpy(fileresf,"F_"); 
     strcat(fileresf,fileresu);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   
     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=pow(2,cptcoveff);
     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,"#****** Routine prevforecast **\n");
     
   /*            if (h==(int)(YEARM*yearp)){ */
     for(k=1;k<=i1;k++){
       if(invalidvarcomb[k]){
         printf("\nCombination (%d) projection ignored because no cases \n",k); 
         continue;
       }
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficresf," yearproj age");
       for(j=1; j<=nlstate+ndeath;j++){ 
         for(i=1; i<=nlstate;i++)        
           fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresf," wp.%d",j);
       }
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+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;
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
           
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+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][k];
                 else {
                   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 */
           } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end  k */
           
     fclose(ficresf);
     printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
   
   }
   
   /* /\************** Back Forecasting ******************\/ */
   /* 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  */
   /*      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;} */
     
   /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
     
   /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
           
   /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
   /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
   /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
   /*       k=k+1; */
   /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
   /*       for(j=1;j<=cptcoveff;j++) { */
   /*                              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 *\/ */
           
   /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
           
   /*   fclose(ficresfb); */
   /*   printf("End of Computing Back forecasting \n"); */
   /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
           
   /* } */
   
   /************** Forecasting *****not tested NB*************/
   /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
     
   /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
   /*   int *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,fileresu); */
   /*   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; */
   /*   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)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# 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" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=1;i<=imx ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     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,"<br><br><img src=\"graphmort.svg\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.svg\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \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,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0, iv=0;
     int lstra;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
   
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
       fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
       
       /* Loops on waves */
       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, ' '); 
         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 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);
             return 1;
           }
         }
         
         s[j][i]=lval;
         
         /* Date of Interview */
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* End loop on waves */
       
       /* Date of death */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }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);
         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;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       /* Date of birth */
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }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);
         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;
       }
       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);
         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;
         
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       /* Sample weight */
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       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--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing covariate value */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);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;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     
     *imax=i-1; /* Number of individuals */
     fclose(fic);
     
     return (0);
     /* endread: */
     printf("Exiting readdata: ");
     fclose(fic);
     return (1);
   }
   
   void removespace(char **stri){/*, char stro[]) {*/
     char *p1 = *stri, *p2 = *stri;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
     *stri=p1; 
   }
   
   int decoderesult ( char resultline[])
   /**< This routine decode one result line and returns the combination # of dummy covariates only **/
   {
     int j=0, k=0;
     char resultsav[MAXLINE];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     removespace(&resultline);
     printf("decoderesult=%s\n",resultline);
   
     if (strstr(resultline,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
       fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
       return 1;
     }
     trimbb(resultsav, resultline);
     if (strlen(resultsav) >1){
       j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
     }
   
     for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                                        resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
       cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
       Tvalsel[k]=atof(strc); /* 1 */
   
       cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
       Tvarsel[k]=atoi(strc);
       /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
       /* cptcovsel++;     */
       if (nbocc(stra,'=') >0)
         strcpy(resultsav,stra); /* and analyzes it */
     }
     return (0);
   }
   int selected( int kvar){ /* Selected combination of covariates */
     if(Tvarsel[kvar])
       return (0);
     else
       return(1);
   }
   int decodemodel( char model[], int lastobs)
    /**< This routine decodes the model and returns:
           * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
           * - nagesqr = 1 if age*age in the model, otherwise 0.
           * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
           * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
           * - cptcovage number of covariates with age*products =2
           * - cptcovs number of simple covariates
           * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
           *     which is a new column after the 9 (ncovcol) variables. 
           * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
           * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
           *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
           * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
           */
   {
     int i, j, k, ks;
     int  j1, k1, k2, k3, k4;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
     char *strpt;
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       if (strstr(model,"AGE") !=0){
         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);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       strcpy(modelsav,model); 
       if ((strpt=strstr(model,"age*age")) !=0){
         printf(" strpt=%s, model=%s\n",strpt, model);
         if(strpt != model){
           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 \
    corresponding column of parameters.\n",model);
           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 \
    corresponding column of parameters.\n",model); fflush(ficlog);
           return 1;
         }
         nagesqr=1;
         if (strstr(model,"+age*age") !=0)
           substrchaine(modelsav, model, "+age*age");
         else if (strstr(model,"age*age+") !=0)
           substrchaine(modelsav, model, "age*age+");
         else 
           substrchaine(modelsav, model, "age*age");
       }else
         nagesqr=0;
       if (strlen(modelsav) >1){
         j=nbocc(modelsav,'+'); /**< j=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 =5-3=2  */
         cptcovt= j+1; /* Number of total covariates in the model, not including
                        * cst, age and age*age 
                        * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
         /* including age products which are counted in cptcovage.
          * but the covariates which are products must be treated 
          * separately: ncovn=4- 2=2 (V1+V3). */
         cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
         
         
         /*   Design
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
          *  <          ncovcol=8                >
          * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
          *   k=  1    2      3       4     5       6      7        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[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
          *  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 
          *  Tage[++cptcovage]=k
          *       if products, new covar are created after ncovcol with k1
          *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
          *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
          *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
          *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
          *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
          *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
          *  <          ncovcol=8                >
          *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
          *          k=  1    2      3       4     5       6      7        8    9   10   11  12
          *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
          * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          * p Tprod[1]@2={                         6, 5}
          *p Tvard[1][1]@4= {7, 8, 5, 6}
          * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
          *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          *How to reorganize?
          * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
          * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
          *       {2,   1,     4,      8,    5,      6,     3,       7}
          * Struct []
          */
         
         /* 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 */
         /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
         /*        k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
         /*        k=3 V4 Tvar[k=3]= 4 (from V4) */
         /*        k=2 V1 Tvar[k=2]= 1 (from V1) */
         /*        k=1 Tvar[1]=2 (from V2) */
         /*        k=5 Tvar[5] */
         /* for (k=1; k<=cptcovn;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]]][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 */
         for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
           Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
         }
         cptcovage=0;
         for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                            modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
           if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
           /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           /*scanf("%d",i);*/
           if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
             cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
             if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
               /* covar is not filled and then is empty */
               cptcovprod--;
               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 */
               Typevar[k]=1;  /* 1 for age 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 */
               /*printf("stre=%s ", stre);*/
             } else if (strcmp(strd,"age")==0) { /* or age*Vn */
               cptcovprod--;
               cutl(stre,strb,strc,'V');
               Tvar[k]=atoi(stre);
               Typevar[k]=1;  /* 1 for age product */
               cptcovage++;
               Tage[cptcovage]=k;
             } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
               /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
               cptcovn++;
               cptcovprodnoage++;k1++;
               cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
               Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                      because this model-covariate is a construction we invent a new column
                                      which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                      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 */
               Typevar[k]=2;  /* 2 for double fixed dummy covariates */
               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  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
               Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
               Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
               k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
               /* 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) *\/ */
               /*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++){
                 /* 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[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
               }
             } /* End age is not in the model */
           } /* End if model includes a product */
           else { /* no more sum */
             /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
             /*  scanf("%d",i);*/
             cutl(strd,strc,strb,'V');
             ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
             cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
             Tvar[k]=atoi(strd);
             Typevar[k]=0;  /* 0 for simple covariates */
           }
           strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
                                   /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                     scanf("%d",i);*/
         } /* end of loop + on total covariates */
       } /* end if strlen(modelsave == 0) age*age might exist */
     } /* 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.
       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("cptcovprod=%d ", cptcovprod);
        fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
        scanf("%d ",i);*/
   
   
   /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
      of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
   /* 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++;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=Tvar[k]; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
         Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;
         TvarFQ[nqfveff]=Tvar[k]; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
         Fixed[k]= 1;
         Dummy[k]= 0;
         ntveff++; /* Only simple time varying dummy variable */
         TvarVD[ntvveff]=Tvar[k]; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         TvarVDind[ntveff++]=k; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
         printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
         printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
           Fixed[k]= 1;
           Dummy[k]= 1;
           TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
           /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
           printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
         printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
       }else if (Typevar[k] == 1) {  /* product with age */
         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 */ 
     /*endread:*/
     printf("Exiting decodemodel: ");
     return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
     int firstone=0;
     
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           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){
           *nberr = *nberr + 1;
           if(firstone == 0){
             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;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         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(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
                 /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           } /* end if */
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    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]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           } /* en if 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;
             s[m][i]=-1;
           }
         }
         else if(s[m][i]==0) /*= 0 Unknown */
           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(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo(int logged)
    {
      /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              if(logged) fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for "); if (logged) fprintf(ficlog, " for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");if(logged) fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
            if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
   }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
   
     strcpy(filerespl,"PL_");
     strcat(filerespl,fileresu);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       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;
     }
     printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
     pstamp(ficrespl);
     fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
     agebase=ageminpar;
     agelim=agemaxpar;
   
     /* i1=pow(2,ncoveff); */
     i1=pow(2,cptcoveff); /* Number of dummy covariates */
     if (cptcovn < 1){i1=1;}
   
     for(k=1; k<=i1;k++){
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       /* k=k+1; */
       /* to clean */
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       fprintf(ficrespl,"#******");
       printf("#******");
       fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
         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]][codtabm(k,j)]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficrespl,"******\n");
       printf("******\n");
       fprintf(ficlog,"******\n");
       if(invalidvarcomb[k]){
         printf("\nCombination (%d) ignored because no case \n",k); 
         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
                                                   continue;
       }
   
       fprintf(ficrespl,"#Age ");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
       fprintf(ficrespl,"Total Years_to_converge\n");
       
       for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */
         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
         fprintf(ficrespl,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         tot=0.;
         for(i=1; i<=nlstate;i++){
           tot +=  prlim[i][i];
           fprintf(ficrespl," %.5f", prlim[i][i]);
         }
         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
       } /* Age */
       /* was end of cptcod */
     } /* cptcov */
     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){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i 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(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           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);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
       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 */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     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 ncvyear=0; /* Number of years needed for the period prevalence to converge */
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb=0.;
   
     double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
     double fret;
     double dum=0.; /* Dummy variable */
     double ***p3mat;
     /* double ***mobaverage; */
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
     char resultline[MAXLINE];
     
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt, c2;
     int jl=0;
     int i1, j1, jk, stepsize=0;
     int count=0;
   
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
     int mobilav=0,popforecast=0;
     int hstepm=0, nhstepm=0;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110., age, agelim=0., agebase=0.;
     double ftolpl=FTOL;
     double **prlim;
     double **bprlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double **hess; /* Hessian matrix */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     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;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
     syscompilerinfo(0);
     printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       if(!fgets(pathr,FILENAMELENGTH,stdin)){
         printf("ERROR Empty parameter file name\n");
         goto end;
       }
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
       }
       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);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Main Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"Version %s %s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo(1);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileresu, optionfilefiname); /* Without r in front */
     strcat(fileres,".txt");    /* Other files have txt extension */
     strcat(fileresu,".txt");    /* Other files have txt extension */
   
     /* Main ---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileresu);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   
       /* First 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,"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++;
       printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     }
     /* Second 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,"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);
     /* if(model[0]=='#'|| model[0]== '\0'){ */
     if(model[0]=='#'){
       printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
    'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
    'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
       if(mle != -1){
         printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
         exit(1);
       }
     }
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       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);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     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*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
     else
       ncovmodel=2; /* Constant and age */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }  else if(mle==-5) { /* Main Wizard */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You chose 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);
       matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
     }  else{ /* Begin of mle != -1 or -5 */
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
                           j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
                                   if(jj==i) continue;
                                   j++;
                                   fscanf(ficpar,"%1d%1d",&i1,&j1);
                                   if ((i1 != i) || (j1 != jj)){
                                           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 \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
                                           exit(1);
                                   }
                                   fprintf(ficparo,"%1d%1d",i1,j1);
                                   if(mle==1)
                                           printf("%1d%1d",i,jj);
                                   fprintf(ficlog,"%1d%1d",i,jj);
                                   for(k=1; k<=ncovmodel;k++){
                                           fscanf(ficpar," %lf",&param[i][j][k]);
                                           if(mle==1){
                                                   printf(" %lf",param[i][j][k]);
                                                   fprintf(ficlog," %lf",param[i][j][k]);
                                           }
                                           else
                                                   fprintf(ficlog," %lf",param[i][j][k]);
                                           fprintf(ficparo," %lf",param[i][j][k]);
                                   }
                                   fscanf(ficpar,"\n");
                                   numlinepar++;
                                   if(mle==1)
                                           printf("\n");
                                   fprintf(ficlog,"\n");
                                   fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
                                   fscanf(ficpar,"%1d%1d",&i1,&j1);
                                   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);
                                           exit(1);
                                   }
                                   printf("%1d%1d",i,j);
                                   fprintf(ficparo,"%1d%1d",i1,j1);
                                   fprintf(ficlog,"%1d%1d",i1,j1);
                                   for(k=1; k<=ncovmodel;k++){
                                           fscanf(ficpar,"%le",&delti3[i][j][k]);
                                           printf(" %le",delti3[i][j][k]);
                                           fprintf(ficparo," %le",delti3[i][j][k]);
                                           fprintf(ficlog," %le",delti3[i][j][k]);
                                   }
                                   fscanf(ficpar,"\n");
                                   numlinepar++;
                                   printf("\n");
                                   fprintf(ficparo,"\n");
                                   fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
                   
       /* Reads covariance matrix */
       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 */
                   
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
                   
       matcov=matrix(1,npar,1,npar);
       hess=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
                   
       /* Scans npar lines */
       for(i=1; i <=npar; i++){
         count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
         if(count != 3){
           printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
   This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
   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++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
                                   printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       /* End of read covariance matrix npar lines */
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", rfileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
     
     /*  Main data
      */
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     weight=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     for(i=1;i<=n;i++){
                   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);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     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 */
     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 */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     Tvarsel=ivector(1,NCOVMAX); /*  */
     Tvalsel=vector(1,NCOVMAX); /*  */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         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.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     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
        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 */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
     Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 , 
                                   * V1 df, V2 qf, V3 & V4 dv, V5 qv
                                   * Tmodelind[1]@9={9,0,3,2,}*/
     TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
     TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual quantitative, fixed or varying:
                                   * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                   * 3, 1, 0, 0, 0, 0, 0, 0},
                                   * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   /* Main decodemodel */
   
   
     if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     /* free_vector(moisdc,1,n); */
     /* free_vector(andc,1,n); */
     /* */
     
     wav=ivector(1,imx);
     /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
     /* bh=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: 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);
     /* */
    
     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); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     cptcoveff=0;
     if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
       tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     }
     
     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).*/
     /* 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) */
     /*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).*/
     /* 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) */
     m=pow(2,cptcoveff);
    
             /**< 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 m=2**k
              * 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
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     2
              *    10     2     1     1     2
              *    11 i=6 1     2     1     2
              *    12     2     2     1     2
              *    13 i=7 1 i=4 1     2     2    
              *    14     2     1     2     2
              *    15 i=8 1     2     2     2
              *    16     2     2     2     2
              */
     /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
        /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
        * and the value of each covariate?
        * 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
        * We are keeping this crazy system in order to be able (in the future?) 
        * to have more than 2 values (0 or 1) for a covariate.
        * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
        * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
        *              bbbbbbbb
        *              76543210     
        *   h-1        00000101 (6-1=5)
        *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
        *           &
        *     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);
   
   
       
     /* Initialisation of ----------- gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-MORT_");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# IMaCh-%s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
   
   
     /* Initialisation of --------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-MORT_");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     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\
   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);
     }
   
     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\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
        and prints on file fileres'p'. */
     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,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= 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 */
           savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
           oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
     /* 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] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
     if (mle==-3){
       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); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
                   
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
       
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
           
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"POW-MORT_"); 
       strcat(filerespow,fileresu);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
       /*     gsl_vector_set(x, 0, 0.0268); */
       /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
                                   matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       fprintf(ficlog,"\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
                                   printf("%f ",matcov[i][j]);
                                   fprintf(ficlog,"%f ",matcov[i][j]);
         }
         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);
       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]));
         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);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   ageminpar=50;
                   agemaxpar=100;
       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,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
       free_matrix(ximort,1,NDIM,1,NDIM);
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
   #ifdef GSL
   #endif
     } /* Endof if mle==-3 mortality only */
     /* Standard  */
     else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
       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 */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       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 */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       
       /*--------- results files --------------*/
       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");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\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);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               fprintf(ficres,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle != 0){
         /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
         ftolhess=ftol; /* Usually correct */
         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");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\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) /* 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");
       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\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.7e",matcov[jj][ll]); 
                           fprintf(ficlog," %.7e",matcov[jj][ll]); 
                           fprintf(ficres," %.7e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       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;
       }
       
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
       
       estepm=0;
       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 (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       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 ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
       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 */    
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficlog,"pop_based=%d\n",popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"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(ficparo,"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);
       printf("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(ficlog,"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.*/
       
       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.*/
       
       /* Results */
       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;
       }
       while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
         if (num_filled == 0)
           resultline[0]='\0';
         else if (num_filled != 1){
           printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
         }
         printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
         decoderesult(resultline);
         while(fgets(line, MAXLINE, ficpar)) {
           /* If line starts with a # it is a comment */
           if (line[0] == '#') {
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
             continue;
           }else
             break;
         }
         if (feof(ficpar))
           break;
         else{ /* Processess output results for this combination of covariate values */
         }                            
       }
   
   
       
       /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       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{
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
       }
       printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
                    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_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
                   
                   
       /* Other results (useful)*/
                   
                   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
       
       /* ncovcombmax=  pow(2,cptcoveff); */
       /*-------------- Variance of one-step probabilities---*/
       k=1;
       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,nlstate+ndeath, 1,ncovcombmax);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
           for(k=1;k<=ncovcombmax;k++)
             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 ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       }
       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------------ */
   
       free_ivector(wav,1,imx);
       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);   
                   
                   
       /*---------- Health expectancies, no variances ------------*/
                   
       strcpy(filerese,"E_");
       strcat(filerese,fileresu);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("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' ...", filerese);fflush(stdout);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
                   
       for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         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);
       }
       fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
                   
       /*---------- State-specific expectancies and variances ------------*/
                   
                   
       strcpy(filerest,"T_");
       strcat(filerest,fileresu);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("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); fflush(stdout);
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
                   
   
       strcpy(fileresstde,"STDE_");
       strcat(fileresstde,fileresu);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with State specific 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 State-specific 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_");
       strcat(filerescve,fileresu);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. State-specific 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 State-specific Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"V_");
       strcat(fileresv,fileresu);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("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 State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
       fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);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++){
         printf("\n#****** ");
         fprintf(ficrest,"\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         fprintf(ficrest,"******\n");
         fprintf(ficlog,"******\n");
         printf("******\n");
         
         fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");
         
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvij,"******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         printf(" cvevsij combination#=%d, ",k);
         fprintf(ficlog, " cvevsij combination#=%d, ",k);
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
         printf(" end cvevsij \n ");
         fprintf(ficlog, " end cvevsij \n ");
         
         /*
          */
         /* goto endfree; */
         
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         pstamp(ficrest);
         
         
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           cptcod= 0; /* To be deleted */
           printf("varevsij vpopbased=%d \n",vpopbased);
           fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           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);
           else
             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");
           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
           epj=vector(1,nlstate+1);
           printf("Computing age specific period (stable) prevalences in each health state \n");
           fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
             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];
               }
             }
             
             fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
             /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
             /* printf(" age %4.0f ",age); */
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               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]); */
               }
               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");
           }
         } /* End vpopbased */
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
         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_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
       
       
       /*---------- End : free ----------------*/
       if (mobilav!=0 ||mobilavproj !=0)
         free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
       free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     }  /* mle==-3 arrives here for freeing */
     /* endfree:*/
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
     free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
     free_matrix(coqvar,1,maxwav,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     free_matrix(hess,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     
     free_ivector(ncodemax,1,NCOVMAX);
     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(Tvarsel,1,NCOVMAX);
     free_vector(Tvalsel,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     free_ivector(TmodelInvind,1,NCOVMAX);
     free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */
     fflush(fichtm);
     fflush(ficgp);
     
     
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     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); 
     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));
     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));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
     
     
     printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
     if (_chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(_getcwd(pathcd,MAXLINE) > 0)
   #else
       if(chdir(pathcd) != 0)
         printf("Can't move to directory %s!\n", path);
     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     
     if((outcmd=system(plotcmd)) != 0){
       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");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
   end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: "); fflush(stdout);
       scanf("%s",z);
     }
   }

Removed from v.1.2  
changed lines
  Added in v.1.230


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