Annotation of imach096d/src/imach.c, revision 1.53

1.53    ! brouard     1: /* $Id: imach.c,v 1.52 2002/07/19 18:49:30 brouard Exp $
        !             2:    Interpolated Markov Chain
        !             3: 
        !             4:   Short summary of the programme:
        !             5:   
        !             6:   This program computes Healthy Life Expectancies from
        !             7:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
        !             8:   first survey ("cross") where individuals from different ages are
        !             9:   interviewed on their health status or degree of disability (in the
        !            10:   case of a health survey which is our main interest) -2- at least a
        !            11:   second wave of interviews ("longitudinal") which measure each change
        !            12:   (if any) in individual health status.  Health expectancies are
        !            13:   computed from the time spent in each health state according to a
        !            14:   model. More health states you consider, more time is necessary to reach the
        !            15:   Maximum Likelihood of the parameters involved in the model.  The
        !            16:   simplest model is the multinomial logistic model where pij is the
        !            17:   probability to be observed in state j at the second wave
        !            18:   conditional to be observed in state i at the first wave. Therefore
        !            19:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
        !            20:   'age' is age and 'sex' is a covariate. If you want to have a more
        !            21:   complex model than "constant and age", you should modify the program
        !            22:   where the markup *Covariates have to be included here again* invites
        !            23:   you to do it.  More covariates you add, slower the
        !            24:   convergence.
        !            25: 
        !            26:   The advantage of this computer programme, compared to a simple
        !            27:   multinomial logistic model, is clear when the delay between waves is not
        !            28:   identical for each individual. Also, if a individual missed an
        !            29:   intermediate interview, the information is lost, but taken into
        !            30:   account using an interpolation or extrapolation.  
        !            31: 
        !            32:   hPijx is the probability to be observed in state i at age x+h
        !            33:   conditional to the observed state i at age x. The delay 'h' can be
        !            34:   split into an exact number (nh*stepm) of unobserved intermediate
        !            35:   states. This elementary transition (by month or quarter trimester,
        !            36:   semester or year) is model as a multinomial logistic.  The hPx
        !            37:   matrix is simply the matrix product of nh*stepm elementary matrices
        !            38:   and the contribution of each individual to the likelihood is simply
        !            39:   hPijx.
        !            40: 
        !            41:   Also this programme outputs the covariance matrix of the parameters but also
        !            42:   of the life expectancies. It also computes the prevalence limits. 
        !            43:   
        !            44:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
        !            45:            Institut national d'études démographiques, Paris.
        !            46:   This software have been partly granted by Euro-REVES, a concerted action
        !            47:   from the European Union.
        !            48:   It is copyrighted identically to a GNU software product, ie programme and
        !            49:   software can be distributed freely for non commercial use. Latest version
        !            50:   can be accessed at http://euroreves.ined.fr/imach .
        !            51:   **********************************************************************/
        !            52:  
        !            53: #include <math.h>
        !            54: #include <stdio.h>
        !            55: #include <stdlib.h>
        !            56: #include <unistd.h>
        !            57: 
        !            58: #define MAXLINE 256
        !            59: #define GNUPLOTPROGRAM "gnuplot"
        !            60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
        !            61: #define FILENAMELENGTH 80
        !            62: /*#define DEBUG*/
        !            63: #define unix
        !            64: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
        !            65: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
        !            66: 
        !            67: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
        !            68: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
        !            69: 
        !            70: #define NINTERVMAX 8
        !            71: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
        !            72: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
        !            73: #define NCOVMAX 8 /* Maximum number of covariates */
        !            74: #define MAXN 20000
        !            75: #define YEARM 12. /* Number of months per year */
        !            76: #define AGESUP 130
        !            77: #define AGEBASE 40
        !            78: #ifdef windows
        !            79: #define DIRSEPARATOR '\\'
        !            80: #define ODIRSEPARATOR '/'
        !            81: #else
        !            82: #define DIRSEPARATOR '/'
        !            83: #define ODIRSEPARATOR '\\'
        !            84: #endif
        !            85: 
        !            86: char version[80]="Imach version 0.8j, July 2002, INED-EUROREVES ";
        !            87: int erreur; /* Error number */
        !            88: int nvar;
        !            89: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
        !            90: int npar=NPARMAX;
        !            91: int nlstate=2; /* Number of live states */
        !            92: int ndeath=1; /* Number of dead states */
        !            93: int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
        !            94: int popbased=0;
        !            95: 
        !            96: int *wav; /* Number of waves for this individuual 0 is possible */
        !            97: int maxwav; /* Maxim number of waves */
        !            98: int jmin, jmax; /* min, max spacing between 2 waves */
        !            99: int mle, weightopt;
        !           100: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
        !           101: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
        !           102: double jmean; /* Mean space between 2 waves */
        !           103: double **oldm, **newm, **savm; /* Working pointers to matrices */
        !           104: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
        !           105: FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
        !           106: FILE *ficlog;
        !           107: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
        !           108: FILE *ficresprobmorprev;
        !           109: FILE *fichtm; /* Html File */
        !           110: FILE *ficreseij;
        !           111: char filerese[FILENAMELENGTH];
        !           112: FILE  *ficresvij;
        !           113: char fileresv[FILENAMELENGTH];
        !           114: FILE  *ficresvpl;
        !           115: char fileresvpl[FILENAMELENGTH];
        !           116: char title[MAXLINE];
        !           117: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
        !           118: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
        !           119: 
        !           120: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
        !           121: char filelog[FILENAMELENGTH]; /* Log file */
        !           122: char filerest[FILENAMELENGTH];
        !           123: char fileregp[FILENAMELENGTH];
        !           124: char popfile[FILENAMELENGTH];
        !           125: 
        !           126: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
        !           127: 
        !           128: #define NR_END 1
        !           129: #define FREE_ARG char*
        !           130: #define FTOL 1.0e-10
        !           131: 
        !           132: #define NRANSI 
        !           133: #define ITMAX 200 
        !           134: 
        !           135: #define TOL 2.0e-4 
        !           136: 
        !           137: #define CGOLD 0.3819660 
        !           138: #define ZEPS 1.0e-10 
        !           139: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
        !           140: 
        !           141: #define GOLD 1.618034 
        !           142: #define GLIMIT 100.0 
        !           143: #define TINY 1.0e-20 
        !           144: 
        !           145: static double maxarg1,maxarg2;
        !           146: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
        !           147: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
        !           148:   
        !           149: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
        !           150: #define rint(a) floor(a+0.5)
        !           151: 
        !           152: static double sqrarg;
        !           153: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
        !           154: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
        !           155: 
        !           156: int imx; 
        !           157: int stepm;
        !           158: /* Stepm, step in month: minimum step interpolation*/
        !           159: 
        !           160: int estepm;
        !           161: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
        !           162: 
        !           163: int m,nb;
        !           164: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
        !           165: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
        !           166: double **pmmij, ***probs, ***mobaverage;
        !           167: double dateintmean=0;
        !           168: 
        !           169: double *weight;
        !           170: int **s; /* Status */
        !           171: double *agedc, **covar, idx;
        !           172: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
        !           173: 
        !           174: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
        !           175: double ftolhess; /* Tolerance for computing hessian */
        !           176: 
        !           177: /**************** split *************************/
        !           178: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
        !           179: {
        !           180:    char        *s;                             /* pointer */
        !           181:    int l1, l2;                         /* length counters */
        !           182: 
        !           183:    l1 = strlen( path );                        /* length of path */
        !           184:    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
        !           185:    s= strrchr( path, DIRSEPARATOR );           /* find last / */
        !           186:    if ( s == NULL ) {                  /* no directory, so use current */
        !           187:      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
        !           188:        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        !           189: #if    defined(__bsd__)                /* get current working directory */
        !           190:       extern char      *getwd( );
        !           191: 
        !           192:       if ( getwd( dirc ) == NULL ) {
        !           193: #else
        !           194:       extern char      *getcwd( );
        !           195: 
        !           196:       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
        !           197: #endif
        !           198:          return( GLOCK_ERROR_GETCWD );
        !           199:       }
        !           200:       strcpy( name, path );            /* we've got it */
        !           201:    } else {                            /* strip direcotry from path */
        !           202:       s++;                             /* after this, the filename */
        !           203:       l2 = strlen( s );                        /* length of filename */
        !           204:       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        !           205:       strcpy( name, s );               /* save file name */
        !           206:       strncpy( dirc, path, l1 - l2 );  /* now the directory */
        !           207:       dirc[l1-l2] = 0;                 /* add zero */
        !           208:    }
        !           209:    l1 = strlen( dirc );                        /* length of directory */
        !           210: #ifdef windows
        !           211:    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
        !           212: #else
        !           213:    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
        !           214: #endif
        !           215:    s = strrchr( name, '.' );           /* find last / */
        !           216:    s++;
        !           217:    strcpy(ext,s);                      /* save extension */
        !           218:    l1= strlen( name);
        !           219:    l2= strlen( s)+1;
        !           220:    strncpy( finame, name, l1-l2);
        !           221:    finame[l1-l2]= 0;
        !           222:    return( 0 );                                /* we're done */
        !           223: }
        !           224: 
        !           225: 
        !           226: /******************************************/
        !           227: 
        !           228: void replace(char *s, char*t)
        !           229: {
        !           230:   int i;
        !           231:   int lg=20;
        !           232:   i=0;
        !           233:   lg=strlen(t);
        !           234:   for(i=0; i<= lg; i++) {
        !           235:     (s[i] = t[i]);
        !           236:     if (t[i]== '\\') s[i]='/';
        !           237:   }
        !           238: }
        !           239: 
        !           240: int nbocc(char *s, char occ)
        !           241: {
        !           242:   int i,j=0;
        !           243:   int lg=20;
        !           244:   i=0;
        !           245:   lg=strlen(s);
        !           246:   for(i=0; i<= lg; i++) {
        !           247:   if  (s[i] == occ ) j++;
        !           248:   }
        !           249:   return j;
        !           250: }
        !           251: 
        !           252: void cutv(char *u,char *v, char*t, char occ)
        !           253: {
        !           254:   /* cuts string t into u and v where u is ended by char occ excluding it
        !           255:      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        !           256:      gives u="abcedf" and v="ghi2j" */
        !           257:   int i,lg,j,p=0;
        !           258:   i=0;
        !           259:   for(j=0; j<=strlen(t)-1; j++) {
        !           260:     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
        !           261:   }
        !           262: 
        !           263:   lg=strlen(t);
        !           264:   for(j=0; j<p; j++) {
        !           265:     (u[j] = t[j]);
        !           266:   }
        !           267:      u[p]='\0';
        !           268: 
        !           269:    for(j=0; j<= lg; j++) {
        !           270:     if (j>=(p+1))(v[j-p-1] = t[j]);
        !           271:   }
        !           272: }
        !           273: 
        !           274: /********************** nrerror ********************/
        !           275: 
        !           276: void nrerror(char error_text[])
        !           277: {
        !           278:   fprintf(stderr,"ERREUR ...\n");
        !           279:   fprintf(stderr,"%s\n",error_text);
        !           280:   exit(1);
        !           281: }
        !           282: /*********************** vector *******************/
        !           283: double *vector(int nl, int nh)
        !           284: {
        !           285:   double *v;
        !           286:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
        !           287:   if (!v) nrerror("allocation failure in vector");
        !           288:   return v-nl+NR_END;
        !           289: }
        !           290: 
        !           291: /************************ free vector ******************/
        !           292: void free_vector(double*v, int nl, int nh)
        !           293: {
        !           294:   free((FREE_ARG)(v+nl-NR_END));
        !           295: }
        !           296: 
        !           297: /************************ivector *******************************/
        !           298: int *ivector(long nl,long nh)
        !           299: {
        !           300:   int *v;
        !           301:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
        !           302:   if (!v) nrerror("allocation failure in ivector");
        !           303:   return v-nl+NR_END;
        !           304: }
        !           305: 
        !           306: /******************free ivector **************************/
        !           307: void free_ivector(int *v, long nl, long nh)
        !           308: {
        !           309:   free((FREE_ARG)(v+nl-NR_END));
        !           310: }
        !           311: 
        !           312: /******************* imatrix *******************************/
        !           313: int **imatrix(long nrl, long nrh, long ncl, long nch) 
        !           314:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
        !           315: { 
        !           316:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
        !           317:   int **m; 
        !           318:   
        !           319:   /* allocate pointers to rows */ 
        !           320:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
        !           321:   if (!m) nrerror("allocation failure 1 in matrix()"); 
        !           322:   m += NR_END; 
        !           323:   m -= nrl; 
        !           324:   
        !           325:   
        !           326:   /* allocate rows and set pointers to them */ 
        !           327:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
        !           328:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
        !           329:   m[nrl] += NR_END; 
        !           330:   m[nrl] -= ncl; 
        !           331:   
        !           332:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
        !           333:   
        !           334:   /* return pointer to array of pointers to rows */ 
        !           335:   return m; 
        !           336: } 
        !           337: 
        !           338: /****************** free_imatrix *************************/
        !           339: void free_imatrix(m,nrl,nrh,ncl,nch)
        !           340:       int **m;
        !           341:       long nch,ncl,nrh,nrl; 
        !           342:      /* free an int matrix allocated by imatrix() */ 
        !           343: { 
        !           344:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
        !           345:   free((FREE_ARG) (m+nrl-NR_END)); 
        !           346: } 
        !           347: 
        !           348: /******************* matrix *******************************/
        !           349: double **matrix(long nrl, long nrh, long ncl, long nch)
        !           350: {
        !           351:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
        !           352:   double **m;
        !           353: 
        !           354:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
        !           355:   if (!m) nrerror("allocation failure 1 in matrix()");
        !           356:   m += NR_END;
        !           357:   m -= nrl;
        !           358: 
        !           359:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
        !           360:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
        !           361:   m[nrl] += NR_END;
        !           362:   m[nrl] -= ncl;
        !           363: 
        !           364:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
        !           365:   return m;
        !           366: }
        !           367: 
        !           368: /*************************free matrix ************************/
        !           369: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
        !           370: {
        !           371:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
        !           372:   free((FREE_ARG)(m+nrl-NR_END));
        !           373: }
        !           374: 
        !           375: /******************* ma3x *******************************/
        !           376: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
        !           377: {
        !           378:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
        !           379:   double ***m;
        !           380: 
        !           381:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
        !           382:   if (!m) nrerror("allocation failure 1 in matrix()");
        !           383:   m += NR_END;
        !           384:   m -= nrl;
        !           385: 
        !           386:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
        !           387:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
        !           388:   m[nrl] += NR_END;
        !           389:   m[nrl] -= ncl;
        !           390: 
        !           391:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
        !           392: 
        !           393:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
        !           394:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
        !           395:   m[nrl][ncl] += NR_END;
        !           396:   m[nrl][ncl] -= nll;
        !           397:   for (j=ncl+1; j<=nch; j++) 
        !           398:     m[nrl][j]=m[nrl][j-1]+nlay;
        !           399:   
        !           400:   for (i=nrl+1; i<=nrh; i++) {
        !           401:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
        !           402:     for (j=ncl+1; j<=nch; j++) 
        !           403:       m[i][j]=m[i][j-1]+nlay;
        !           404:   }
        !           405:   return m;
        !           406: }
        !           407: 
        !           408: /*************************free ma3x ************************/
        !           409: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
        !           410: {
        !           411:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
        !           412:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
        !           413:   free((FREE_ARG)(m+nrl-NR_END));
        !           414: }
        !           415: 
        !           416: /***************** f1dim *************************/
        !           417: extern int ncom; 
        !           418: extern double *pcom,*xicom;
        !           419: extern double (*nrfunc)(double []); 
        !           420:  
        !           421: double f1dim(double x) 
        !           422: { 
        !           423:   int j; 
        !           424:   double f;
        !           425:   double *xt; 
        !           426:  
        !           427:   xt=vector(1,ncom); 
        !           428:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
        !           429:   f=(*nrfunc)(xt); 
        !           430:   free_vector(xt,1,ncom); 
        !           431:   return f; 
        !           432: } 
        !           433: 
        !           434: /*****************brent *************************/
        !           435: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
        !           436: { 
        !           437:   int iter; 
        !           438:   double a,b,d,etemp;
        !           439:   double fu,fv,fw,fx;
        !           440:   double ftemp;
        !           441:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
        !           442:   double e=0.0; 
        !           443:  
        !           444:   a=(ax < cx ? ax : cx); 
        !           445:   b=(ax > cx ? ax : cx); 
        !           446:   x=w=v=bx; 
        !           447:   fw=fv=fx=(*f)(x); 
        !           448:   for (iter=1;iter<=ITMAX;iter++) { 
        !           449:     xm=0.5*(a+b); 
        !           450:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
        !           451:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        !           452:     printf(".");fflush(stdout);
        !           453:     fprintf(ficlog,".");fflush(ficlog);
        !           454: #ifdef DEBUG
        !           455:     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);
        !           456:     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);
        !           457:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
        !           458: #endif
        !           459:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
        !           460:       *xmin=x; 
        !           461:       return fx; 
        !           462:     } 
        !           463:     ftemp=fu;
        !           464:     if (fabs(e) > tol1) { 
        !           465:       r=(x-w)*(fx-fv); 
        !           466:       q=(x-v)*(fx-fw); 
        !           467:       p=(x-v)*q-(x-w)*r; 
        !           468:       q=2.0*(q-r); 
        !           469:       if (q > 0.0) p = -p; 
        !           470:       q=fabs(q); 
        !           471:       etemp=e; 
        !           472:       e=d; 
        !           473:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
        !           474:        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
        !           475:       else { 
        !           476:        d=p/q; 
        !           477:        u=x+d; 
        !           478:        if (u-a < tol2 || b-u < tol2) 
        !           479:          d=SIGN(tol1,xm-x); 
        !           480:       } 
        !           481:     } else { 
        !           482:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
        !           483:     } 
        !           484:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        !           485:     fu=(*f)(u); 
        !           486:     if (fu <= fx) { 
        !           487:       if (u >= x) a=x; else b=x; 
        !           488:       SHFT(v,w,x,u) 
        !           489:        SHFT(fv,fw,fx,fu) 
        !           490:        } else { 
        !           491:          if (u < x) a=u; else b=u; 
        !           492:          if (fu <= fw || w == x) { 
        !           493:            v=w; 
        !           494:            w=u; 
        !           495:            fv=fw; 
        !           496:            fw=fu; 
        !           497:          } else if (fu <= fv || v == x || v == w) { 
        !           498:            v=u; 
        !           499:            fv=fu; 
        !           500:          } 
        !           501:        } 
        !           502:   } 
        !           503:   nrerror("Too many iterations in brent"); 
        !           504:   *xmin=x; 
        !           505:   return fx; 
        !           506: } 
        !           507: 
        !           508: /****************** mnbrak ***********************/
        !           509: 
        !           510: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
        !           511:            double (*func)(double)) 
        !           512: { 
        !           513:   double ulim,u,r,q, dum;
        !           514:   double fu; 
        !           515:  
        !           516:   *fa=(*func)(*ax); 
        !           517:   *fb=(*func)(*bx); 
        !           518:   if (*fb > *fa) { 
        !           519:     SHFT(dum,*ax,*bx,dum) 
        !           520:       SHFT(dum,*fb,*fa,dum) 
        !           521:       } 
        !           522:   *cx=(*bx)+GOLD*(*bx-*ax); 
        !           523:   *fc=(*func)(*cx); 
        !           524:   while (*fb > *fc) { 
        !           525:     r=(*bx-*ax)*(*fb-*fc); 
        !           526:     q=(*bx-*cx)*(*fb-*fa); 
        !           527:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
        !           528:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        !           529:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
        !           530:     if ((*bx-u)*(u-*cx) > 0.0) { 
        !           531:       fu=(*func)(u); 
        !           532:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
        !           533:       fu=(*func)(u); 
        !           534:       if (fu < *fc) { 
        !           535:        SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
        !           536:          SHFT(*fb,*fc,fu,(*func)(u)) 
        !           537:          } 
        !           538:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
        !           539:       u=ulim; 
        !           540:       fu=(*func)(u); 
        !           541:     } else { 
        !           542:       u=(*cx)+GOLD*(*cx-*bx); 
        !           543:       fu=(*func)(u); 
        !           544:     } 
        !           545:     SHFT(*ax,*bx,*cx,u) 
        !           546:       SHFT(*fa,*fb,*fc,fu) 
        !           547:       } 
        !           548: } 
        !           549: 
        !           550: /*************** linmin ************************/
        !           551: 
        !           552: int ncom; 
        !           553: double *pcom,*xicom;
        !           554: double (*nrfunc)(double []); 
        !           555:  
        !           556: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
        !           557: { 
        !           558:   double brent(double ax, double bx, double cx, 
        !           559:               double (*f)(double), double tol, double *xmin); 
        !           560:   double f1dim(double x); 
        !           561:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
        !           562:              double *fc, double (*func)(double)); 
        !           563:   int j; 
        !           564:   double xx,xmin,bx,ax; 
        !           565:   double fx,fb,fa;
        !           566:  
        !           567:   ncom=n; 
        !           568:   pcom=vector(1,n); 
        !           569:   xicom=vector(1,n); 
        !           570:   nrfunc=func; 
        !           571:   for (j=1;j<=n;j++) { 
        !           572:     pcom[j]=p[j]; 
        !           573:     xicom[j]=xi[j]; 
        !           574:   } 
        !           575:   ax=0.0; 
        !           576:   xx=1.0; 
        !           577:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
        !           578:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
        !           579: #ifdef DEBUG
        !           580:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
        !           581:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
        !           582: #endif
        !           583:   for (j=1;j<=n;j++) { 
        !           584:     xi[j] *= xmin; 
        !           585:     p[j] += xi[j]; 
        !           586:   } 
        !           587:   free_vector(xicom,1,n); 
        !           588:   free_vector(pcom,1,n); 
        !           589: } 
        !           590: 
        !           591: /*************** powell ************************/
        !           592: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
        !           593:            double (*func)(double [])) 
        !           594: { 
        !           595:   void linmin(double p[], double xi[], int n, double *fret, 
        !           596:              double (*func)(double [])); 
        !           597:   int i,ibig,j; 
        !           598:   double del,t,*pt,*ptt,*xit;
        !           599:   double fp,fptt;
        !           600:   double *xits;
        !           601:   pt=vector(1,n); 
        !           602:   ptt=vector(1,n); 
        !           603:   xit=vector(1,n); 
        !           604:   xits=vector(1,n); 
        !           605:   *fret=(*func)(p); 
        !           606:   for (j=1;j<=n;j++) pt[j]=p[j]; 
        !           607:   for (*iter=1;;++(*iter)) { 
        !           608:     fp=(*fret); 
        !           609:     ibig=0; 
        !           610:     del=0.0; 
        !           611:     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
        !           612:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
        !           613:     for (i=1;i<=n;i++) 
        !           614:       printf(" %d %.12f",i, p[i]);
        !           615:     fprintf(ficlog," %d %.12f",i, p[i]);
        !           616:     printf("\n");
        !           617:     fprintf(ficlog,"\n");
        !           618:     for (i=1;i<=n;i++) { 
        !           619:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
        !           620:       fptt=(*fret); 
        !           621: #ifdef DEBUG
        !           622:       printf("fret=%lf \n",*fret);
        !           623:       fprintf(ficlog,"fret=%lf \n",*fret);
        !           624: #endif
        !           625:       printf("%d",i);fflush(stdout);
        !           626:       fprintf(ficlog,"%d",i);fflush(ficlog);
        !           627:       linmin(p,xit,n,fret,func); 
        !           628:       if (fabs(fptt-(*fret)) > del) { 
        !           629:        del=fabs(fptt-(*fret)); 
        !           630:        ibig=i; 
        !           631:       } 
        !           632: #ifdef DEBUG
        !           633:       printf("%d %.12e",i,(*fret));
        !           634:       fprintf(ficlog,"%d %.12e",i,(*fret));
        !           635:       for (j=1;j<=n;j++) {
        !           636:        xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
        !           637:        printf(" x(%d)=%.12e",j,xit[j]);
        !           638:        fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        !           639:       }
        !           640:       for(j=1;j<=n;j++) {
        !           641:        printf(" p=%.12e",p[j]);
        !           642:        fprintf(ficlog," p=%.12e",p[j]);
        !           643:       }
        !           644:       printf("\n");
        !           645:       fprintf(ficlog,"\n");
        !           646: #endif
        !           647:     } 
        !           648:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
        !           649: #ifdef DEBUG
        !           650:       int k[2],l;
        !           651:       k[0]=1;
        !           652:       k[1]=-1;
        !           653:       printf("Max: %.12e",(*func)(p));
        !           654:       fprintf(ficlog,"Max: %.12e",(*func)(p));
        !           655:       for (j=1;j<=n;j++) {
        !           656:        printf(" %.12e",p[j]);
        !           657:        fprintf(ficlog," %.12e",p[j]);
        !           658:       }
        !           659:       printf("\n");
        !           660:       fprintf(ficlog,"\n");
        !           661:       for(l=0;l<=1;l++) {
        !           662:        for (j=1;j<=n;j++) {
        !           663:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
        !           664:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
        !           665:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
        !           666:        }
        !           667:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        !           668:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        !           669:       }
        !           670: #endif
        !           671: 
        !           672: 
        !           673:       free_vector(xit,1,n); 
        !           674:       free_vector(xits,1,n); 
        !           675:       free_vector(ptt,1,n); 
        !           676:       free_vector(pt,1,n); 
        !           677:       return; 
        !           678:     } 
        !           679:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        !           680:     for (j=1;j<=n;j++) { 
        !           681:       ptt[j]=2.0*p[j]-pt[j]; 
        !           682:       xit[j]=p[j]-pt[j]; 
        !           683:       pt[j]=p[j]; 
        !           684:     } 
        !           685:     fptt=(*func)(ptt); 
        !           686:     if (fptt < fp) { 
        !           687:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
        !           688:       if (t < 0.0) { 
        !           689:        linmin(p,xit,n,fret,func); 
        !           690:        for (j=1;j<=n;j++) { 
        !           691:          xi[j][ibig]=xi[j][n]; 
        !           692:          xi[j][n]=xit[j]; 
        !           693:        }
        !           694: #ifdef DEBUG
        !           695:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
        !           696:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
        !           697:        for(j=1;j<=n;j++){
        !           698:          printf(" %.12e",xit[j]);
        !           699:          fprintf(ficlog," %.12e",xit[j]);
        !           700:        }
        !           701:        printf("\n");
        !           702:        fprintf(ficlog,"\n");
        !           703: #endif
        !           704:       } 
        !           705:     } 
        !           706:   } 
        !           707: } 
        !           708: 
        !           709: /**** Prevalence limit ****************/
        !           710: 
        !           711: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
        !           712: {
        !           713:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        !           714:      matrix by transitions matrix until convergence is reached */
        !           715: 
        !           716:   int i, ii,j,k;
        !           717:   double min, max, maxmin, maxmax,sumnew=0.;
        !           718:   double **matprod2();
        !           719:   double **out, cov[NCOVMAX], **pmij();
        !           720:   double **newm;
        !           721:   double agefin, delaymax=50 ; /* Max number of years to converge */
        !           722: 
        !           723:   for (ii=1;ii<=nlstate+ndeath;ii++)
        !           724:     for (j=1;j<=nlstate+ndeath;j++){
        !           725:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        !           726:     }
        !           727: 
        !           728:    cov[1]=1.;
        !           729:  
        !           730:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        !           731:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        !           732:     newm=savm;
        !           733:     /* Covariates have to be included here again */
        !           734:      cov[2]=agefin;
        !           735:   
        !           736:       for (k=1; k<=cptcovn;k++) {
        !           737:        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        !           738:        /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
        !           739:       }
        !           740:       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        !           741:       for (k=1; k<=cptcovprod;k++)
        !           742:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        !           743: 
        !           744:       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        !           745:       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
        !           746:       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
        !           747:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
        !           748: 
        !           749:     savm=oldm;
        !           750:     oldm=newm;
        !           751:     maxmax=0.;
        !           752:     for(j=1;j<=nlstate;j++){
        !           753:       min=1.;
        !           754:       max=0.;
        !           755:       for(i=1; i<=nlstate; i++) {
        !           756:        sumnew=0;
        !           757:        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
        !           758:        prlim[i][j]= newm[i][j]/(1-sumnew);
        !           759:        max=FMAX(max,prlim[i][j]);
        !           760:        min=FMIN(min,prlim[i][j]);
        !           761:       }
        !           762:       maxmin=max-min;
        !           763:       maxmax=FMAX(maxmax,maxmin);
        !           764:     }
        !           765:     if(maxmax < ftolpl){
        !           766:       return prlim;
        !           767:     }
        !           768:   }
        !           769: }
        !           770: 
        !           771: /*************** transition probabilities ***************/ 
        !           772: 
        !           773: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
        !           774: {
        !           775:   double s1, s2;
        !           776:   /*double t34;*/
        !           777:   int i,j,j1, nc, ii, jj;
        !           778: 
        !           779:     for(i=1; i<= nlstate; i++){
        !           780:     for(j=1; j<i;j++){
        !           781:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
        !           782:        /*s2 += param[i][j][nc]*cov[nc];*/
        !           783:        s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
        !           784:        /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
        !           785:       }
        !           786:       ps[i][j]=s2;
        !           787:       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
        !           788:     }
        !           789:     for(j=i+1; j<=nlstate+ndeath;j++){
        !           790:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
        !           791:        s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
        !           792:        /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
        !           793:       }
        !           794:       ps[i][j]=s2;
        !           795:     }
        !           796:   }
        !           797:     /*ps[3][2]=1;*/
        !           798: 
        !           799:   for(i=1; i<= nlstate; i++){
        !           800:      s1=0;
        !           801:     for(j=1; j<i; j++)
        !           802:       s1+=exp(ps[i][j]);
        !           803:     for(j=i+1; j<=nlstate+ndeath; j++)
        !           804:       s1+=exp(ps[i][j]);
        !           805:     ps[i][i]=1./(s1+1.);
        !           806:     for(j=1; j<i; j++)
        !           807:       ps[i][j]= exp(ps[i][j])*ps[i][i];
        !           808:     for(j=i+1; j<=nlstate+ndeath; j++)
        !           809:       ps[i][j]= exp(ps[i][j])*ps[i][i];
        !           810:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        !           811:   } /* end i */
        !           812: 
        !           813:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        !           814:     for(jj=1; jj<= nlstate+ndeath; jj++){
        !           815:       ps[ii][jj]=0;
        !           816:       ps[ii][ii]=1;
        !           817:     }
        !           818:   }
        !           819: 
        !           820: 
        !           821:   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
        !           822:     for(jj=1; jj<= nlstate+ndeath; jj++){
        !           823:      printf("%lf ",ps[ii][jj]);
        !           824:    }
        !           825:     printf("\n ");
        !           826:     }
        !           827:     printf("\n ");printf("%lf ",cov[2]);*/
        !           828: /*
        !           829:   for(i=1; i<= npar; i++) printf("%f ",x[i]);
        !           830:   goto end;*/
        !           831:     return ps;
        !           832: }
        !           833: 
        !           834: /**************** Product of 2 matrices ******************/
        !           835: 
        !           836: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
        !           837: {
        !           838:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        !           839:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
        !           840:   /* in, b, out are matrice of pointers which should have been initialized 
        !           841:      before: only the contents of out is modified. The function returns
        !           842:      a pointer to pointers identical to out */
        !           843:   long i, j, k;
        !           844:   for(i=nrl; i<= nrh; i++)
        !           845:     for(k=ncolol; k<=ncoloh; k++)
        !           846:       for(j=ncl,out[i][k]=0.; j<=nch; j++)
        !           847:        out[i][k] +=in[i][j]*b[j][k];
        !           848: 
        !           849:   return out;
        !           850: }
        !           851: 
        !           852: 
        !           853: /************* Higher Matrix Product ***************/
        !           854: 
        !           855: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
        !           856: {
        !           857:   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
        !           858:      duration (i.e. until
        !           859:      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
        !           860:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        !           861:      (typically every 2 years instead of every month which is too big).
        !           862:      Model is determined by parameters x and covariates have to be 
        !           863:      included manually here. 
        !           864: 
        !           865:      */
        !           866: 
        !           867:   int i, j, d, h, k;
        !           868:   double **out, cov[NCOVMAX];
        !           869:   double **newm;
        !           870: 
        !           871:   /* Hstepm could be zero and should return the unit matrix */
        !           872:   for (i=1;i<=nlstate+ndeath;i++)
        !           873:     for (j=1;j<=nlstate+ndeath;j++){
        !           874:       oldm[i][j]=(i==j ? 1.0 : 0.0);
        !           875:       po[i][j][0]=(i==j ? 1.0 : 0.0);
        !           876:     }
        !           877:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        !           878:   for(h=1; h <=nhstepm; h++){
        !           879:     for(d=1; d <=hstepm; d++){
        !           880:       newm=savm;
        !           881:       /* Covariates have to be included here again */
        !           882:       cov[1]=1.;
        !           883:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
        !           884:       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        !           885:       for (k=1; k<=cptcovage;k++)
        !           886:        cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        !           887:       for (k=1; k<=cptcovprod;k++)
        !           888:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        !           889: 
        !           890: 
        !           891:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        !           892:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        !           893:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
        !           894:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
        !           895:       savm=oldm;
        !           896:       oldm=newm;
        !           897:     }
        !           898:     for(i=1; i<=nlstate+ndeath; i++)
        !           899:       for(j=1;j<=nlstate+ndeath;j++) {
        !           900:        po[i][j][h]=newm[i][j];
        !           901:        /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
        !           902:         */
        !           903:       }
        !           904:   } /* end h */
        !           905:   return po;
        !           906: }
        !           907: 
        !           908: 
        !           909: /*************** log-likelihood *************/
        !           910: double func( double *x)
        !           911: {
        !           912:   int i, ii, j, k, mi, d, kk;
        !           913:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
        !           914:   double **out;
        !           915:   double sw; /* Sum of weights */
        !           916:   double lli; /* Individual log likelihood */
        !           917:   long ipmx;
        !           918:   /*extern weight */
        !           919:   /* We are differentiating ll according to initial status */
        !           920:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        !           921:   /*for(i=1;i<imx;i++) 
        !           922:     printf(" %d\n",s[4][i]);
        !           923:   */
        !           924:   cov[1]=1.;
        !           925: 
        !           926:   for(k=1; k<=nlstate; k++) ll[k]=0.;
        !           927:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        !           928:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        !           929:     for(mi=1; mi<= wav[i]-1; mi++){
        !           930:       for (ii=1;ii<=nlstate+ndeath;ii++)
        !           931:        for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        !           932:       for(d=0; d<dh[mi][i]; d++){
        !           933:        newm=savm;
        !           934:        cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        !           935:        for (kk=1; kk<=cptcovage;kk++) {
        !           936:          cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        !           937:        }
        !           938:        
        !           939:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        !           940:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        !           941:        savm=oldm;
        !           942:        oldm=newm;
        !           943:        
        !           944:        
        !           945:       } /* end mult */
        !           946:       
        !           947:       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
        !           948:       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
        !           949:       ipmx +=1;
        !           950:       sw += weight[i];
        !           951:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        !           952:     } /* end of wave */
        !           953:   } /* end of individual */
        !           954: 
        !           955:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        !           956:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        !           957:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        !           958:   return -l;
        !           959: }
        !           960: 
        !           961: 
        !           962: /*********** Maximum Likelihood Estimation ***************/
        !           963: 
        !           964: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
        !           965: {
        !           966:   int i,j, iter;
        !           967:   double **xi,*delti;
        !           968:   double fret;
        !           969:   xi=matrix(1,npar,1,npar);
        !           970:   for (i=1;i<=npar;i++)
        !           971:     for (j=1;j<=npar;j++)
        !           972:       xi[i][j]=(i==j ? 1.0 : 0.0);
        !           973:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
        !           974:   powell(p,xi,npar,ftol,&iter,&fret,func);
        !           975: 
        !           976:    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
        !           977:   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        !           978:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        !           979: 
        !           980: }
        !           981: 
        !           982: /**** Computes Hessian and covariance matrix ***/
        !           983: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        !           984: {
        !           985:   double  **a,**y,*x,pd;
        !           986:   double **hess;
        !           987:   int i, j,jk;
        !           988:   int *indx;
        !           989: 
        !           990:   double hessii(double p[], double delta, int theta, double delti[]);
        !           991:   double hessij(double p[], double delti[], int i, int j);
        !           992:   void lubksb(double **a, int npar, int *indx, double b[]) ;
        !           993:   void ludcmp(double **a, int npar, int *indx, double *d) ;
        !           994: 
        !           995:   hess=matrix(1,npar,1,npar);
        !           996: 
        !           997:   printf("\nCalculation of the hessian matrix. Wait...\n");
        !           998:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
        !           999:   for (i=1;i<=npar;i++){
        !          1000:     printf("%d",i);fflush(stdout);
        !          1001:     fprintf(ficlog,"%d",i);fflush(ficlog);
        !          1002:     hess[i][i]=hessii(p,ftolhess,i,delti);
        !          1003:     /*printf(" %f ",p[i]);*/
        !          1004:     /*printf(" %lf ",hess[i][i]);*/
        !          1005:   }
        !          1006:   
        !          1007:   for (i=1;i<=npar;i++) {
        !          1008:     for (j=1;j<=npar;j++)  {
        !          1009:       if (j>i) { 
        !          1010:        printf(".%d%d",i,j);fflush(stdout);
        !          1011:        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
        !          1012:        hess[i][j]=hessij(p,delti,i,j);
        !          1013:        hess[j][i]=hess[i][j];    
        !          1014:        /*printf(" %lf ",hess[i][j]);*/
        !          1015:       }
        !          1016:     }
        !          1017:   }
        !          1018:   printf("\n");
        !          1019:   fprintf(ficlog,"\n");
        !          1020: 
        !          1021:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        !          1022:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        !          1023:   
        !          1024:   a=matrix(1,npar,1,npar);
        !          1025:   y=matrix(1,npar,1,npar);
        !          1026:   x=vector(1,npar);
        !          1027:   indx=ivector(1,npar);
        !          1028:   for (i=1;i<=npar;i++)
        !          1029:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        !          1030:   ludcmp(a,npar,indx,&pd);
        !          1031: 
        !          1032:   for (j=1;j<=npar;j++) {
        !          1033:     for (i=1;i<=npar;i++) x[i]=0;
        !          1034:     x[j]=1;
        !          1035:     lubksb(a,npar,indx,x);
        !          1036:     for (i=1;i<=npar;i++){ 
        !          1037:       matcov[i][j]=x[i];
        !          1038:     }
        !          1039:   }
        !          1040: 
        !          1041:   printf("\n#Hessian matrix#\n");
        !          1042:   fprintf(ficlog,"\n#Hessian matrix#\n");
        !          1043:   for (i=1;i<=npar;i++) { 
        !          1044:     for (j=1;j<=npar;j++) { 
        !          1045:       printf("%.3e ",hess[i][j]);
        !          1046:       fprintf(ficlog,"%.3e ",hess[i][j]);
        !          1047:     }
        !          1048:     printf("\n");
        !          1049:     fprintf(ficlog,"\n");
        !          1050:   }
        !          1051: 
        !          1052:   /* Recompute Inverse */
        !          1053:   for (i=1;i<=npar;i++)
        !          1054:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
        !          1055:   ludcmp(a,npar,indx,&pd);
        !          1056: 
        !          1057:   /*  printf("\n#Hessian matrix recomputed#\n");
        !          1058: 
        !          1059:   for (j=1;j<=npar;j++) {
        !          1060:     for (i=1;i<=npar;i++) x[i]=0;
        !          1061:     x[j]=1;
        !          1062:     lubksb(a,npar,indx,x);
        !          1063:     for (i=1;i<=npar;i++){ 
        !          1064:       y[i][j]=x[i];
        !          1065:       printf("%.3e ",y[i][j]);
        !          1066:       fprintf(ficlog,"%.3e ",y[i][j]);
        !          1067:     }
        !          1068:     printf("\n");
        !          1069:     fprintf(ficlog,"\n");
        !          1070:   }
        !          1071:   */
        !          1072: 
        !          1073:   free_matrix(a,1,npar,1,npar);
        !          1074:   free_matrix(y,1,npar,1,npar);
        !          1075:   free_vector(x,1,npar);
        !          1076:   free_ivector(indx,1,npar);
        !          1077:   free_matrix(hess,1,npar,1,npar);
        !          1078: 
        !          1079: 
        !          1080: }
        !          1081: 
        !          1082: /*************** hessian matrix ****************/
        !          1083: double hessii( double x[], double delta, int theta, double delti[])
        !          1084: {
        !          1085:   int i;
        !          1086:   int l=1, lmax=20;
        !          1087:   double k1,k2;
        !          1088:   double p2[NPARMAX+1];
        !          1089:   double res;
        !          1090:   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        !          1091:   double fx;
        !          1092:   int k=0,kmax=10;
        !          1093:   double l1;
        !          1094: 
        !          1095:   fx=func(x);
        !          1096:   for (i=1;i<=npar;i++) p2[i]=x[i];
        !          1097:   for(l=0 ; l <=lmax; l++){
        !          1098:     l1=pow(10,l);
        !          1099:     delts=delt;
        !          1100:     for(k=1 ; k <kmax; k=k+1){
        !          1101:       delt = delta*(l1*k);
        !          1102:       p2[theta]=x[theta] +delt;
        !          1103:       k1=func(p2)-fx;
        !          1104:       p2[theta]=x[theta]-delt;
        !          1105:       k2=func(p2)-fx;
        !          1106:       /*res= (k1-2.0*fx+k2)/delt/delt; */
        !          1107:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
        !          1108:       
        !          1109: #ifdef DEBUG
        !          1110:       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);
        !          1111:       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);
        !          1112: #endif
        !          1113:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        !          1114:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
        !          1115:        k=kmax;
        !          1116:       }
        !          1117:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
        !          1118:        k=kmax; l=lmax*10.;
        !          1119:       }
        !          1120:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
        !          1121:        delts=delt;
        !          1122:       }
        !          1123:     }
        !          1124:   }
        !          1125:   delti[theta]=delts;
        !          1126:   return res; 
        !          1127:   
        !          1128: }
        !          1129: 
        !          1130: double hessij( double x[], double delti[], int thetai,int thetaj)
        !          1131: {
        !          1132:   int i;
        !          1133:   int l=1, l1, lmax=20;
        !          1134:   double k1,k2,k3,k4,res,fx;
        !          1135:   double p2[NPARMAX+1];
        !          1136:   int k;
        !          1137: 
        !          1138:   fx=func(x);
        !          1139:   for (k=1; k<=2; k++) {
        !          1140:     for (i=1;i<=npar;i++) p2[i]=x[i];
        !          1141:     p2[thetai]=x[thetai]+delti[thetai]/k;
        !          1142:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        !          1143:     k1=func(p2)-fx;
        !          1144:   
        !          1145:     p2[thetai]=x[thetai]+delti[thetai]/k;
        !          1146:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        !          1147:     k2=func(p2)-fx;
        !          1148:   
        !          1149:     p2[thetai]=x[thetai]-delti[thetai]/k;
        !          1150:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        !          1151:     k3=func(p2)-fx;
        !          1152:   
        !          1153:     p2[thetai]=x[thetai]-delti[thetai]/k;
        !          1154:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        !          1155:     k4=func(p2)-fx;
        !          1156:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
        !          1157: #ifdef DEBUG
        !          1158:     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);
        !          1159:     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);
        !          1160: #endif
        !          1161:   }
        !          1162:   return res;
        !          1163: }
        !          1164: 
        !          1165: /************** Inverse of matrix **************/
        !          1166: void ludcmp(double **a, int n, int *indx, double *d) 
        !          1167: { 
        !          1168:   int i,imax,j,k; 
        !          1169:   double big,dum,sum,temp; 
        !          1170:   double *vv; 
        !          1171:  
        !          1172:   vv=vector(1,n); 
        !          1173:   *d=1.0; 
        !          1174:   for (i=1;i<=n;i++) { 
        !          1175:     big=0.0; 
        !          1176:     for (j=1;j<=n;j++) 
        !          1177:       if ((temp=fabs(a[i][j])) > big) big=temp; 
        !          1178:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        !          1179:     vv[i]=1.0/big; 
        !          1180:   } 
        !          1181:   for (j=1;j<=n;j++) { 
        !          1182:     for (i=1;i<j;i++) { 
        !          1183:       sum=a[i][j]; 
        !          1184:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
        !          1185:       a[i][j]=sum; 
        !          1186:     } 
        !          1187:     big=0.0; 
        !          1188:     for (i=j;i<=n;i++) { 
        !          1189:       sum=a[i][j]; 
        !          1190:       for (k=1;k<j;k++) 
        !          1191:        sum -= a[i][k]*a[k][j]; 
        !          1192:       a[i][j]=sum; 
        !          1193:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
        !          1194:        big=dum; 
        !          1195:        imax=i; 
        !          1196:       } 
        !          1197:     } 
        !          1198:     if (j != imax) { 
        !          1199:       for (k=1;k<=n;k++) { 
        !          1200:        dum=a[imax][k]; 
        !          1201:        a[imax][k]=a[j][k]; 
        !          1202:        a[j][k]=dum; 
        !          1203:       } 
        !          1204:       *d = -(*d); 
        !          1205:       vv[imax]=vv[j]; 
        !          1206:     } 
        !          1207:     indx[j]=imax; 
        !          1208:     if (a[j][j] == 0.0) a[j][j]=TINY; 
        !          1209:     if (j != n) { 
        !          1210:       dum=1.0/(a[j][j]); 
        !          1211:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        !          1212:     } 
        !          1213:   } 
        !          1214:   free_vector(vv,1,n);  /* Doesn't work */
        !          1215: ;
        !          1216: } 
        !          1217: 
        !          1218: void lubksb(double **a, int n, int *indx, double b[]) 
        !          1219: { 
        !          1220:   int i,ii=0,ip,j; 
        !          1221:   double sum; 
        !          1222:  
        !          1223:   for (i=1;i<=n;i++) { 
        !          1224:     ip=indx[i]; 
        !          1225:     sum=b[ip]; 
        !          1226:     b[ip]=b[i]; 
        !          1227:     if (ii) 
        !          1228:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        !          1229:     else if (sum) ii=i; 
        !          1230:     b[i]=sum; 
        !          1231:   } 
        !          1232:   for (i=n;i>=1;i--) { 
        !          1233:     sum=b[i]; 
        !          1234:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        !          1235:     b[i]=sum/a[i][i]; 
        !          1236:   } 
        !          1237: } 
        !          1238: 
        !          1239: /************ Frequencies ********************/
        !          1240: void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
        !          1241: {  /* Some frequencies */
        !          1242:   
        !          1243:   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
        !          1244:   int first;
        !          1245:   double ***freq; /* Frequencies */
        !          1246:   double *pp;
        !          1247:   double pos, k2, dateintsum=0,k2cpt=0;
        !          1248:   FILE *ficresp;
        !          1249:   char fileresp[FILENAMELENGTH];
        !          1250:   
        !          1251:   pp=vector(1,nlstate);
        !          1252:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          1253:   strcpy(fileresp,"p");
        !          1254:   strcat(fileresp,fileres);
        !          1255:   if((ficresp=fopen(fileresp,"w"))==NULL) {
        !          1256:     printf("Problem with prevalence resultfile: %s\n", fileresp);
        !          1257:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        !          1258:     exit(0);
        !          1259:   }
        !          1260:   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
        !          1261:   j1=0;
        !          1262:   
        !          1263:   j=cptcoveff;
        !          1264:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
        !          1265: 
        !          1266:   first=1;
        !          1267: 
        !          1268:   for(k1=1; k1<=j;k1++){
        !          1269:     for(i1=1; i1<=ncodemax[k1];i1++){
        !          1270:       j1++;
        !          1271:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
        !          1272:        scanf("%d", i);*/
        !          1273:       for (i=-1; i<=nlstate+ndeath; i++)  
        !          1274:        for (jk=-1; jk<=nlstate+ndeath; jk++)  
        !          1275:          for(m=agemin; m <= agemax+3; m++)
        !          1276:            freq[i][jk][m]=0;
        !          1277:       
        !          1278:       dateintsum=0;
        !          1279:       k2cpt=0;
        !          1280:       for (i=1; i<=imx; i++) {
        !          1281:        bool=1;
        !          1282:        if  (cptcovn>0) {
        !          1283:          for (z1=1; z1<=cptcoveff; z1++) 
        !          1284:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        !          1285:              bool=0;
        !          1286:        }
        !          1287:        if (bool==1) {
        !          1288:          for(m=firstpass; m<=lastpass; m++){
        !          1289:            k2=anint[m][i]+(mint[m][i]/12.);
        !          1290:            if ((k2>=dateprev1) && (k2<=dateprev2)) {
        !          1291:              if(agev[m][i]==0) agev[m][i]=agemax+1;
        !          1292:              if(agev[m][i]==1) agev[m][i]=agemax+2;
        !          1293:              if (m<lastpass) {
        !          1294:                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        !          1295:                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
        !          1296:              }
        !          1297:              
        !          1298:              if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
        !          1299:                dateintsum=dateintsum+k2;
        !          1300:                k2cpt++;
        !          1301:              }
        !          1302:            }
        !          1303:          }
        !          1304:        }
        !          1305:       }
        !          1306:        
        !          1307:       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
        !          1308: 
        !          1309:       if  (cptcovn>0) {
        !          1310:        fprintf(ficresp, "\n#********** Variable "); 
        !          1311:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          1312:        fprintf(ficresp, "**********\n#");
        !          1313:       }
        !          1314:       for(i=1; i<=nlstate;i++) 
        !          1315:        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        !          1316:       fprintf(ficresp, "\n");
        !          1317:       
        !          1318:       for(i=(int)agemin; i <= (int)agemax+3; i++){
        !          1319:        if(i==(int)agemax+3){
        !          1320:          fprintf(ficlog,"Total");
        !          1321:        }else{
        !          1322:          if(first==1){
        !          1323:            first=0;
        !          1324:            printf("See log file for details...\n");
        !          1325:          }
        !          1326:          fprintf(ficlog,"Age %d", i);
        !          1327:        }
        !          1328:        for(jk=1; jk <=nlstate ; jk++){
        !          1329:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        !          1330:            pp[jk] += freq[jk][m][i]; 
        !          1331:        }
        !          1332:        for(jk=1; jk <=nlstate ; jk++){
        !          1333:          for(m=-1, pos=0; m <=0 ; m++)
        !          1334:            pos += freq[jk][m][i];
        !          1335:          if(pp[jk]>=1.e-10){
        !          1336:            if(first==1){
        !          1337:            printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        !          1338:            }
        !          1339:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        !          1340:          }else{
        !          1341:            if(first==1)
        !          1342:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        !          1343:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        !          1344:          }
        !          1345:        }
        !          1346: 
        !          1347:        for(jk=1; jk <=nlstate ; jk++){
        !          1348:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
        !          1349:            pp[jk] += freq[jk][m][i];
        !          1350:        }
        !          1351: 
        !          1352:        for(jk=1,pos=0; jk <=nlstate ; jk++)
        !          1353:          pos += pp[jk];
        !          1354:        for(jk=1; jk <=nlstate ; jk++){
        !          1355:          if(pos>=1.e-5){
        !          1356:            if(first==1)
        !          1357:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        !          1358:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        !          1359:          }else{
        !          1360:            if(first==1)
        !          1361:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        !          1362:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        !          1363:          }
        !          1364:          if( i <= (int) agemax){
        !          1365:            if(pos>=1.e-5){
        !          1366:              fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
        !          1367:              probs[i][jk][j1]= pp[jk]/pos;
        !          1368:              /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
        !          1369:            }
        !          1370:            else
        !          1371:              fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
        !          1372:          }
        !          1373:        }
        !          1374:        
        !          1375:        for(jk=-1; jk <=nlstate+ndeath; jk++)
        !          1376:          for(m=-1; m <=nlstate+ndeath; m++)
        !          1377:            if(freq[jk][m][i] !=0 ) {
        !          1378:            if(first==1)
        !          1379:              printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        !          1380:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
        !          1381:            }
        !          1382:        if(i <= (int) agemax)
        !          1383:          fprintf(ficresp,"\n");
        !          1384:        if(first==1)
        !          1385:          printf("Others in log...\n");
        !          1386:        fprintf(ficlog,"\n");
        !          1387:       }
        !          1388:     }
        !          1389:   }
        !          1390:   dateintmean=dateintsum/k2cpt; 
        !          1391:  
        !          1392:   fclose(ficresp);
        !          1393:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
        !          1394:   free_vector(pp,1,nlstate);
        !          1395:   
        !          1396:   /* End of Freq */
        !          1397: }
        !          1398: 
        !          1399: /************ Prevalence ********************/
        !          1400: void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
        !          1401: {  /* Some frequencies */
        !          1402:  
        !          1403:   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
        !          1404:   double ***freq; /* Frequencies */
        !          1405:   double *pp;
        !          1406:   double pos, k2;
        !          1407: 
        !          1408:   pp=vector(1,nlstate);
        !          1409:   
        !          1410:   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
        !          1411:   j1=0;
        !          1412:   
        !          1413:   j=cptcoveff;
        !          1414:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
        !          1415:   
        !          1416:   for(k1=1; k1<=j;k1++){
        !          1417:     for(i1=1; i1<=ncodemax[k1];i1++){
        !          1418:       j1++;
        !          1419:       
        !          1420:       for (i=-1; i<=nlstate+ndeath; i++)  
        !          1421:        for (jk=-1; jk<=nlstate+ndeath; jk++)  
        !          1422:          for(m=agemin; m <= agemax+3; m++)
        !          1423:            freq[i][jk][m]=0;
        !          1424:      
        !          1425:       for (i=1; i<=imx; i++) {
        !          1426:        bool=1;
        !          1427:        if  (cptcovn>0) {
        !          1428:          for (z1=1; z1<=cptcoveff; z1++) 
        !          1429:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        !          1430:              bool=0;
        !          1431:        } 
        !          1432:        if (bool==1) { 
        !          1433:          for(m=firstpass; m<=lastpass; m++){
        !          1434:            k2=anint[m][i]+(mint[m][i]/12.);
        !          1435:            if ((k2>=dateprev1) && (k2<=dateprev2)) {
        !          1436:              if(agev[m][i]==0) agev[m][i]=agemax+1;
        !          1437:              if(agev[m][i]==1) agev[m][i]=agemax+2;
        !          1438:              if (m<lastpass) {
        !          1439:                if (calagedate>0) 
        !          1440:                  freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
        !          1441:                else
        !          1442:                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        !          1443:                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
        !          1444:              }
        !          1445:            }
        !          1446:          }
        !          1447:        }
        !          1448:       }
        !          1449:       for(i=(int)agemin; i <= (int)agemax+3; i++){ 
        !          1450:        for(jk=1; jk <=nlstate ; jk++){
        !          1451:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        !          1452:            pp[jk] += freq[jk][m][i]; 
        !          1453:        }
        !          1454:        for(jk=1; jk <=nlstate ; jk++){
        !          1455:          for(m=-1, pos=0; m <=0 ; m++)
        !          1456:            pos += freq[jk][m][i];
        !          1457:        }
        !          1458:        
        !          1459:        for(jk=1; jk <=nlstate ; jk++){
        !          1460:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
        !          1461:            pp[jk] += freq[jk][m][i];
        !          1462:        }
        !          1463:        
        !          1464:        for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
        !          1465:        
        !          1466:        for(jk=1; jk <=nlstate ; jk++){    
        !          1467:          if( i <= (int) agemax){
        !          1468:            if(pos>=1.e-5){
        !          1469:              probs[i][jk][j1]= pp[jk]/pos;
        !          1470:            }
        !          1471:          }
        !          1472:        }/* end jk */
        !          1473:       }/* end i */
        !          1474:     } /* end i1 */
        !          1475:   } /* end k1 */
        !          1476: 
        !          1477:   
        !          1478:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
        !          1479:   free_vector(pp,1,nlstate);
        !          1480:   
        !          1481: }  /* End of Freq */
        !          1482: 
        !          1483: /************* Waves Concatenation ***************/
        !          1484: 
        !          1485: void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
        !          1486: {
        !          1487:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        !          1488:      Death is a valid wave (if date is known).
        !          1489:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        !          1490:      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
        !          1491:      and mw[mi+1][i]. dh depends on stepm.
        !          1492:      */
        !          1493: 
        !          1494:   int i, mi, m;
        !          1495:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        !          1496:      double sum=0., jmean=0.;*/
        !          1497:   int first;
        !          1498:   int j, k=0,jk, ju, jl;
        !          1499:   double sum=0.;
        !          1500:   first=0;
        !          1501:   jmin=1e+5;
        !          1502:   jmax=-1;
        !          1503:   jmean=0.;
        !          1504:   for(i=1; i<=imx; i++){
        !          1505:     mi=0;
        !          1506:     m=firstpass;
        !          1507:     while(s[m][i] <= nlstate){
        !          1508:       if(s[m][i]>=1)
        !          1509:        mw[++mi][i]=m;
        !          1510:       if(m >=lastpass)
        !          1511:        break;
        !          1512:       else
        !          1513:        m++;
        !          1514:     }/* end while */
        !          1515:     if (s[m][i] > nlstate){
        !          1516:       mi++;    /* Death is another wave */
        !          1517:       /* if(mi==0)  never been interviewed correctly before death */
        !          1518:         /* Only death is a correct wave */
        !          1519:       mw[mi][i]=m;
        !          1520:     }
        !          1521: 
        !          1522:     wav[i]=mi;
        !          1523:     if(mi==0){
        !          1524:       if(first==0){
        !          1525:        printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
        !          1526:        first=1;
        !          1527:       }
        !          1528:       if(first==1){
        !          1529:        fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
        !          1530:       }
        !          1531:     } /* end mi==0 */
        !          1532:   }
        !          1533: 
        !          1534:   for(i=1; i<=imx; i++){
        !          1535:     for(mi=1; mi<wav[i];mi++){
        !          1536:       if (stepm <=0)
        !          1537:        dh[mi][i]=1;
        !          1538:       else{
        !          1539:        if (s[mw[mi+1][i]][i] > nlstate) {
        !          1540:          if (agedc[i] < 2*AGESUP) {
        !          1541:          j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
        !          1542:          if(j==0) j=1;  /* Survives at least one month after exam */
        !          1543:          k=k+1;
        !          1544:          if (j >= jmax) jmax=j;
        !          1545:          if (j <= jmin) jmin=j;
        !          1546:          sum=sum+j;
        !          1547:          /*if (j<0) printf("j=%d num=%d \n",j,i); */
        !          1548:          }
        !          1549:        }
        !          1550:        else{
        !          1551:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
        !          1552:          k=k+1;
        !          1553:          if (j >= jmax) jmax=j;
        !          1554:          else if (j <= jmin)jmin=j;
        !          1555:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        !          1556:          sum=sum+j;
        !          1557:        }
        !          1558:        jk= j/stepm;
        !          1559:        jl= j -jk*stepm;
        !          1560:        ju= j -(jk+1)*stepm;
        !          1561:        if(jl <= -ju)
        !          1562:          dh[mi][i]=jk;
        !          1563:        else
        !          1564:          dh[mi][i]=jk+1;
        !          1565:        if(dh[mi][i]==0)
        !          1566:          dh[mi][i]=1; /* At least one step */
        !          1567:       }
        !          1568:     }
        !          1569:   }
        !          1570:   jmean=sum/k;
        !          1571:   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        !          1572:   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        !          1573:  }
        !          1574: 
        !          1575: /*********** Tricode ****************************/
        !          1576: void tricode(int *Tvar, int **nbcode, int imx)
        !          1577: {
        !          1578:   int Ndum[20],ij=1, k, j, i;
        !          1579:   int cptcode=0;
        !          1580:   cptcoveff=0; 
        !          1581:  
        !          1582:   for (k=0; k<19; k++) Ndum[k]=0;
        !          1583:   for (k=1; k<=7; k++) ncodemax[k]=0;
        !          1584: 
        !          1585:   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
        !          1586:     for (i=1; i<=imx; i++) {
        !          1587:       ij=(int)(covar[Tvar[j]][i]);
        !          1588:       Ndum[ij]++; 
        !          1589:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
        !          1590:       if (ij > cptcode) cptcode=ij; 
        !          1591:     }
        !          1592: 
        !          1593:     for (i=0; i<=cptcode; i++) {
        !          1594:       if(Ndum[i]!=0) ncodemax[j]++;
        !          1595:     }
        !          1596:     ij=1; 
        !          1597: 
        !          1598: 
        !          1599:     for (i=1; i<=ncodemax[j]; i++) {
        !          1600:       for (k=0; k<=19; k++) {
        !          1601:        if (Ndum[k] != 0) {
        !          1602:          nbcode[Tvar[j]][ij]=k; 
        !          1603:          
        !          1604:          ij++;
        !          1605:        }
        !          1606:        if (ij > ncodemax[j]) break; 
        !          1607:       }  
        !          1608:     } 
        !          1609:   }  
        !          1610: 
        !          1611:  for (k=0; k<19; k++) Ndum[k]=0;
        !          1612: 
        !          1613:  for (i=1; i<=ncovmodel-2; i++) {
        !          1614:    ij=Tvar[i];
        !          1615:    Ndum[ij]++; 
        !          1616:  }
        !          1617: 
        !          1618:  ij=1;
        !          1619:  for (i=1; i<=10; i++) {
        !          1620:    if((Ndum[i]!=0) && (i<=ncovcol)){
        !          1621:      Tvaraff[ij]=i; 
        !          1622:      ij++;
        !          1623:    }
        !          1624:  }
        !          1625:  
        !          1626:  cptcoveff=ij-1;
        !          1627: }
        !          1628: 
        !          1629: /*********** Health Expectancies ****************/
        !          1630: 
        !          1631: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
        !          1632: 
        !          1633: {
        !          1634:   /* Health expectancies */
        !          1635:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        !          1636:   double age, agelim, hf;
        !          1637:   double ***p3mat,***varhe;
        !          1638:   double **dnewm,**doldm;
        !          1639:   double *xp;
        !          1640:   double **gp, **gm;
        !          1641:   double ***gradg, ***trgradg;
        !          1642:   int theta;
        !          1643: 
        !          1644:   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
        !          1645:   xp=vector(1,npar);
        !          1646:   dnewm=matrix(1,nlstate*2,1,npar);
        !          1647:   doldm=matrix(1,nlstate*2,1,nlstate*2);
        !          1648:   
        !          1649:   fprintf(ficreseij,"# Health expectancies\n");
        !          1650:   fprintf(ficreseij,"# Age");
        !          1651:   for(i=1; i<=nlstate;i++)
        !          1652:     for(j=1; j<=nlstate;j++)
        !          1653:       fprintf(ficreseij," %1d-%1d (SE)",i,j);
        !          1654:   fprintf(ficreseij,"\n");
        !          1655: 
        !          1656:   if(estepm < stepm){
        !          1657:     printf ("Problem %d lower than %d\n",estepm, stepm);
        !          1658:   }
        !          1659:   else  hstepm=estepm;   
        !          1660:   /* We compute the life expectancy from trapezoids spaced every estepm months
        !          1661:    * This is mainly to measure the difference between two models: for example
        !          1662:    * if stepm=24 months pijx are given only every 2 years and by summing them
        !          1663:    * we are calculating an estimate of the Life Expectancy assuming a linear 
        !          1664:    * progression inbetween and thus overestimating or underestimating according
        !          1665:    * to the curvature of the survival function. If, for the same date, we 
        !          1666:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
        !          1667:    * to compare the new estimate of Life expectancy with the same linear 
        !          1668:    * hypothesis. A more precise result, taking into account a more precise
        !          1669:    * curvature will be obtained if estepm is as small as stepm. */
        !          1670: 
        !          1671:   /* For example we decided to compute the life expectancy with the smallest unit */
        !          1672:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        !          1673:      nhstepm is the number of hstepm from age to agelim 
        !          1674:      nstepm is the number of stepm from age to agelin. 
        !          1675:      Look at hpijx to understand the reason of that which relies in memory size
        !          1676:      and note for a fixed period like estepm months */
        !          1677:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        !          1678:      survival function given by stepm (the optimization length). Unfortunately it
        !          1679:      means that if the survival funtion is printed only each two years of age and if
        !          1680:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        !          1681:      results. So we changed our mind and took the option of the best precision.
        !          1682:   */
        !          1683:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        !          1684: 
        !          1685:   agelim=AGESUP;
        !          1686:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        !          1687:     /* nhstepm age range expressed in number of stepm */
        !          1688:     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        !          1689:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        !          1690:     /* if (stepm >= YEARM) hstepm=1;*/
        !          1691:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        !          1692:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          1693:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
        !          1694:     gp=matrix(0,nhstepm,1,nlstate*2);
        !          1695:     gm=matrix(0,nhstepm,1,nlstate*2);
        !          1696: 
        !          1697:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
        !          1698:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        !          1699:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
        !          1700:  
        !          1701: 
        !          1702:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        !          1703: 
        !          1704:     /* Computing Variances of health expectancies */
        !          1705: 
        !          1706:      for(theta=1; theta <=npar; theta++){
        !          1707:       for(i=1; i<=npar; i++){ 
        !          1708:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
        !          1709:       }
        !          1710:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        !          1711:   
        !          1712:       cptj=0;
        !          1713:       for(j=1; j<= nlstate; j++){
        !          1714:        for(i=1; i<=nlstate; i++){
        !          1715:          cptj=cptj+1;
        !          1716:          for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
        !          1717:            gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        !          1718:          }
        !          1719:        }
        !          1720:       }
        !          1721:      
        !          1722:      
        !          1723:       for(i=1; i<=npar; i++) 
        !          1724:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
        !          1725:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        !          1726:       
        !          1727:       cptj=0;
        !          1728:       for(j=1; j<= nlstate; j++){
        !          1729:        for(i=1;i<=nlstate;i++){
        !          1730:          cptj=cptj+1;
        !          1731:          for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
        !          1732:            gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        !          1733:          }
        !          1734:        }
        !          1735:       }
        !          1736:       for(j=1; j<= nlstate*2; j++)
        !          1737:        for(h=0; h<=nhstepm-1; h++){
        !          1738:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        !          1739:        }
        !          1740:      } 
        !          1741:    
        !          1742: /* End theta */
        !          1743: 
        !          1744:      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
        !          1745: 
        !          1746:      for(h=0; h<=nhstepm-1; h++)
        !          1747:       for(j=1; j<=nlstate*2;j++)
        !          1748:        for(theta=1; theta <=npar; theta++)
        !          1749:          trgradg[h][j][theta]=gradg[h][theta][j];
        !          1750:      
        !          1751: 
        !          1752:      for(i=1;i<=nlstate*2;i++)
        !          1753:       for(j=1;j<=nlstate*2;j++)
        !          1754:        varhe[i][j][(int)age] =0.;
        !          1755: 
        !          1756:      printf("%d|",(int)age);fflush(stdout);
        !          1757:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        !          1758:      for(h=0;h<=nhstepm-1;h++){
        !          1759:       for(k=0;k<=nhstepm-1;k++){
        !          1760:        matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
        !          1761:        matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
        !          1762:        for(i=1;i<=nlstate*2;i++)
        !          1763:          for(j=1;j<=nlstate*2;j++)
        !          1764:            varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
        !          1765:       }
        !          1766:     }
        !          1767:     /* Computing expectancies */
        !          1768:     for(i=1; i<=nlstate;i++)
        !          1769:       for(j=1; j<=nlstate;j++)
        !          1770:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        !          1771:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
        !          1772:          
        !          1773: /* 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]);*/
        !          1774: 
        !          1775:        }
        !          1776: 
        !          1777:     fprintf(ficreseij,"%3.0f",age );
        !          1778:     cptj=0;
        !          1779:     for(i=1; i<=nlstate;i++)
        !          1780:       for(j=1; j<=nlstate;j++){
        !          1781:        cptj++;
        !          1782:        fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
        !          1783:       }
        !          1784:     fprintf(ficreseij,"\n");
        !          1785:    
        !          1786:     free_matrix(gm,0,nhstepm,1,nlstate*2);
        !          1787:     free_matrix(gp,0,nhstepm,1,nlstate*2);
        !          1788:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
        !          1789:     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
        !          1790:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          1791:   }
        !          1792:   printf("\n");
        !          1793:   fprintf(ficlog,"\n");
        !          1794: 
        !          1795:   free_vector(xp,1,npar);
        !          1796:   free_matrix(dnewm,1,nlstate*2,1,npar);
        !          1797:   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
        !          1798:   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
        !          1799: }
        !          1800: 
        !          1801: /************ Variance ******************/
        !          1802: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
        !          1803: {
        !          1804:   /* Variance of health expectancies */
        !          1805:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        !          1806:   /* double **newm;*/
        !          1807:   double **dnewm,**doldm;
        !          1808:   double **dnewmp,**doldmp;
        !          1809:   int i, j, nhstepm, hstepm, h, nstepm ;
        !          1810:   int k, cptcode;
        !          1811:   double *xp;
        !          1812:   double **gp, **gm;  /* for var eij */
        !          1813:   double ***gradg, ***trgradg; /*for var eij */
        !          1814:   double **gradgp, **trgradgp; /* for var p point j */
        !          1815:   double *gpp, *gmp; /* for var p point j */
        !          1816:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        !          1817:   double ***p3mat;
        !          1818:   double age,agelim, hf;
        !          1819:   double ***mobaverage;
        !          1820:   int theta;
        !          1821:   char digit[4];
        !          1822:   char digitp[16];
        !          1823: 
        !          1824:   char fileresprobmorprev[FILENAMELENGTH];
        !          1825: 
        !          1826:   if(popbased==1)
        !          1827:     strcpy(digitp,"-populbased-");
        !          1828:   else
        !          1829:     strcpy(digitp,"-stablbased-");
        !          1830:   if(mobilav==1)
        !          1831:     strcat(digitp,"mobilav-");
        !          1832:   else
        !          1833:     strcat(digitp,"nomobil-");
        !          1834:   if (mobilav==1) {
        !          1835:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          1836:     movingaverage(probs, bage, fage, mobaverage);
        !          1837:   }
        !          1838: 
        !          1839:   strcpy(fileresprobmorprev,"prmorprev"); 
        !          1840:   sprintf(digit,"%-d",ij);
        !          1841:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        !          1842:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
        !          1843:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        !          1844:   strcat(fileresprobmorprev,fileres);
        !          1845:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        !          1846:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
        !          1847:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        !          1848:   }
        !          1849:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        !          1850:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        !          1851:   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
        !          1852:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
        !          1853:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        !          1854:     fprintf(ficresprobmorprev," p.%-d SE",j);
        !          1855:     for(i=1; i<=nlstate;i++)
        !          1856:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
        !          1857:   }  
        !          1858:   fprintf(ficresprobmorprev,"\n");
        !          1859:   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        !          1860:     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        !          1861:     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        !          1862:     exit(0);
        !          1863:   }
        !          1864:   else{
        !          1865:     fprintf(ficgp,"\n# Routine varevsij");
        !          1866:   }
        !          1867:   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        !          1868:     printf("Problem with html file: %s\n", optionfilehtm);
        !          1869:     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        !          1870:     exit(0);
        !          1871:   }
        !          1872:   else{
        !          1873:     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
        !          1874:     fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
        !          1875:   }
        !          1876:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        !          1877: 
        !          1878:   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
        !          1879:   fprintf(ficresvij,"# Age");
        !          1880:   for(i=1; i<=nlstate;i++)
        !          1881:     for(j=1; j<=nlstate;j++)
        !          1882:       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
        !          1883:   fprintf(ficresvij,"\n");
        !          1884: 
        !          1885:   xp=vector(1,npar);
        !          1886:   dnewm=matrix(1,nlstate,1,npar);
        !          1887:   doldm=matrix(1,nlstate,1,nlstate);
        !          1888:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        !          1889:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        !          1890: 
        !          1891:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
        !          1892:   gpp=vector(nlstate+1,nlstate+ndeath);
        !          1893:   gmp=vector(nlstate+1,nlstate+ndeath);
        !          1894:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        !          1895:   
        !          1896:   if(estepm < stepm){
        !          1897:     printf ("Problem %d lower than %d\n",estepm, stepm);
        !          1898:   }
        !          1899:   else  hstepm=estepm;   
        !          1900:   /* For example we decided to compute the life expectancy with the smallest unit */
        !          1901:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        !          1902:      nhstepm is the number of hstepm from age to agelim 
        !          1903:      nstepm is the number of stepm from age to agelin. 
        !          1904:      Look at hpijx to understand the reason of that which relies in memory size
        !          1905:      and note for a fixed period like k years */
        !          1906:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        !          1907:      survival function given by stepm (the optimization length). Unfortunately it
        !          1908:      means that if the survival funtion is printed only each two years of age and if
        !          1909:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        !          1910:      results. So we changed our mind and took the option of the best precision.
        !          1911:   */
        !          1912:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        !          1913:   agelim = AGESUP;
        !          1914:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        !          1915:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        !          1916:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        !          1917:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          1918:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        !          1919:     gp=matrix(0,nhstepm,1,nlstate);
        !          1920:     gm=matrix(0,nhstepm,1,nlstate);
        !          1921: 
        !          1922: 
        !          1923:     for(theta=1; theta <=npar; theta++){
        !          1924:       for(i=1; i<=npar; i++){ /* Computes gradient */
        !          1925:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
        !          1926:       }
        !          1927:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        !          1928:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        !          1929: 
        !          1930:       if (popbased==1) {
        !          1931:        if(mobilav !=1){
        !          1932:          for(i=1; i<=nlstate;i++)
        !          1933:            prlim[i][i]=probs[(int)age][i][ij];
        !          1934:        }else{ /* mobilav=1 */ 
        !          1935:          for(i=1; i<=nlstate;i++)
        !          1936:            prlim[i][i]=mobaverage[(int)age][i][ij];
        !          1937:        }
        !          1938:       }
        !          1939:   
        !          1940:       for(j=1; j<= nlstate; j++){
        !          1941:        for(h=0; h<=nhstepm; h++){
        !          1942:          for(i=1, gp[h][j]=0.;i<=nlstate;i++)
        !          1943:            gp[h][j] += prlim[i][i]*p3mat[i][j][h];
        !          1944:        }
        !          1945:       }
        !          1946:       /* This for computing forces of mortality (h=1)as a weighted average */
        !          1947:       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
        !          1948:        for(i=1; i<= nlstate; i++)
        !          1949:          gpp[j] += prlim[i][i]*p3mat[i][j][1];
        !          1950:       }    
        !          1951:       /* end force of mortality */
        !          1952: 
        !          1953:       for(i=1; i<=npar; i++) /* Computes gradient */
        !          1954:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
        !          1955:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        !          1956:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        !          1957:  
        !          1958:       if (popbased==1) {
        !          1959:        if(mobilav !=1){
        !          1960:          for(i=1; i<=nlstate;i++)
        !          1961:            prlim[i][i]=probs[(int)age][i][ij];
        !          1962:        }else{ /* mobilav=1 */ 
        !          1963:          for(i=1; i<=nlstate;i++)
        !          1964:            prlim[i][i]=mobaverage[(int)age][i][ij];
        !          1965:        }
        !          1966:       }
        !          1967: 
        !          1968:       for(j=1; j<= nlstate; j++){
        !          1969:        for(h=0; h<=nhstepm; h++){
        !          1970:          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
        !          1971:            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
        !          1972:        }
        !          1973:       }
        !          1974:       /* This for computing force of mortality (h=1)as a weighted average */
        !          1975:       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
        !          1976:        for(i=1; i<= nlstate; i++)
        !          1977:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
        !          1978:       }    
        !          1979:       /* end force of mortality */
        !          1980: 
        !          1981:       for(j=1; j<= nlstate; j++) /* vareij */
        !          1982:        for(h=0; h<=nhstepm; h++){
        !          1983:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        !          1984:        }
        !          1985:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
        !          1986:        gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        !          1987:       }
        !          1988: 
        !          1989:     } /* End theta */
        !          1990: 
        !          1991:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
        !          1992: 
        !          1993:     for(h=0; h<=nhstepm; h++) /* veij */
        !          1994:       for(j=1; j<=nlstate;j++)
        !          1995:        for(theta=1; theta <=npar; theta++)
        !          1996:          trgradg[h][j][theta]=gradg[h][theta][j];
        !          1997: 
        !          1998:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        !          1999:       for(theta=1; theta <=npar; theta++)
        !          2000:        trgradgp[j][theta]=gradgp[theta][j];
        !          2001: 
        !          2002:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        !          2003:     for(i=1;i<=nlstate;i++)
        !          2004:       for(j=1;j<=nlstate;j++)
        !          2005:        vareij[i][j][(int)age] =0.;
        !          2006: 
        !          2007:     for(h=0;h<=nhstepm;h++){
        !          2008:       for(k=0;k<=nhstepm;k++){
        !          2009:        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
        !          2010:        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
        !          2011:        for(i=1;i<=nlstate;i++)
        !          2012:          for(j=1;j<=nlstate;j++)
        !          2013:            vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
        !          2014:       }
        !          2015:     }
        !          2016: 
        !          2017:     /* pptj */
        !          2018:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        !          2019:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        !          2020:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
        !          2021:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
        !          2022:        varppt[j][i]=doldmp[j][i];
        !          2023:     /* end ppptj */
        !          2024:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        !          2025:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
        !          2026:  
        !          2027:     if (popbased==1) {
        !          2028:       if(mobilav !=1){
        !          2029:        for(i=1; i<=nlstate;i++)
        !          2030:          prlim[i][i]=probs[(int)age][i][ij];
        !          2031:       }else{ /* mobilav=1 */ 
        !          2032:        for(i=1; i<=nlstate;i++)
        !          2033:          prlim[i][i]=mobaverage[(int)age][i][ij];
        !          2034:       }
        !          2035:     }
        !          2036:     
        !          2037:     /* This for computing force of mortality (h=1)as a weighted average */
        !          2038:     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
        !          2039:       for(i=1; i<= nlstate; i++)
        !          2040:        gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        !          2041:     }    
        !          2042:     /* end force of mortality */
        !          2043: 
        !          2044:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        !          2045:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        !          2046:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
        !          2047:       for(i=1; i<=nlstate;i++){
        !          2048:        fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
        !          2049:       }
        !          2050:     } 
        !          2051:     fprintf(ficresprobmorprev,"\n");
        !          2052: 
        !          2053:     fprintf(ficresvij,"%.0f ",age );
        !          2054:     for(i=1; i<=nlstate;i++)
        !          2055:       for(j=1; j<=nlstate;j++){
        !          2056:        fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        !          2057:       }
        !          2058:     fprintf(ficresvij,"\n");
        !          2059:     free_matrix(gp,0,nhstepm,1,nlstate);
        !          2060:     free_matrix(gm,0,nhstepm,1,nlstate);
        !          2061:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        !          2062:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        !          2063:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          2064:   } /* End age */
        !          2065:   free_vector(gpp,nlstate+1,nlstate+ndeath);
        !          2066:   free_vector(gmp,nlstate+1,nlstate+ndeath);
        !          2067:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        !          2068:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        !          2069:   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
        !          2070:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        !          2071:   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
        !          2072:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
        !          2073:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
        !          2074:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
        !          2075:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
        !          2076:   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
        !          2077:   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
        !          2078: */
        !          2079:   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
        !          2080: 
        !          2081:   free_vector(xp,1,npar);
        !          2082:   free_matrix(doldm,1,nlstate,1,nlstate);
        !          2083:   free_matrix(dnewm,1,nlstate,1,npar);
        !          2084:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        !          2085:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        !          2086:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        !          2087:   free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2088:   fclose(ficresprobmorprev);
        !          2089:   fclose(ficgp);
        !          2090:   fclose(fichtm);
        !          2091: 
        !          2092: }
        !          2093: 
        !          2094: /************ Variance of prevlim ******************/
        !          2095: 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)
        !          2096: {
        !          2097:   /* Variance of prevalence limit */
        !          2098:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        !          2099:   double **newm;
        !          2100:   double **dnewm,**doldm;
        !          2101:   int i, j, nhstepm, hstepm;
        !          2102:   int k, cptcode;
        !          2103:   double *xp;
        !          2104:   double *gp, *gm;
        !          2105:   double **gradg, **trgradg;
        !          2106:   double age,agelim;
        !          2107:   int theta;
        !          2108:    
        !          2109:   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
        !          2110:   fprintf(ficresvpl,"# Age");
        !          2111:   for(i=1; i<=nlstate;i++)
        !          2112:       fprintf(ficresvpl," %1d-%1d",i,i);
        !          2113:   fprintf(ficresvpl,"\n");
        !          2114: 
        !          2115:   xp=vector(1,npar);
        !          2116:   dnewm=matrix(1,nlstate,1,npar);
        !          2117:   doldm=matrix(1,nlstate,1,nlstate);
        !          2118:   
        !          2119:   hstepm=1*YEARM; /* Every year of age */
        !          2120:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
        !          2121:   agelim = AGESUP;
        !          2122:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        !          2123:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        !          2124:     if (stepm >= YEARM) hstepm=1;
        !          2125:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        !          2126:     gradg=matrix(1,npar,1,nlstate);
        !          2127:     gp=vector(1,nlstate);
        !          2128:     gm=vector(1,nlstate);
        !          2129: 
        !          2130:     for(theta=1; theta <=npar; theta++){
        !          2131:       for(i=1; i<=npar; i++){ /* Computes gradient */
        !          2132:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
        !          2133:       }
        !          2134:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        !          2135:       for(i=1;i<=nlstate;i++)
        !          2136:        gp[i] = prlim[i][i];
        !          2137:     
        !          2138:       for(i=1; i<=npar; i++) /* Computes gradient */
        !          2139:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
        !          2140:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        !          2141:       for(i=1;i<=nlstate;i++)
        !          2142:        gm[i] = prlim[i][i];
        !          2143: 
        !          2144:       for(i=1;i<=nlstate;i++)
        !          2145:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        !          2146:     } /* End theta */
        !          2147: 
        !          2148:     trgradg =matrix(1,nlstate,1,npar);
        !          2149: 
        !          2150:     for(j=1; j<=nlstate;j++)
        !          2151:       for(theta=1; theta <=npar; theta++)
        !          2152:        trgradg[j][theta]=gradg[theta][j];
        !          2153: 
        !          2154:     for(i=1;i<=nlstate;i++)
        !          2155:       varpl[i][(int)age] =0.;
        !          2156:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        !          2157:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        !          2158:     for(i=1;i<=nlstate;i++)
        !          2159:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
        !          2160: 
        !          2161:     fprintf(ficresvpl,"%.0f ",age );
        !          2162:     for(i=1; i<=nlstate;i++)
        !          2163:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        !          2164:     fprintf(ficresvpl,"\n");
        !          2165:     free_vector(gp,1,nlstate);
        !          2166:     free_vector(gm,1,nlstate);
        !          2167:     free_matrix(gradg,1,npar,1,nlstate);
        !          2168:     free_matrix(trgradg,1,nlstate,1,npar);
        !          2169:   } /* End age */
        !          2170: 
        !          2171:   free_vector(xp,1,npar);
        !          2172:   free_matrix(doldm,1,nlstate,1,npar);
        !          2173:   free_matrix(dnewm,1,nlstate,1,nlstate);
        !          2174: 
        !          2175: }
        !          2176: 
        !          2177: /************ Variance of one-step probabilities  ******************/
        !          2178: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
        !          2179: {
        !          2180:   int i, j=0,  i1, k1, l1, t, tj;
        !          2181:   int k2, l2, j1,  z1;
        !          2182:   int k=0,l, cptcode;
        !          2183:   int first=1, first1;
        !          2184:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        !          2185:   double **dnewm,**doldm;
        !          2186:   double *xp;
        !          2187:   double *gp, *gm;
        !          2188:   double **gradg, **trgradg;
        !          2189:   double **mu;
        !          2190:   double age,agelim, cov[NCOVMAX];
        !          2191:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        !          2192:   int theta;
        !          2193:   char fileresprob[FILENAMELENGTH];
        !          2194:   char fileresprobcov[FILENAMELENGTH];
        !          2195:   char fileresprobcor[FILENAMELENGTH];
        !          2196: 
        !          2197:   double ***varpij;
        !          2198: 
        !          2199:   strcpy(fileresprob,"prob"); 
        !          2200:   strcat(fileresprob,fileres);
        !          2201:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        !          2202:     printf("Problem with resultfile: %s\n", fileresprob);
        !          2203:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        !          2204:   }
        !          2205:   strcpy(fileresprobcov,"probcov"); 
        !          2206:   strcat(fileresprobcov,fileres);
        !          2207:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        !          2208:     printf("Problem with resultfile: %s\n", fileresprobcov);
        !          2209:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        !          2210:   }
        !          2211:   strcpy(fileresprobcor,"probcor"); 
        !          2212:   strcat(fileresprobcor,fileres);
        !          2213:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        !          2214:     printf("Problem with resultfile: %s\n", fileresprobcor);
        !          2215:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
        !          2216:   }
        !          2217:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        !          2218:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        !          2219:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        !          2220:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        !          2221:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        !          2222:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        !          2223:   
        !          2224:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        !          2225:   fprintf(ficresprob,"# Age");
        !          2226:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        !          2227:   fprintf(ficresprobcov,"# Age");
        !          2228:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
        !          2229:   fprintf(ficresprobcov,"# Age");
        !          2230: 
        !          2231: 
        !          2232:   for(i=1; i<=nlstate;i++)
        !          2233:     for(j=1; j<=(nlstate+ndeath);j++){
        !          2234:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        !          2235:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
        !          2236:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
        !          2237:     }  
        !          2238:   fprintf(ficresprob,"\n");
        !          2239:   fprintf(ficresprobcov,"\n");
        !          2240:   fprintf(ficresprobcor,"\n");
        !          2241:   xp=vector(1,npar);
        !          2242:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        !          2243:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        !          2244:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        !          2245:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
        !          2246:   first=1;
        !          2247:   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        !          2248:     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        !          2249:     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
        !          2250:     exit(0);
        !          2251:   }
        !          2252:   else{
        !          2253:     fprintf(ficgp,"\n# Routine varprob");
        !          2254:   }
        !          2255:   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
        !          2256:     printf("Problem with html file: %s\n", optionfilehtm);
        !          2257:     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
        !          2258:     exit(0);
        !          2259:   }
        !          2260:   else{
        !          2261:     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        !          2262:     fprintf(fichtm,"\n");
        !          2263: 
        !          2264:     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
        !          2265:     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
        !          2266:     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix 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> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
        !          2267: 
        !          2268:   }
        !          2269: 
        !          2270:  
        !          2271:   cov[1]=1;
        !          2272:   tj=cptcoveff;
        !          2273:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
        !          2274:   j1=0;
        !          2275:   for(t=1; t<=tj;t++){
        !          2276:     for(i1=1; i1<=ncodemax[t];i1++){ 
        !          2277:       j1++;
        !          2278:       
        !          2279:       if  (cptcovn>0) {
        !          2280:        fprintf(ficresprob, "\n#********** Variable "); 
        !          2281:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          2282:        fprintf(ficresprob, "**********\n#");
        !          2283:        fprintf(ficresprobcov, "\n#********** Variable "); 
        !          2284:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          2285:        fprintf(ficresprobcov, "**********\n#");
        !          2286:        
        !          2287:        fprintf(ficgp, "\n#********** Variable "); 
        !          2288:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          2289:        fprintf(ficgp, "**********\n#");
        !          2290:        
        !          2291:        
        !          2292:        fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
        !          2293:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          2294:        fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
        !          2295:        
        !          2296:        fprintf(ficresprobcor, "\n#********** Variable ");    
        !          2297:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        !          2298:        fprintf(ficgp, "**********\n#");    
        !          2299:       }
        !          2300:       
        !          2301:       for (age=bage; age<=fage; age ++){ 
        !          2302:        cov[2]=age;
        !          2303:        for (k=1; k<=cptcovn;k++) {
        !          2304:          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
        !          2305:        }
        !          2306:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        !          2307:        for (k=1; k<=cptcovprod;k++)
        !          2308:          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        !          2309:        
        !          2310:        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
        !          2311:        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        !          2312:        gp=vector(1,(nlstate)*(nlstate+ndeath));
        !          2313:        gm=vector(1,(nlstate)*(nlstate+ndeath));
        !          2314:     
        !          2315:        for(theta=1; theta <=npar; theta++){
        !          2316:          for(i=1; i<=npar; i++)
        !          2317:            xp[i] = x[i] + (i==theta ?delti[theta]:0);
        !          2318:          
        !          2319:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
        !          2320:          
        !          2321:          k=0;
        !          2322:          for(i=1; i<= (nlstate); i++){
        !          2323:            for(j=1; j<=(nlstate+ndeath);j++){
        !          2324:              k=k+1;
        !          2325:              gp[k]=pmmij[i][j];
        !          2326:            }
        !          2327:          }
        !          2328:          
        !          2329:          for(i=1; i<=npar; i++)
        !          2330:            xp[i] = x[i] - (i==theta ?delti[theta]:0);
        !          2331:     
        !          2332:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
        !          2333:          k=0;
        !          2334:          for(i=1; i<=(nlstate); i++){
        !          2335:            for(j=1; j<=(nlstate+ndeath);j++){
        !          2336:              k=k+1;
        !          2337:              gm[k]=pmmij[i][j];
        !          2338:            }
        !          2339:          }
        !          2340:      
        !          2341:          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
        !          2342:            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
        !          2343:        }
        !          2344: 
        !          2345:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        !          2346:          for(theta=1; theta <=npar; theta++)
        !          2347:            trgradg[j][theta]=gradg[theta][j];
        !          2348:        
        !          2349:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
        !          2350:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
        !          2351:        
        !          2352:        pmij(pmmij,cov,ncovmodel,x,nlstate);
        !          2353:        
        !          2354:        k=0;
        !          2355:        for(i=1; i<=(nlstate); i++){
        !          2356:          for(j=1; j<=(nlstate+ndeath);j++){
        !          2357:            k=k+1;
        !          2358:            mu[k][(int) age]=pmmij[i][j];
        !          2359:          }
        !          2360:        }
        !          2361:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
        !          2362:          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
        !          2363:            varpij[i][j][(int)age] = doldm[i][j];
        !          2364: 
        !          2365:        /*printf("\n%d ",(int)age);
        !          2366:      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        !          2367:        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        !          2368:        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        !          2369:      }*/
        !          2370: 
        !          2371:        fprintf(ficresprob,"\n%d ",(int)age);
        !          2372:        fprintf(ficresprobcov,"\n%d ",(int)age);
        !          2373:        fprintf(ficresprobcor,"\n%d ",(int)age);
        !          2374: 
        !          2375:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
        !          2376:          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
        !          2377:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
        !          2378:          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
        !          2379:          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
        !          2380:        }
        !          2381:        i=0;
        !          2382:        for (k=1; k<=(nlstate);k++){
        !          2383:          for (l=1; l<=(nlstate+ndeath);l++){ 
        !          2384:            i=i++;
        !          2385:            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
        !          2386:            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
        !          2387:            for (j=1; j<=i;j++){
        !          2388:              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
        !          2389:              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
        !          2390:            }
        !          2391:          }
        !          2392:        }/* end of loop for state */
        !          2393:       } /* end of loop for age */
        !          2394: 
        !          2395:       /* Confidence intervalle of pij  */
        !          2396:       /*
        !          2397:       fprintf(ficgp,"\nset noparametric;unset label");
        !          2398:       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
        !          2399:       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
        !          2400:       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);
        !          2401:       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
        !          2402:       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
        !          2403:       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
        !          2404:       */
        !          2405: 
        !          2406:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        !          2407:       first1=1;
        !          2408:       for (k2=1; k2<=(nlstate);k2++){
        !          2409:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
        !          2410:          if(l2==k2) continue;
        !          2411:          j=(k2-1)*(nlstate+ndeath)+l2;
        !          2412:          for (k1=1; k1<=(nlstate);k1++){
        !          2413:            for (l1=1; l1<=(nlstate+ndeath);l1++){ 
        !          2414:              if(l1==k1) continue;
        !          2415:              i=(k1-1)*(nlstate+ndeath)+l1;
        !          2416:              if(i<=j) continue;
        !          2417:              for (age=bage; age<=fage; age ++){ 
        !          2418:                if ((int)age %5==0){
        !          2419:                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
        !          2420:                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
        !          2421:                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
        !          2422:                  mu1=mu[i][(int) age]/stepm*YEARM ;
        !          2423:                  mu2=mu[j][(int) age]/stepm*YEARM;
        !          2424:                  c12=cv12/sqrt(v1*v2);
        !          2425:                  /* Computing eigen value of matrix of covariance */
        !          2426:                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
        !          2427:                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
        !          2428:                  /* Eigen vectors */
        !          2429:                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
        !          2430:                  /*v21=sqrt(1.-v11*v11); *//* error */
        !          2431:                  v21=(lc1-v1)/cv12*v11;
        !          2432:                  v12=-v21;
        !          2433:                  v22=v11;
        !          2434:                  tnalp=v21/v11;
        !          2435:                  if(first1==1){
        !          2436:                    first1=0;
        !          2437:                    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);
        !          2438:                  }
        !          2439:                  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);
        !          2440:                  /*printf(fignu*/
        !          2441:                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
        !          2442:                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
        !          2443:                  if(first==1){
        !          2444:                    first=0;
        !          2445:                    fprintf(ficgp,"\nset parametric;unset label");
        !          2446:                    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);
        !          2447:                    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
        !          2448:                    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
        !          2449:                    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
        !          2450:                    fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
        !          2451:                    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
        !          2452:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
        !          2453:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
        !          2454:                    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",\
        !          2455:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
        !          2456:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        !          2457:                  }else{
        !          2458:                    first=0;
        !          2459:                    fprintf(fichtm," %d (%.3f),",(int) age, c12);
        !          2460:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
        !          2461:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
        !          2462:                    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",\
        !          2463:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
        !          2464:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        !          2465:                  }/* if first */
        !          2466:                } /* age mod 5 */
        !          2467:              } /* end loop age */
        !          2468:              fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
        !          2469:              first=1;
        !          2470:            } /*l12 */
        !          2471:          } /* k12 */
        !          2472:        } /*l1 */
        !          2473:       }/* k1 */
        !          2474:     } /* loop covariates */
        !          2475:     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
        !          2476:     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        !          2477:     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        !          2478:     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
        !          2479:     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        !          2480:     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        !          2481:   }
        !          2482:   free_vector(xp,1,npar);
        !          2483:   fclose(ficresprob);
        !          2484:   fclose(ficresprobcov);
        !          2485:   fclose(ficresprobcor);
        !          2486:   fclose(ficgp);
        !          2487:   fclose(fichtm);
        !          2488: }
        !          2489: 
        !          2490: 
        !          2491: /******************* Printing html file ***********/
        !          2492: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
        !          2493:                  int lastpass, int stepm, int weightopt, char model[],\
        !          2494:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
        !          2495:                  int popforecast, int estepm ,\
        !          2496:                  double jprev1, double mprev1,double anprev1, \
        !          2497:                  double jprev2, double mprev2,double anprev2){
        !          2498:   int jj1, k1, i1, cpt;
        !          2499:   /*char optionfilehtm[FILENAMELENGTH];*/
        !          2500:   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
        !          2501:     printf("Problem with %s \n",optionfilehtm), exit(0);
        !          2502:     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
        !          2503:   }
        !          2504: 
        !          2505:    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
        !          2506:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
        !          2507:  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
        !          2508:  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
        !          2509:  - Life expectancies by age and initial health status (estepm=%2d months): 
        !          2510:    <a href=\"e%s\">e%s</a> <br>\n</li>", \
        !          2511:   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
        !          2512: 
        !          2513: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
        !          2514: 
        !          2515:  m=cptcoveff;
        !          2516:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        !          2517: 
        !          2518:  jj1=0;
        !          2519:  for(k1=1; k1<=m;k1++){
        !          2520:    for(i1=1; i1<=ncodemax[k1];i1++){
        !          2521:      jj1++;
        !          2522:      if (cptcovn > 0) {
        !          2523:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        !          2524:        for (cpt=1; cpt<=cptcoveff;cpt++) 
        !          2525:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        !          2526:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        !          2527:      }
        !          2528:      /* Pij */
        !          2529:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
        !          2530: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        !          2531:      /* Quasi-incidences */
        !          2532:      fprintf(fichtm,"<br>- Pij 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: pe%s%d2.png<br>
        !          2533: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
        !          2534:        /* Stable prevalence in each health state */
        !          2535:        for(cpt=1; cpt<nlstate;cpt++){
        !          2536:         fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
        !          2537: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        !          2538:        }
        !          2539:      for(cpt=1; cpt<=nlstate;cpt++) {
        !          2540:         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
        !          2541: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        !          2542:      }
        !          2543:      fprintf(fichtm,"\n<br>- Total life expectancy by age and
        !          2544: health expectancies in states (1) and (2): e%s%d.png<br>
        !          2545: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
        !          2546:    } /* end i1 */
        !          2547:  }/* End k1 */
        !          2548:  fprintf(fichtm,"</ul>");
        !          2549: 
        !          2550: 
        !          2551:  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
        !          2552:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
        !          2553:  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
        !          2554:  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
        !          2555:  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
        !          2556:  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
        !          2557:  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
        !          2558:  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
        !          2559: 
        !          2560:  if(popforecast==1) fprintf(fichtm,"\n
        !          2561:  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
        !          2562:  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
        !          2563:        <br>",fileres,fileres,fileres,fileres);
        !          2564:  else 
        !          2565:    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);
        !          2566: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        !          2567: 
        !          2568:  m=cptcoveff;
        !          2569:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
        !          2570: 
        !          2571:  jj1=0;
        !          2572:  for(k1=1; k1<=m;k1++){
        !          2573:    for(i1=1; i1<=ncodemax[k1];i1++){
        !          2574:      jj1++;
        !          2575:      if (cptcovn > 0) {
        !          2576:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        !          2577:        for (cpt=1; cpt<=cptcoveff;cpt++) 
        !          2578:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        !          2579:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        !          2580:      }
        !          2581:      for(cpt=1; cpt<=nlstate;cpt++) {
        !          2582:        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
        !          2583: interval) in state (%d): v%s%d%d.png <br>
        !          2584: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        !          2585:      }
        !          2586:    } /* end i1 */
        !          2587:  }/* End k1 */
        !          2588:  fprintf(fichtm,"</ul>");
        !          2589: fclose(fichtm);
        !          2590: }
        !          2591: 
        !          2592: /******************* Gnuplot file **************/
        !          2593: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
        !          2594: 
        !          2595:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
        !          2596:   int ng;
        !          2597:   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        !          2598:     printf("Problem with file %s",optionfilegnuplot);
        !          2599:     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
        !          2600:   }
        !          2601: 
        !          2602: #ifdef windows
        !          2603:     fprintf(ficgp,"cd \"%s\" \n",pathc);
        !          2604: #endif
        !          2605: m=pow(2,cptcoveff);
        !          2606:   
        !          2607:  /* 1eme*/
        !          2608:   for (cpt=1; cpt<= nlstate ; cpt ++) {
        !          2609:    for (k1=1; k1<= m ; k1 ++) {
        !          2610:      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        !          2611:      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
        !          2612: 
        !          2613:      for (i=1; i<= nlstate ; i ++) {
        !          2614:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        !          2615:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2616:      }
        !          2617:      fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
        !          2618:      for (i=1; i<= nlstate ; i ++) {
        !          2619:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        !          2620:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2621:      } 
        !          2622:      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
        !          2623:      for (i=1; i<= nlstate ; i ++) {
        !          2624:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        !          2625:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2626:      }  
        !          2627:      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
        !          2628:    }
        !          2629:   }
        !          2630:   /*2 eme*/
        !          2631:   
        !          2632:   for (k1=1; k1<= m ; k1 ++) { 
        !          2633:     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
        !          2634:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        !          2635:     
        !          2636:     for (i=1; i<= nlstate+1 ; i ++) {
        !          2637:       k=2*i;
        !          2638:       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
        !          2639:       for (j=1; j<= nlstate+1 ; j ++) {
        !          2640:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        !          2641:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2642:       }   
        !          2643:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
        !          2644:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
        !          2645:       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
        !          2646:       for (j=1; j<= nlstate+1 ; j ++) {
        !          2647:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        !          2648:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2649:       }   
        !          2650:       fprintf(ficgp,"\" t\"\" w l 0,");
        !          2651:       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
        !          2652:       for (j=1; j<= nlstate+1 ; j ++) {
        !          2653:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        !          2654:        else fprintf(ficgp," \%%*lf (\%%*lf)");
        !          2655:       }   
        !          2656:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
        !          2657:       else fprintf(ficgp,"\" t\"\" w l 0,");
        !          2658:     }
        !          2659:   }
        !          2660:   
        !          2661:   /*3eme*/
        !          2662:   
        !          2663:   for (k1=1; k1<= m ; k1 ++) { 
        !          2664:     for (cpt=1; cpt<= nlstate ; cpt ++) {
        !          2665:       k=2+nlstate*(2*cpt-2);
        !          2666:       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        !          2667:       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
        !          2668:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
        !          2669:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
        !          2670:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        !          2671:        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
        !          2672:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
        !          2673:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        !          2674:        
        !          2675:       */
        !          2676:       for (i=1; i< nlstate ; i ++) {
        !          2677:        fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
        !          2678:        
        !          2679:       } 
        !          2680:     }
        !          2681:   }
        !          2682:   
        !          2683:   /* CV preval stat */
        !          2684:   for (k1=1; k1<= m ; k1 ++) { 
        !          2685:     for (cpt=1; cpt<nlstate ; cpt ++) {
        !          2686:       k=3;
        !          2687:       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        !          2688:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
        !          2689:       
        !          2690:       for (i=1; i< nlstate ; i ++)
        !          2691:        fprintf(ficgp,"+$%d",k+i+1);
        !          2692:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
        !          2693:       
        !          2694:       l=3+(nlstate+ndeath)*cpt;
        !          2695:       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
        !          2696:       for (i=1; i< nlstate ; i ++) {
        !          2697:        l=3+(nlstate+ndeath)*cpt;
        !          2698:        fprintf(ficgp,"+$%d",l+i+1);
        !          2699:       }
        !          2700:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
        !          2701:     } 
        !          2702:   }  
        !          2703:   
        !          2704:   /* proba elementaires */
        !          2705:   for(i=1,jk=1; i <=nlstate; i++){
        !          2706:     for(k=1; k <=(nlstate+ndeath); k++){
        !          2707:       if (k != i) {
        !          2708:        for(j=1; j <=ncovmodel; j++){
        !          2709:          fprintf(ficgp,"p%d=%f ",jk,p[jk]);
        !          2710:          jk++; 
        !          2711:          fprintf(ficgp,"\n");
        !          2712:        }
        !          2713:       }
        !          2714:     }
        !          2715:    }
        !          2716: 
        !          2717:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        !          2718:      for(jk=1; jk <=m; jk++) {
        !          2719:        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
        !          2720:        if (ng==2)
        !          2721:         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        !          2722:        else
        !          2723:         fprintf(ficgp,"\nset title \"Probability\"\n");
        !          2724:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        !          2725:        i=1;
        !          2726:        for(k2=1; k2<=nlstate; k2++) {
        !          2727:         k3=i;
        !          2728:         for(k=1; k<=(nlstate+ndeath); k++) {
        !          2729:           if (k != k2){
        !          2730:             if(ng==2)
        !          2731:               fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
        !          2732:             else
        !          2733:               fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
        !          2734:             ij=1;
        !          2735:             for(j=3; j <=ncovmodel; j++) {
        !          2736:               if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
        !          2737:                 fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
        !          2738:                 ij++;
        !          2739:               }
        !          2740:               else
        !          2741:                 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
        !          2742:             }
        !          2743:             fprintf(ficgp,")/(1");
        !          2744:             
        !          2745:             for(k1=1; k1 <=nlstate; k1++){   
        !          2746:               fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
        !          2747:               ij=1;
        !          2748:               for(j=3; j <=ncovmodel; j++){
        !          2749:                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
        !          2750:                   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
        !          2751:                   ij++;
        !          2752:                 }
        !          2753:                 else
        !          2754:                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
        !          2755:               }
        !          2756:               fprintf(ficgp,")");
        !          2757:             }
        !          2758:             fprintf(ficgp,") t \"p%d%d\" ", k2,k);
        !          2759:             if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
        !          2760:             i=i+ncovmodel;
        !          2761:           }
        !          2762:         } /* end k */
        !          2763:        } /* end k2 */
        !          2764:      } /* end jk */
        !          2765:    } /* end ng */
        !          2766:    fclose(ficgp); 
        !          2767: }  /* end gnuplot */
        !          2768: 
        !          2769: 
        !          2770: /*************** Moving average **************/
        !          2771: void movingaverage(double ***probs, double bage,double fage, double ***mobaverage){
        !          2772: 
        !          2773:   int i, cpt, cptcod;
        !          2774:   double age;
        !          2775:   for (age=bage; age<=fage; age++)
        !          2776:     for (i=1; i<=nlstate;i++)
        !          2777:       for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
        !          2778:        mobaverage[(int)age][i][cptcod]=0.;
        !          2779:   
        !          2780:   for (age=bage+4; age<=fage; age++){
        !          2781:     for (i=1; i<=nlstate;i++){
        !          2782:       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        !          2783:        for (cpt=0;cpt<=4;cpt++){
        !          2784:          mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]+probs[(int)age-cpt][i][cptcod];
        !          2785:        }
        !          2786:        mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]/5;
        !          2787:       }
        !          2788:     }
        !          2789:   }
        !          2790:   
        !          2791: }
        !          2792: 
        !          2793: 
        !          2794: /************** Forecasting ******************/
        !          2795: prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
        !          2796:   
        !          2797:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
        !          2798:   int *popage;
        !          2799:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
        !          2800:   double *popeffectif,*popcount;
        !          2801:   double ***p3mat;
        !          2802:   char fileresf[FILENAMELENGTH];
        !          2803: 
        !          2804:  agelim=AGESUP;
        !          2805: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
        !          2806: 
        !          2807:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        !          2808:  
        !          2809:  
        !          2810:   strcpy(fileresf,"f"); 
        !          2811:   strcat(fileresf,fileres);
        !          2812:   if((ficresf=fopen(fileresf,"w"))==NULL) {
        !          2813:     printf("Problem with forecast resultfile: %s\n", fileresf);
        !          2814:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
        !          2815:   }
        !          2816:   printf("Computing forecasting: result on file '%s' \n", fileresf);
        !          2817:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
        !          2818: 
        !          2819:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
        !          2820: 
        !          2821:   if (mobilav==1) {
        !          2822:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2823:     movingaverage(probs, ageminpar,fage, mobaverage);
        !          2824:   }
        !          2825: 
        !          2826:   stepsize=(int) (stepm+YEARM-1)/YEARM;
        !          2827:   if (stepm<=12) stepsize=1;
        !          2828:   
        !          2829:   agelim=AGESUP;
        !          2830:   
        !          2831:   hstepm=1;
        !          2832:   hstepm=hstepm/stepm; 
        !          2833:   yp1=modf(dateintmean,&yp);
        !          2834:   anprojmean=yp;
        !          2835:   yp2=modf((yp1*12),&yp);
        !          2836:   mprojmean=yp;
        !          2837:   yp1=modf((yp2*30.5),&yp);
        !          2838:   jprojmean=yp;
        !          2839:   if(jprojmean==0) jprojmean=1;
        !          2840:   if(mprojmean==0) jprojmean=1;
        !          2841:   
        !          2842:   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
        !          2843:   
        !          2844:   for(cptcov=1;cptcov<=i2;cptcov++){
        !          2845:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        !          2846:       k=k+1;
        !          2847:       fprintf(ficresf,"\n#******");
        !          2848:       for(j=1;j<=cptcoveff;j++) {
        !          2849:        fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          2850:       }
        !          2851:       fprintf(ficresf,"******\n");
        !          2852:       fprintf(ficresf,"# StartingAge FinalAge");
        !          2853:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
        !          2854:       
        !          2855:       
        !          2856:       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
        !          2857:        fprintf(ficresf,"\n");
        !          2858:        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
        !          2859: 
        !          2860:        for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
        !          2861:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
        !          2862:          nhstepm = nhstepm/hstepm; 
        !          2863:          
        !          2864:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          2865:          oldm=oldms;savm=savms;
        !          2866:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        !          2867:        
        !          2868:          for (h=0; h<=nhstepm; h++){
        !          2869:            if (h==(int) (calagedate+YEARM*cpt)) {
        !          2870:              fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
        !          2871:            } 
        !          2872:            for(j=1; j<=nlstate+ndeath;j++) {
        !          2873:              kk1=0.;kk2=0;
        !          2874:              for(i=1; i<=nlstate;i++) {              
        !          2875:                if (mobilav==1) 
        !          2876:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
        !          2877:                else {
        !          2878:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
        !          2879:                }
        !          2880:                
        !          2881:              }
        !          2882:              if (h==(int)(calagedate+12*cpt)){
        !          2883:                fprintf(ficresf," %.3f", kk1);
        !          2884:                        
        !          2885:              }
        !          2886:            }
        !          2887:          }
        !          2888:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          2889:        }
        !          2890:       }
        !          2891:     }
        !          2892:   }
        !          2893:        
        !          2894:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2895: 
        !          2896:   fclose(ficresf);
        !          2897: }
        !          2898: /************** Forecasting ******************/
        !          2899: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
        !          2900:   
        !          2901:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
        !          2902:   int *popage;
        !          2903:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
        !          2904:   double *popeffectif,*popcount;
        !          2905:   double ***p3mat,***tabpop,***tabpopprev;
        !          2906:   char filerespop[FILENAMELENGTH];
        !          2907: 
        !          2908:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2909:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2910:   agelim=AGESUP;
        !          2911:   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
        !          2912:   
        !          2913:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        !          2914:   
        !          2915:   
        !          2916:   strcpy(filerespop,"pop"); 
        !          2917:   strcat(filerespop,fileres);
        !          2918:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
        !          2919:     printf("Problem with forecast resultfile: %s\n", filerespop);
        !          2920:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
        !          2921:   }
        !          2922:   printf("Computing forecasting: result on file '%s' \n", filerespop);
        !          2923:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
        !          2924: 
        !          2925:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
        !          2926: 
        !          2927:   if (mobilav==1) {
        !          2928:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          2929:     movingaverage(probs, ageminpar, fage, mobaverage);
        !          2930:   }
        !          2931: 
        !          2932:   stepsize=(int) (stepm+YEARM-1)/YEARM;
        !          2933:   if (stepm<=12) stepsize=1;
        !          2934:   
        !          2935:   agelim=AGESUP;
        !          2936:   
        !          2937:   hstepm=1;
        !          2938:   hstepm=hstepm/stepm; 
        !          2939:   
        !          2940:   if (popforecast==1) {
        !          2941:     if((ficpop=fopen(popfile,"r"))==NULL) {
        !          2942:       printf("Problem with population file : %s\n",popfile);exit(0);
        !          2943:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
        !          2944:     } 
        !          2945:     popage=ivector(0,AGESUP);
        !          2946:     popeffectif=vector(0,AGESUP);
        !          2947:     popcount=vector(0,AGESUP);
        !          2948:     
        !          2949:     i=1;   
        !          2950:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
        !          2951:    
        !          2952:     imx=i;
        !          2953:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
        !          2954:   }
        !          2955: 
        !          2956:   for(cptcov=1;cptcov<=i2;cptcov++){
        !          2957:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
        !          2958:       k=k+1;
        !          2959:       fprintf(ficrespop,"\n#******");
        !          2960:       for(j=1;j<=cptcoveff;j++) {
        !          2961:        fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          2962:       }
        !          2963:       fprintf(ficrespop,"******\n");
        !          2964:       fprintf(ficrespop,"# Age");
        !          2965:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
        !          2966:       if (popforecast==1)  fprintf(ficrespop," [Population]");
        !          2967:       
        !          2968:       for (cpt=0; cpt<=0;cpt++) { 
        !          2969:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
        !          2970:        
        !          2971:        for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
        !          2972:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
        !          2973:          nhstepm = nhstepm/hstepm; 
        !          2974:          
        !          2975:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          2976:          oldm=oldms;savm=savms;
        !          2977:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        !          2978:        
        !          2979:          for (h=0; h<=nhstepm; h++){
        !          2980:            if (h==(int) (calagedate+YEARM*cpt)) {
        !          2981:              fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
        !          2982:            } 
        !          2983:            for(j=1; j<=nlstate+ndeath;j++) {
        !          2984:              kk1=0.;kk2=0;
        !          2985:              for(i=1; i<=nlstate;i++) {              
        !          2986:                if (mobilav==1) 
        !          2987:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
        !          2988:                else {
        !          2989:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
        !          2990:                }
        !          2991:              }
        !          2992:              if (h==(int)(calagedate+12*cpt)){
        !          2993:                tabpop[(int)(agedeb)][j][cptcod]=kk1;
        !          2994:                  /*fprintf(ficrespop," %.3f", kk1);
        !          2995:                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
        !          2996:              }
        !          2997:            }
        !          2998:            for(i=1; i<=nlstate;i++){
        !          2999:              kk1=0.;
        !          3000:                for(j=1; j<=nlstate;j++){
        !          3001:                  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
        !          3002:                }
        !          3003:                  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
        !          3004:            }
        !          3005: 
        !          3006:            if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
        !          3007:              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
        !          3008:          }
        !          3009:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          3010:        }
        !          3011:       }
        !          3012:  
        !          3013:   /******/
        !          3014: 
        !          3015:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
        !          3016:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
        !          3017:        for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
        !          3018:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
        !          3019:          nhstepm = nhstepm/hstepm; 
        !          3020:          
        !          3021:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          3022:          oldm=oldms;savm=savms;
        !          3023:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        !          3024:          for (h=0; h<=nhstepm; h++){
        !          3025:            if (h==(int) (calagedate+YEARM*cpt)) {
        !          3026:              fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
        !          3027:            } 
        !          3028:            for(j=1; j<=nlstate+ndeath;j++) {
        !          3029:              kk1=0.;kk2=0;
        !          3030:              for(i=1; i<=nlstate;i++) {              
        !          3031:                kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
        !          3032:              }
        !          3033:              if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); 
        !          3034:            }
        !          3035:          }
        !          3036:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          3037:        }
        !          3038:       }
        !          3039:    } 
        !          3040:   }
        !          3041:  
        !          3042:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          3043: 
        !          3044:   if (popforecast==1) {
        !          3045:     free_ivector(popage,0,AGESUP);
        !          3046:     free_vector(popeffectif,0,AGESUP);
        !          3047:     free_vector(popcount,0,AGESUP);
        !          3048:   }
        !          3049:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          3050:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          3051:   fclose(ficrespop);
        !          3052: }
        !          3053: 
        !          3054: /***********************************************/
        !          3055: /**************** Main Program *****************/
        !          3056: /***********************************************/
        !          3057: 
        !          3058: int main(int argc, char *argv[])
        !          3059: {
        !          3060: 
        !          3061:   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
        !          3062:   double agedeb, agefin,hf;
        !          3063:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
        !          3064: 
        !          3065:   double fret;
        !          3066:   double **xi,tmp,delta;
        !          3067: 
        !          3068:   double dum; /* Dummy variable */
        !          3069:   double ***p3mat;
        !          3070:   double ***mobaverage;
        !          3071:   int *indx;
        !          3072:   char line[MAXLINE], linepar[MAXLINE];
        !          3073:   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
        !          3074:   int firstobs=1, lastobs=10;
        !          3075:   int sdeb, sfin; /* Status at beginning and end */
        !          3076:   int c,  h , cpt,l;
        !          3077:   int ju,jl, mi;
        !          3078:   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
        !          3079:   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
        !          3080:   int mobilav=0,popforecast=0;
        !          3081:   int hstepm, nhstepm;
        !          3082:   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
        !          3083: 
        !          3084:   double bage, fage, age, agelim, agebase;
        !          3085:   double ftolpl=FTOL;
        !          3086:   double **prlim;
        !          3087:   double *severity;
        !          3088:   double ***param; /* Matrix of parameters */
        !          3089:   double  *p;
        !          3090:   double **matcov; /* Matrix of covariance */
        !          3091:   double ***delti3; /* Scale */
        !          3092:   double *delti; /* Scale */
        !          3093:   double ***eij, ***vareij;
        !          3094:   double **varpl; /* Variances of prevalence limits by age */
        !          3095:   double *epj, vepp;
        !          3096:   double kk1, kk2;
        !          3097:   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
        !          3098:   
        !          3099: 
        !          3100:   char *alph[]={"a","a","b","c","d","e"}, str[4];
        !          3101: 
        !          3102: 
        !          3103:   char z[1]="c", occ;
        !          3104: #include <sys/time.h>
        !          3105: #include <time.h>
        !          3106:   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
        !          3107:  
        !          3108:   /* long total_usecs;
        !          3109:   struct timeval start_time, end_time;
        !          3110:   
        !          3111:   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
        !          3112:   getcwd(pathcd, size);
        !          3113: 
        !          3114:   printf("\n%s",version);
        !          3115:   if(argc <=1){
        !          3116:     printf("\nEnter the parameter file name: ");
        !          3117:     scanf("%s",pathtot);
        !          3118:   }
        !          3119:   else{
        !          3120:     strcpy(pathtot,argv[1]);
        !          3121:   }
        !          3122:   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
        !          3123:   /*cygwin_split_path(pathtot,path,optionfile);
        !          3124:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
        !          3125:   /* cutv(path,optionfile,pathtot,'\\');*/
        !          3126: 
        !          3127:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
        !          3128:    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
        !          3129:   chdir(path);
        !          3130:   replace(pathc,path);
        !          3131: 
        !          3132: /*-------- arguments in the command line --------*/
        !          3133: 
        !          3134:   /* Log file */
        !          3135:   strcat(filelog, optionfilefiname);
        !          3136:   strcat(filelog,".log");    /* */
        !          3137:   if((ficlog=fopen(filelog,"w"))==NULL)    {
        !          3138:     printf("Problem with logfile %s\n",filelog);
        !          3139:     goto end;
        !          3140:   }
        !          3141:   fprintf(ficlog,"Log filename:%s\n",filelog);
        !          3142:   fprintf(ficlog,"\n%s",version);
        !          3143:   fprintf(ficlog,"\nEnter the parameter file name: ");
        !          3144:   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
        !          3145:   fflush(ficlog);
        !          3146: 
        !          3147:   /* */
        !          3148:   strcpy(fileres,"r");
        !          3149:   strcat(fileres, optionfilefiname);
        !          3150:   strcat(fileres,".txt");    /* Other files have txt extension */
        !          3151: 
        !          3152:   /*---------arguments file --------*/
        !          3153: 
        !          3154:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
        !          3155:     printf("Problem with optionfile %s\n",optionfile);
        !          3156:     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
        !          3157:     goto end;
        !          3158:   }
        !          3159: 
        !          3160:   strcpy(filereso,"o");
        !          3161:   strcat(filereso,fileres);
        !          3162:   if((ficparo=fopen(filereso,"w"))==NULL) {
        !          3163:     printf("Problem with Output resultfile: %s\n", filereso);
        !          3164:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
        !          3165:     goto end;
        !          3166:   }
        !          3167: 
        !          3168:   /* Reads comments: lines beginning with '#' */
        !          3169:   while((c=getc(ficpar))=='#' && c!= EOF){
        !          3170:     ungetc(c,ficpar);
        !          3171:     fgets(line, MAXLINE, ficpar);
        !          3172:     puts(line);
        !          3173:     fputs(line,ficparo);
        !          3174:   }
        !          3175:   ungetc(c,ficpar);
        !          3176: 
        !          3177:   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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
        !          3178:   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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
        !          3179:   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
        !          3180: while((c=getc(ficpar))=='#' && c!= EOF){
        !          3181:     ungetc(c,ficpar);
        !          3182:     fgets(line, MAXLINE, ficpar);
        !          3183:     puts(line);
        !          3184:     fputs(line,ficparo);
        !          3185:   }
        !          3186:   ungetc(c,ficpar);
        !          3187:   
        !          3188:    
        !          3189:   covar=matrix(0,NCOVMAX,1,n); 
        !          3190:   cptcovn=0; 
        !          3191:   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
        !          3192: 
        !          3193:   ncovmodel=2+cptcovn;
        !          3194:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
        !          3195:   
        !          3196:   /* Read guess parameters */
        !          3197:   /* Reads comments: lines beginning with '#' */
        !          3198:   while((c=getc(ficpar))=='#' && c!= EOF){
        !          3199:     ungetc(c,ficpar);
        !          3200:     fgets(line, MAXLINE, ficpar);
        !          3201:     puts(line);
        !          3202:     fputs(line,ficparo);
        !          3203:   }
        !          3204:   ungetc(c,ficpar);
        !          3205:   
        !          3206:   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
        !          3207:     for(i=1; i <=nlstate; i++)
        !          3208:     for(j=1; j <=nlstate+ndeath-1; j++){
        !          3209:       fscanf(ficpar,"%1d%1d",&i1,&j1);
        !          3210:       fprintf(ficparo,"%1d%1d",i1,j1);
        !          3211:       if(mle==1)
        !          3212:        printf("%1d%1d",i,j);
        !          3213:       fprintf(ficlog,"%1d%1d",i,j);
        !          3214:       for(k=1; k<=ncovmodel;k++){
        !          3215:        fscanf(ficpar," %lf",&param[i][j][k]);
        !          3216:        if(mle==1){
        !          3217:          printf(" %lf",param[i][j][k]);
        !          3218:          fprintf(ficlog," %lf",param[i][j][k]);
        !          3219:        }
        !          3220:        else
        !          3221:          fprintf(ficlog," %lf",param[i][j][k]);
        !          3222:        fprintf(ficparo," %lf",param[i][j][k]);
        !          3223:       }
        !          3224:       fscanf(ficpar,"\n");
        !          3225:       if(mle==1)
        !          3226:        printf("\n");
        !          3227:       fprintf(ficlog,"\n");
        !          3228:       fprintf(ficparo,"\n");
        !          3229:     }
        !          3230:   
        !          3231:     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
        !          3232: 
        !          3233:   p=param[1][1];
        !          3234:   
        !          3235:   /* Reads comments: lines beginning with '#' */
        !          3236:   while((c=getc(ficpar))=='#' && c!= EOF){
        !          3237:     ungetc(c,ficpar);
        !          3238:     fgets(line, MAXLINE, ficpar);
        !          3239:     puts(line);
        !          3240:     fputs(line,ficparo);
        !          3241:   }
        !          3242:   ungetc(c,ficpar);
        !          3243: 
        !          3244:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
        !          3245:   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
        !          3246:   for(i=1; i <=nlstate; i++){
        !          3247:     for(j=1; j <=nlstate+ndeath-1; j++){
        !          3248:       fscanf(ficpar,"%1d%1d",&i1,&j1);
        !          3249:       printf("%1d%1d",i,j);
        !          3250:       fprintf(ficparo,"%1d%1d",i1,j1);
        !          3251:       for(k=1; k<=ncovmodel;k++){
        !          3252:        fscanf(ficpar,"%le",&delti3[i][j][k]);
        !          3253:        printf(" %le",delti3[i][j][k]);
        !          3254:        fprintf(ficparo," %le",delti3[i][j][k]);
        !          3255:       }
        !          3256:       fscanf(ficpar,"\n");
        !          3257:       printf("\n");
        !          3258:       fprintf(ficparo,"\n");
        !          3259:     }
        !          3260:   }
        !          3261:   delti=delti3[1][1];
        !          3262:   
        !          3263:   /* Reads comments: lines beginning with '#' */
        !          3264:   while((c=getc(ficpar))=='#' && c!= EOF){
        !          3265:     ungetc(c,ficpar);
        !          3266:     fgets(line, MAXLINE, ficpar);
        !          3267:     puts(line);
        !          3268:     fputs(line,ficparo);
        !          3269:   }
        !          3270:   ungetc(c,ficpar);
        !          3271:   
        !          3272:   matcov=matrix(1,npar,1,npar);
        !          3273:   for(i=1; i <=npar; i++){
        !          3274:     fscanf(ficpar,"%s",&str);
        !          3275:     if(mle==1)
        !          3276:       printf("%s",str);
        !          3277:     fprintf(ficlog,"%s",str);
        !          3278:     fprintf(ficparo,"%s",str);
        !          3279:     for(j=1; j <=i; j++){
        !          3280:       fscanf(ficpar," %le",&matcov[i][j]);
        !          3281:       if(mle==1){
        !          3282:        printf(" %.5le",matcov[i][j]);
        !          3283:        fprintf(ficlog," %.5le",matcov[i][j]);
        !          3284:       }
        !          3285:       else
        !          3286:        fprintf(ficlog," %.5le",matcov[i][j]);
        !          3287:       fprintf(ficparo," %.5le",matcov[i][j]);
        !          3288:     }
        !          3289:     fscanf(ficpar,"\n");
        !          3290:     if(mle==1)
        !          3291:       printf("\n");
        !          3292:     fprintf(ficlog,"\n");
        !          3293:     fprintf(ficparo,"\n");
        !          3294:   }
        !          3295:   for(i=1; i <=npar; i++)
        !          3296:     for(j=i+1;j<=npar;j++)
        !          3297:       matcov[i][j]=matcov[j][i];
        !          3298:    
        !          3299:   if(mle==1)
        !          3300:     printf("\n");
        !          3301:   fprintf(ficlog,"\n");
        !          3302: 
        !          3303: 
        !          3304:     /*-------- Rewriting paramater file ----------*/
        !          3305:      strcpy(rfileres,"r");    /* "Rparameterfile */
        !          3306:      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
        !          3307:      strcat(rfileres,".");    /* */
        !          3308:      strcat(rfileres,optionfilext);    /* Other files have txt extension */
        !          3309:     if((ficres =fopen(rfileres,"w"))==NULL) {
        !          3310:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
        !          3311:       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
        !          3312:     }
        !          3313:     fprintf(ficres,"#%s\n",version);
        !          3314:     
        !          3315:     /*-------- data file ----------*/
        !          3316:     if((fic=fopen(datafile,"r"))==NULL)    {
        !          3317:       printf("Problem with datafile: %s\n", datafile);goto end;
        !          3318:       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
        !          3319:     }
        !          3320: 
        !          3321:     n= lastobs;
        !          3322:     severity = vector(1,maxwav);
        !          3323:     outcome=imatrix(1,maxwav+1,1,n);
        !          3324:     num=ivector(1,n);
        !          3325:     moisnais=vector(1,n);
        !          3326:     annais=vector(1,n);
        !          3327:     moisdc=vector(1,n);
        !          3328:     andc=vector(1,n);
        !          3329:     agedc=vector(1,n);
        !          3330:     cod=ivector(1,n);
        !          3331:     weight=vector(1,n);
        !          3332:     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
        !          3333:     mint=matrix(1,maxwav,1,n);
        !          3334:     anint=matrix(1,maxwav,1,n);
        !          3335:     s=imatrix(1,maxwav+1,1,n);
        !          3336:     adl=imatrix(1,maxwav+1,1,n);    
        !          3337:     tab=ivector(1,NCOVMAX);
        !          3338:     ncodemax=ivector(1,8);
        !          3339: 
        !          3340:     i=1;
        !          3341:     while (fgets(line, MAXLINE, fic) != NULL)    {
        !          3342:       if ((i >= firstobs) && (i <=lastobs)) {
        !          3343:        
        !          3344:        for (j=maxwav;j>=1;j--){
        !          3345:          cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
        !          3346:          strcpy(line,stra);
        !          3347:          cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3348:          cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3349:        }
        !          3350:        
        !          3351:        cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3352:        cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3353: 
        !          3354:        cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3355:        cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3356: 
        !          3357:        cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3358:        for (j=ncovcol;j>=1;j--){
        !          3359:          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
        !          3360:        } 
        !          3361:        num[i]=atol(stra);
        !          3362:        
        !          3363:        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
        !          3364:          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])); ij=ij+1;}*/
        !          3365: 
        !          3366:        i=i+1;
        !          3367:       }
        !          3368:     } 
        !          3369:     /* printf("ii=%d", ij);
        !          3370:        scanf("%d",i);*/
        !          3371:   imx=i-1; /* Number of individuals */
        !          3372: 
        !          3373:   /* for (i=1; i<=imx; i++){
        !          3374:     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
        !          3375:     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
        !          3376:     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
        !          3377:     }*/
        !          3378:    /*  for (i=1; i<=imx; i++){
        !          3379:      if (s[4][i]==9)  s[4][i]=-1; 
        !          3380:      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]));}*/
        !          3381:   
        !          3382:  
        !          3383:   /* Calculation of the number of parameter from char model*/
        !          3384:   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
        !          3385:   Tprod=ivector(1,15); 
        !          3386:   Tvaraff=ivector(1,15); 
        !          3387:   Tvard=imatrix(1,15,1,2);
        !          3388:   Tage=ivector(1,15);      
        !          3389:    
        !          3390:   if (strlen(model) >1){
        !          3391:     j=0, j1=0, k1=1, k2=1;
        !          3392:     j=nbocc(model,'+');
        !          3393:     j1=nbocc(model,'*');
        !          3394:     cptcovn=j+1;
        !          3395:     cptcovprod=j1;
        !          3396:     
        !          3397:     strcpy(modelsav,model); 
        !          3398:     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
        !          3399:       printf("Error. Non available option model=%s ",model);
        !          3400:       fprintf(ficlog,"Error. Non available option model=%s ",model);
        !          3401:       goto end;
        !          3402:     }
        !          3403:     
        !          3404:     for(i=(j+1); i>=1;i--){
        !          3405:       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
        !          3406:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
        !          3407:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
        !          3408:       /*scanf("%d",i);*/
        !          3409:       if (strchr(strb,'*')) {  /* Model includes a product */
        !          3410:        cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
        !          3411:        if (strcmp(strc,"age")==0) { /* Vn*age */
        !          3412:          cptcovprod--;
        !          3413:          cutv(strb,stre,strd,'V');
        !          3414:          Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
        !          3415:          cptcovage++;
        !          3416:            Tage[cptcovage]=i;
        !          3417:            /*printf("stre=%s ", stre);*/
        !          3418:        }
        !          3419:        else if (strcmp(strd,"age")==0) { /* or age*Vn */
        !          3420:          cptcovprod--;
        !          3421:          cutv(strb,stre,strc,'V');
        !          3422:          Tvar[i]=atoi(stre);
        !          3423:          cptcovage++;
        !          3424:          Tage[cptcovage]=i;
        !          3425:        }
        !          3426:        else {  /* Age is not in the model */
        !          3427:          cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
        !          3428:          Tvar[i]=ncovcol+k1;
        !          3429:          cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
        !          3430:          Tprod[k1]=i;
        !          3431:          Tvard[k1][1]=atoi(strc); /* m*/
        !          3432:          Tvard[k1][2]=atoi(stre); /* n */
        !          3433:          Tvar[cptcovn+k2]=Tvard[k1][1];
        !          3434:          Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
        !          3435:          for (k=1; k<=lastobs;k++) 
        !          3436:            covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
        !          3437:          k1++;
        !          3438:          k2=k2+2;
        !          3439:        }
        !          3440:       }
        !          3441:       else { /* no more sum */
        !          3442:        /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
        !          3443:        /*  scanf("%d",i);*/
        !          3444:       cutv(strd,strc,strb,'V');
        !          3445:       Tvar[i]=atoi(strc);
        !          3446:       }
        !          3447:       strcpy(modelsav,stra);  
        !          3448:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
        !          3449:        scanf("%d",i);*/
        !          3450:     } /* end of loop + */
        !          3451:   } /* end model */
        !          3452:   
        !          3453:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
        !          3454:   printf("cptcovprod=%d ", cptcovprod);
        !          3455:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
        !          3456:   scanf("%d ",i);*/
        !          3457:     fclose(fic);
        !          3458: 
        !          3459:     /*  if(mle==1){*/
        !          3460:     if (weightopt != 1) { /* Maximisation without weights*/
        !          3461:       for(i=1;i<=n;i++) weight[i]=1.0;
        !          3462:     }
        !          3463:     /*-calculation of age at interview from date of interview and age at death -*/
        !          3464:     agev=matrix(1,maxwav,1,imx);
        !          3465: 
        !          3466:     for (i=1; i<=imx; i++) {
        !          3467:       for(m=2; (m<= maxwav); m++) {
        !          3468:        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
        !          3469:         anint[m][i]=9999;
        !          3470:         s[m][i]=-1;
        !          3471:        }
        !          3472:      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
        !          3473:       }
        !          3474:     }
        !          3475: 
        !          3476:     for (i=1; i<=imx; i++)  {
        !          3477:       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
        !          3478:       for(m=1; (m<= maxwav); m++){
        !          3479:        if(s[m][i] >0){
        !          3480:          if (s[m][i] >= nlstate+1) {
        !          3481:            if(agedc[i]>0)
        !          3482:              if(moisdc[i]!=99 && andc[i]!=9999)
        !          3483:                agev[m][i]=agedc[i];
        !          3484:            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
        !          3485:           else {
        !          3486:              if (andc[i]!=9999){
        !          3487:              printf("Warning negative age at death: %d line:%d\n",num[i],i);
        !          3488:              fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
        !          3489:              agev[m][i]=-1;
        !          3490:              }
        !          3491:            }
        !          3492:          }
        !          3493:          else if(s[m][i] !=9){ /* Should no more exist */
        !          3494:            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
        !          3495:            if(mint[m][i]==99 || anint[m][i]==9999)
        !          3496:              agev[m][i]=1;
        !          3497:            else if(agev[m][i] <agemin){ 
        !          3498:              agemin=agev[m][i];
        !          3499:              /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
        !          3500:            }
        !          3501:            else if(agev[m][i] >agemax){
        !          3502:              agemax=agev[m][i];
        !          3503:             /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
        !          3504:            }
        !          3505:            /*agev[m][i]=anint[m][i]-annais[i];*/
        !          3506:            /*   agev[m][i] = age[i]+2*m;*/
        !          3507:          }
        !          3508:          else { /* =9 */
        !          3509:            agev[m][i]=1;
        !          3510:            s[m][i]=-1;
        !          3511:          }
        !          3512:        }
        !          3513:        else /*= 0 Unknown */
        !          3514:          agev[m][i]=1;
        !          3515:       }
        !          3516:     
        !          3517:     }
        !          3518:     for (i=1; i<=imx; i++)  {
        !          3519:       for(m=1; (m<= maxwav); m++){
        !          3520:        if (s[m][i] > (nlstate+ndeath)) {
        !          3521:          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);   
        !          3522:          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);   
        !          3523:          goto end;
        !          3524:        }
        !          3525:       }
        !          3526:     }
        !          3527: 
        !          3528: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
        !          3529:  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
        !          3530: 
        !          3531:     free_vector(severity,1,maxwav);
        !          3532:     free_imatrix(outcome,1,maxwav+1,1,n);
        !          3533:     free_vector(moisnais,1,n);
        !          3534:     free_vector(annais,1,n);
        !          3535:     /* free_matrix(mint,1,maxwav,1,n);
        !          3536:        free_matrix(anint,1,maxwav,1,n);*/
        !          3537:     free_vector(moisdc,1,n);
        !          3538:     free_vector(andc,1,n);
        !          3539: 
        !          3540:    
        !          3541:     wav=ivector(1,imx);
        !          3542:     dh=imatrix(1,lastpass-firstpass+1,1,imx);
        !          3543:     mw=imatrix(1,lastpass-firstpass+1,1,imx);
        !          3544:    
        !          3545:     /* Concatenates waves */
        !          3546:       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
        !          3547: 
        !          3548: 
        !          3549:       Tcode=ivector(1,100);
        !          3550:       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
        !          3551:       ncodemax[1]=1;
        !          3552:       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
        !          3553:       
        !          3554:    codtab=imatrix(1,100,1,10);
        !          3555:    h=0;
        !          3556:    m=pow(2,cptcoveff);
        !          3557:  
        !          3558:    for(k=1;k<=cptcoveff; k++){
        !          3559:      for(i=1; i <=(m/pow(2,k));i++){
        !          3560:        for(j=1; j <= ncodemax[k]; j++){
        !          3561:         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
        !          3562:           h++;
        !          3563:           if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
        !          3564:           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
        !          3565:         } 
        !          3566:        }
        !          3567:      }
        !          3568:    } 
        !          3569:    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        !          3570:       codtab[1][2]=1;codtab[2][2]=2; */
        !          3571:    /* for(i=1; i <=m ;i++){ 
        !          3572:       for(k=1; k <=cptcovn; k++){
        !          3573:       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        !          3574:       }
        !          3575:       printf("\n");
        !          3576:       }
        !          3577:       scanf("%d",i);*/
        !          3578:     
        !          3579:    /* Calculates basic frequencies. Computes observed prevalence at single age
        !          3580:        and prints on file fileres'p'. */
        !          3581: 
        !          3582:     
        !          3583:    
        !          3584:     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3585:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3586:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3587:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3588:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
        !          3589:      
        !          3590:     /* For Powell, parameters are in a vector p[] starting at p[1]
        !          3591:        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
        !          3592:     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
        !          3593: 
        !          3594:     if(mle==1){
        !          3595:     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
        !          3596:     }
        !          3597:     
        !          3598:     /*--------- results files --------------*/
        !          3599:     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
        !          3600:   
        !          3601: 
        !          3602:    jk=1;
        !          3603:    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
        !          3604:    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
        !          3605:    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
        !          3606:    for(i=1,jk=1; i <=nlstate; i++){
        !          3607:      for(k=1; k <=(nlstate+ndeath); k++){
        !          3608:        if (k != i) 
        !          3609:         {
        !          3610:           printf("%d%d ",i,k);
        !          3611:           fprintf(ficlog,"%d%d ",i,k);
        !          3612:           fprintf(ficres,"%1d%1d ",i,k);
        !          3613:           for(j=1; j <=ncovmodel; j++){
        !          3614:             printf("%f ",p[jk]);
        !          3615:             fprintf(ficlog,"%f ",p[jk]);
        !          3616:             fprintf(ficres,"%f ",p[jk]);
        !          3617:             jk++; 
        !          3618:           }
        !          3619:           printf("\n");
        !          3620:           fprintf(ficlog,"\n");
        !          3621:           fprintf(ficres,"\n");
        !          3622:         }
        !          3623:      }
        !          3624:    }
        !          3625:    if(mle==1){
        !          3626:      /* Computing hessian and covariance matrix */
        !          3627:      ftolhess=ftol; /* Usually correct */
        !          3628:      hesscov(matcov, p, npar, delti, ftolhess, func);
        !          3629:    }
        !          3630:    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
        !          3631:    printf("# Scales (for hessian or gradient estimation)\n");
        !          3632:    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
        !          3633:    for(i=1,jk=1; i <=nlstate; i++){
        !          3634:      for(j=1; j <=nlstate+ndeath; j++){
        !          3635:        if (j!=i) {
        !          3636:         fprintf(ficres,"%1d%1d",i,j);
        !          3637:         printf("%1d%1d",i,j);
        !          3638:         fprintf(ficlog,"%1d%1d",i,j);
        !          3639:         for(k=1; k<=ncovmodel;k++){
        !          3640:           printf(" %.5e",delti[jk]);
        !          3641:           fprintf(ficlog," %.5e",delti[jk]);
        !          3642:           fprintf(ficres," %.5e",delti[jk]);
        !          3643:           jk++;
        !          3644:         }
        !          3645:         printf("\n");
        !          3646:         fprintf(ficlog,"\n");
        !          3647:         fprintf(ficres,"\n");
        !          3648:        }
        !          3649:      }
        !          3650:    }
        !          3651:    
        !          3652:    k=1;
        !          3653:    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");
        !          3654:    if(mle==1)
        !          3655:      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");
        !          3656:    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");
        !          3657:    for(i=1;i<=npar;i++){
        !          3658:      /*  if (k>nlstate) k=1;
        !          3659:         i1=(i-1)/(ncovmodel*nlstate)+1; 
        !          3660:         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
        !          3661:         printf("%s%d%d",alph[k],i1,tab[i]);*/
        !          3662:      fprintf(ficres,"%3d",i);
        !          3663:      if(mle==1)
        !          3664:        printf("%3d",i);
        !          3665:      fprintf(ficlog,"%3d",i);
        !          3666:      for(j=1; j<=i;j++){
        !          3667:        fprintf(ficres," %.5e",matcov[i][j]);
        !          3668:        if(mle==1)
        !          3669:         printf(" %.5e",matcov[i][j]);
        !          3670:        fprintf(ficlog," %.5e",matcov[i][j]);
        !          3671:      }
        !          3672:      fprintf(ficres,"\n");
        !          3673:      if(mle==1)
        !          3674:        printf("\n");
        !          3675:      fprintf(ficlog,"\n");
        !          3676:      k++;
        !          3677:    }
        !          3678:    
        !          3679:    while((c=getc(ficpar))=='#' && c!= EOF){
        !          3680:      ungetc(c,ficpar);
        !          3681:      fgets(line, MAXLINE, ficpar);
        !          3682:      puts(line);
        !          3683:      fputs(line,ficparo);
        !          3684:    }
        !          3685:    ungetc(c,ficpar);
        !          3686:    estepm=0;
        !          3687:    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
        !          3688:    if (estepm==0 || estepm < stepm) estepm=stepm;
        !          3689:    if (fage <= 2) {
        !          3690:      bage = ageminpar;
        !          3691:      fage = agemaxpar;
        !          3692:    }
        !          3693:    
        !          3694:    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
        !          3695:    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
        !          3696:    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
        !          3697:    
        !          3698:    while((c=getc(ficpar))=='#' && c!= EOF){
        !          3699:      ungetc(c,ficpar);
        !          3700:      fgets(line, MAXLINE, ficpar);
        !          3701:      puts(line);
        !          3702:      fputs(line,ficparo);
        !          3703:    }
        !          3704:    ungetc(c,ficpar);
        !          3705:   
        !          3706:    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);
        !          3707:    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);
        !          3708:    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);
        !          3709:    
        !          3710:    while((c=getc(ficpar))=='#' && c!= EOF){
        !          3711:      ungetc(c,ficpar);
        !          3712:      fgets(line, MAXLINE, ficpar);
        !          3713:      puts(line);
        !          3714:      fputs(line,ficparo);
        !          3715:    }
        !          3716:    ungetc(c,ficpar);
        !          3717:  
        !          3718: 
        !          3719:    dateprev1=anprev1+mprev1/12.+jprev1/365.;
        !          3720:    dateprev2=anprev2+mprev2/12.+jprev2/365.;
        !          3721: 
        !          3722:   fscanf(ficpar,"pop_based=%d\n",&popbased);
        !          3723:   fprintf(ficparo,"pop_based=%d\n",popbased);   
        !          3724:   fprintf(ficres,"pop_based=%d\n",popbased);   
        !          3725:   
        !          3726:   while((c=getc(ficpar))=='#' && c!= EOF){
        !          3727:     ungetc(c,ficpar);
        !          3728:     fgets(line, MAXLINE, ficpar);
        !          3729:     puts(line);
        !          3730:     fputs(line,ficparo);
        !          3731:   }
        !          3732:   ungetc(c,ficpar);
        !          3733: 
        !          3734:   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
        !          3735: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
        !          3736: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
        !          3737: 
        !          3738: 
        !          3739: while((c=getc(ficpar))=='#' && c!= EOF){
        !          3740:     ungetc(c,ficpar);
        !          3741:     fgets(line, MAXLINE, ficpar);
        !          3742:     puts(line);
        !          3743:     fputs(line,ficparo);
        !          3744:   }
        !          3745:   ungetc(c,ficpar);
        !          3746: 
        !          3747:   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
        !          3748:   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
        !          3749:   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
        !          3750: 
        !          3751:  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
        !          3752: /*------------ gnuplot -------------*/
        !          3753:   strcpy(optionfilegnuplot,optionfilefiname);
        !          3754:   strcat(optionfilegnuplot,".gp");
        !          3755:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
        !          3756:     printf("Problem with file %s",optionfilegnuplot);
        !          3757:   }
        !          3758:   fclose(ficgp);
        !          3759:  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
        !          3760: /*--------- index.htm --------*/
        !          3761: 
        !          3762:   strcpy(optionfilehtm,optionfile);
        !          3763:   strcat(optionfilehtm,".htm");
        !          3764:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
        !          3765:     printf("Problem with %s \n",optionfilehtm), exit(0);
        !          3766:   }
        !          3767: 
        !          3768:   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
        !          3769: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
        !          3770: \n
        !          3771: Total number of observations=%d <br>\n
        !          3772: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
        !          3773: <hr  size=\"2\" color=\"#EC5E5E\">
        !          3774:  <ul><li><h4>Parameter files</h4>\n
        !          3775:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
        !          3776:  - Log file of the run: <a href=\"%s\">%s</a><br>\n
        !          3777:  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
        !          3778:   fclose(fichtm);
        !          3779: 
        !          3780:  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
        !          3781:  
        !          3782: /*------------ free_vector  -------------*/
        !          3783:  chdir(path);
        !          3784:  
        !          3785:  free_ivector(wav,1,imx);
        !          3786:  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
        !          3787:  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
        !          3788:  free_ivector(num,1,n);
        !          3789:  free_vector(agedc,1,n);
        !          3790:  /*free_matrix(covar,1,NCOVMAX,1,n);*/
        !          3791:  fclose(ficparo);
        !          3792:  fclose(ficres);
        !          3793: 
        !          3794: 
        !          3795:   /*--------------- Prevalence limit --------------*/
        !          3796:   
        !          3797:   strcpy(filerespl,"pl");
        !          3798:   strcat(filerespl,fileres);
        !          3799:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
        !          3800:     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
        !          3801:     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
        !          3802:   }
        !          3803:   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
        !          3804:   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
        !          3805:   fprintf(ficrespl,"#Prevalence limit\n");
        !          3806:   fprintf(ficrespl,"#Age ");
        !          3807:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
        !          3808:   fprintf(ficrespl,"\n");
        !          3809:   
        !          3810:   prlim=matrix(1,nlstate,1,nlstate);
        !          3811:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3812:   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3813:   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3814:   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
        !          3815:   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
        !          3816:   k=0;
        !          3817:   agebase=ageminpar;
        !          3818:   agelim=agemaxpar;
        !          3819:   ftolpl=1.e-10;
        !          3820:   i1=cptcoveff;
        !          3821:   if (cptcovn < 1){i1=1;}
        !          3822: 
        !          3823:   for(cptcov=1;cptcov<=i1;cptcov++){
        !          3824:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        !          3825:        k=k+1;
        !          3826:        /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
        !          3827:        fprintf(ficrespl,"\n#******");
        !          3828:        printf("\n#******");
        !          3829:        fprintf(ficlog,"\n#******");
        !          3830:        for(j=1;j<=cptcoveff;j++) {
        !          3831:          fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3832:          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3833:          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3834:        }
        !          3835:        fprintf(ficrespl,"******\n");
        !          3836:        printf("******\n");
        !          3837:        fprintf(ficlog,"******\n");
        !          3838:        
        !          3839:        for (age=agebase; age<=agelim; age++){
        !          3840:          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
        !          3841:          fprintf(ficrespl,"%.0f",age );
        !          3842:          for(i=1; i<=nlstate;i++)
        !          3843:          fprintf(ficrespl," %.5f", prlim[i][i]);
        !          3844:          fprintf(ficrespl,"\n");
        !          3845:        }
        !          3846:       }
        !          3847:     }
        !          3848:   fclose(ficrespl);
        !          3849: 
        !          3850:   /*------------- h Pij x at various ages ------------*/
        !          3851:   
        !          3852:   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
        !          3853:   if((ficrespij=fopen(filerespij,"w"))==NULL) {
        !          3854:     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
        !          3855:     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
        !          3856:   }
        !          3857:   printf("Computing pij: result on file '%s' \n", filerespij);
        !          3858:   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
        !          3859:   
        !          3860:   stepsize=(int) (stepm+YEARM-1)/YEARM;
        !          3861:   /*if (stepm<=24) stepsize=2;*/
        !          3862: 
        !          3863:   agelim=AGESUP;
        !          3864:   hstepm=stepsize*YEARM; /* Every year of age */
        !          3865:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
        !          3866: 
        !          3867:   /* hstepm=1;   aff par mois*/
        !          3868: 
        !          3869:   k=0;
        !          3870:   for(cptcov=1;cptcov<=i1;cptcov++){
        !          3871:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        !          3872:       k=k+1;
        !          3873:        fprintf(ficrespij,"\n#****** ");
        !          3874:        for(j=1;j<=cptcoveff;j++) 
        !          3875:          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3876:        fprintf(ficrespij,"******\n");
        !          3877:        
        !          3878:        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
        !          3879:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        !          3880:          nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        !          3881: 
        !          3882:          /*      nhstepm=nhstepm*YEARM; aff par mois*/
        !          3883: 
        !          3884:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          3885:          oldm=oldms;savm=savms;
        !          3886:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
        !          3887:          fprintf(ficrespij,"# Age");
        !          3888:          for(i=1; i<=nlstate;i++)
        !          3889:            for(j=1; j<=nlstate+ndeath;j++)
        !          3890:              fprintf(ficrespij," %1d-%1d",i,j);
        !          3891:          fprintf(ficrespij,"\n");
        !          3892:           for (h=0; h<=nhstepm; h++){
        !          3893:            fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
        !          3894:            for(i=1; i<=nlstate;i++)
        !          3895:              for(j=1; j<=nlstate+ndeath;j++)
        !          3896:                fprintf(ficrespij," %.5f", p3mat[i][j][h]);
        !          3897:            fprintf(ficrespij,"\n");
        !          3898:             }
        !          3899:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        !          3900:          fprintf(ficrespij,"\n");
        !          3901:        }
        !          3902:     }
        !          3903:   }
        !          3904: 
        !          3905:   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
        !          3906: 
        !          3907:   fclose(ficrespij);
        !          3908: 
        !          3909: 
        !          3910:   /*---------- Forecasting ------------------*/
        !          3911:   if((stepm == 1) && (strcmp(model,".")==0)){
        !          3912:     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
        !          3913:     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
        !          3914:   } 
        !          3915:   else{
        !          3916:     erreur=108;
        !          3917:     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
        !          3918:     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
        !          3919:   }
        !          3920:   
        !          3921: 
        !          3922:   /*---------- Health expectancies and variances ------------*/
        !          3923: 
        !          3924:   strcpy(filerest,"t");
        !          3925:   strcat(filerest,fileres);
        !          3926:   if((ficrest=fopen(filerest,"w"))==NULL) {
        !          3927:     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
        !          3928:     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
        !          3929:   }
        !          3930:   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
        !          3931:   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
        !          3932: 
        !          3933: 
        !          3934:   strcpy(filerese,"e");
        !          3935:   strcat(filerese,fileres);
        !          3936:   if((ficreseij=fopen(filerese,"w"))==NULL) {
        !          3937:     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
        !          3938:     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
        !          3939:   }
        !          3940:   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
        !          3941:   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
        !          3942: 
        !          3943:   strcpy(fileresv,"v");
        !          3944:   strcat(fileresv,fileres);
        !          3945:   if((ficresvij=fopen(fileresv,"w"))==NULL) {
        !          3946:     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        !          3947:     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
        !          3948:   }
        !          3949:   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
        !          3950:   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
        !          3951:   calagedate=-1;
        !          3952:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
        !          3953:   if (mobilav==1) {
        !          3954:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          3955:     movingaverage(probs, ageminpar, fage, mobaverage);
        !          3956:   }
        !          3957: 
        !          3958:   k=0;
        !          3959:   for(cptcov=1;cptcov<=i1;cptcov++){
        !          3960:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        !          3961:       k=k+1; 
        !          3962:       fprintf(ficrest,"\n#****** ");
        !          3963:       for(j=1;j<=cptcoveff;j++) 
        !          3964:        fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3965:       fprintf(ficrest,"******\n");
        !          3966: 
        !          3967:       fprintf(ficreseij,"\n#****** ");
        !          3968:       for(j=1;j<=cptcoveff;j++) 
        !          3969:        fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3970:       fprintf(ficreseij,"******\n");
        !          3971: 
        !          3972:       fprintf(ficresvij,"\n#****** ");
        !          3973:       for(j=1;j<=cptcoveff;j++) 
        !          3974:        fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          3975:       fprintf(ficresvij,"******\n");
        !          3976: 
        !          3977:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        !          3978:       oldm=oldms;savm=savms;
        !          3979:       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
        !          3980:  
        !          3981:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        !          3982:       oldm=oldms;savm=savms;
        !          3983:       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
        !          3984:       if(popbased==1){
        !          3985:        varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
        !          3986:        }
        !          3987: 
        !          3988:  
        !          3989:       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
        !          3990:       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
        !          3991:       fprintf(ficrest,"\n");
        !          3992: 
        !          3993:       epj=vector(1,nlstate+1);
        !          3994:       for(age=bage; age <=fage ;age++){
        !          3995:        prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
        !          3996:        if (popbased==1) {
        !          3997:          if(mobilav !=1){
        !          3998:            for(i=1; i<=nlstate;i++)
        !          3999:              prlim[i][i]=probs[(int)age][i][k];
        !          4000:          }else{ /* mobilav=1 */ 
        !          4001:            for(i=1; i<=nlstate;i++)
        !          4002:              prlim[i][i]=mobaverage[(int)age][i][k];
        !          4003:          }
        !          4004:        }
        !          4005:        
        !          4006:        fprintf(ficrest," %4.0f",age);
        !          4007:        for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
        !          4008:          for(i=1, epj[j]=0.;i <=nlstate;i++) {
        !          4009:            epj[j] += prlim[i][i]*eij[i][j][(int)age];
        !          4010:            /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
        !          4011:          }
        !          4012:          epj[nlstate+1] +=epj[j];
        !          4013:        }
        !          4014: 
        !          4015:        for(i=1, vepp=0.;i <=nlstate;i++)
        !          4016:          for(j=1;j <=nlstate;j++)
        !          4017:            vepp += vareij[i][j][(int)age];
        !          4018:        fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
        !          4019:        for(j=1;j <=nlstate;j++){
        !          4020:          fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
        !          4021:        }
        !          4022:        fprintf(ficrest,"\n");
        !          4023:       }
        !          4024:     }
        !          4025:   }
        !          4026: free_matrix(mint,1,maxwav,1,n);
        !          4027:     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
        !          4028:     free_vector(weight,1,n);
        !          4029:   fclose(ficreseij);
        !          4030:   fclose(ficresvij);
        !          4031:   fclose(ficrest);
        !          4032:   fclose(ficpar);
        !          4033:   free_vector(epj,1,nlstate+1);
        !          4034:   
        !          4035:   /*------- Variance limit prevalence------*/   
        !          4036: 
        !          4037:   strcpy(fileresvpl,"vpl");
        !          4038:   strcat(fileresvpl,fileres);
        !          4039:   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
        !          4040:     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
        !          4041:     exit(0);
        !          4042:   }
        !          4043:   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
        !          4044: 
        !          4045:   k=0;
        !          4046:   for(cptcov=1;cptcov<=i1;cptcov++){
        !          4047:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        !          4048:       k=k+1;
        !          4049:       fprintf(ficresvpl,"\n#****** ");
        !          4050:       for(j=1;j<=cptcoveff;j++) 
        !          4051:        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        !          4052:       fprintf(ficresvpl,"******\n");
        !          4053:       
        !          4054:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
        !          4055:       oldm=oldms;savm=savms;
        !          4056:      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
        !          4057:     }
        !          4058:  }
        !          4059: 
        !          4060:   fclose(ficresvpl);
        !          4061: 
        !          4062:   /*---------- End : free ----------------*/
        !          4063:   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
        !          4064:   
        !          4065:   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        !          4066:   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        !          4067:   
        !          4068:   
        !          4069:   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
        !          4070:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
        !          4071:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
        !          4072:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
        !          4073:  
        !          4074:   free_matrix(matcov,1,npar,1,npar);
        !          4075:   free_vector(delti,1,npar);
        !          4076:   free_matrix(agev,1,maxwav,1,imx);
        !          4077:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
        !          4078:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        !          4079: 
        !          4080:   fprintf(fichtm,"\n</body>");
        !          4081:   fclose(fichtm);
        !          4082:   fclose(ficgp);
        !          4083:   
        !          4084: 
        !          4085:   if(erreur >0){
        !          4086:     printf("End of Imach with error or warning %d\n",erreur);
        !          4087:     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
        !          4088:   }else{
        !          4089:    printf("End of Imach\n");
        !          4090:    fprintf(ficlog,"End of Imach\n");
        !          4091:   }
        !          4092:   printf("See log file on %s\n",filelog);
        !          4093:   fclose(ficlog);
        !          4094:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
        !          4095:   
        !          4096:   /* 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);*/
        !          4097:   /*printf("Total time was %d uSec.\n", total_usecs);*/
        !          4098:   /*------ End -----------*/
        !          4099: 
        !          4100: 
        !          4101:  end:
        !          4102: #ifdef windows
        !          4103:   /* chdir(pathcd);*/
        !          4104: #endif 
        !          4105:  /*system("wgnuplot graph.plt");*/
        !          4106:  /*system("../gp37mgw/wgnuplot graph.plt");*/
        !          4107:  /*system("cd ../gp37mgw");*/
        !          4108:  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
        !          4109:  strcpy(plotcmd,GNUPLOTPROGRAM);
        !          4110:  strcat(plotcmd," ");
        !          4111:  strcat(plotcmd,optionfilegnuplot);
        !          4112:  system(plotcmd);
        !          4113: 
        !          4114: #ifdef windows
        !          4115:   while (z[0] != 'q') {
        !          4116:     /* chdir(path); */
        !          4117:     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
        !          4118:     scanf("%s",z);
        !          4119:     if (z[0] == 'c') system("./imach");
        !          4120:     else if (z[0] == 'e') system(optionfilehtm);
        !          4121:     else if (z[0] == 'g') system(plotcmd);
        !          4122:     else if (z[0] == 'q') exit(0);
        !          4123:   }
        !          4124: #endif 
        !          4125: }
        !          4126: 
        !          4127: 

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