File:  [Local Repository] / imach / src / imach.c
Revision 1.37: download - view: text, annotated - select for diffs
Fri Mar 29 15:31:59 2002 UTC (22 years, 2 months ago) by brouard
Branches: MAIN
CVS tags: HEAD
Changed  version to 0.8b

    1: /* $Id: imach.c,v 1.37 2002/03/29 15:31:59 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:   probabibility 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 "wgnuplot"
   60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   61: #define FILENAMELENGTH 80
   62: /*#define DEBUG*/
   63: #define windows
   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: 
   79: 
   80: int erreur; /* Error number */
   81: int nvar;
   82: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
   83: int npar=NPARMAX;
   84: int nlstate=2; /* Number of live states */
   85: int ndeath=1; /* Number of dead states */
   86: int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   87: int popbased=0;
   88: 
   89: int *wav; /* Number of waves for this individuual 0 is possible */
   90: int maxwav; /* Maxim number of waves */
   91: int jmin, jmax; /* min, max spacing between 2 waves */
   92: int mle, weightopt;
   93: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   94: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   95: double jmean; /* Mean space between 2 waves */
   96: double **oldm, **newm, **savm; /* Working pointers to matrices */
   97: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   98: FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   99: FILE *ficgp,*ficresprob,*ficpop;
  100: FILE *ficreseij;
  101:   char filerese[FILENAMELENGTH];
  102:  FILE  *ficresvij;
  103:   char fileresv[FILENAMELENGTH];
  104:  FILE  *ficresvpl;
  105:   char fileresvpl[FILENAMELENGTH];
  106: 
  107: #define NR_END 1
  108: #define FREE_ARG char*
  109: #define FTOL 1.0e-10
  110: 
  111: #define NRANSI 
  112: #define ITMAX 200 
  113: 
  114: #define TOL 2.0e-4 
  115: 
  116: #define CGOLD 0.3819660 
  117: #define ZEPS 1.0e-10 
  118: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
  119: 
  120: #define GOLD 1.618034 
  121: #define GLIMIT 100.0 
  122: #define TINY 1.0e-20 
  123: 
  124: static double maxarg1,maxarg2;
  125: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  126: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
  127:   
  128: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  129: #define rint(a) floor(a+0.5)
  130: 
  131: static double sqrarg;
  132: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  133: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
  134: 
  135: int imx; 
  136: int stepm;
  137: /* Stepm, step in month: minimum step interpolation*/
  138: 
  139: int estepm;
  140: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  141: 
  142: int m,nb;
  143: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  144: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  145: double **pmmij, ***probs, ***mobaverage;
  146: double dateintmean=0;
  147: 
  148: double *weight;
  149: int **s; /* Status */
  150: double *agedc, **covar, idx;
  151: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
  152: 
  153: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  154: double ftolhess; /* Tolerance for computing hessian */
  155: 
  156: /**************** split *************************/
  157: static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
  158: {
  159:    char	*s;				/* pointer */
  160:    int	l1, l2;				/* length counters */
  161: 
  162:    l1 = strlen( path );			/* length of path */
  163:    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
  164: #ifdef windows
  165:    s = strrchr( path, '\\' );		/* find last / */
  166: #else
  167:    s = strrchr( path, '/' );		/* find last / */
  168: #endif
  169:    if ( s == NULL ) {			/* no directory, so use current */
  170: #if	defined(__bsd__)		/* get current working directory */
  171:       extern char	*getwd( );
  172: 
  173:       if ( getwd( dirc ) == NULL ) {
  174: #else
  175:       extern char	*getcwd( );
  176: 
  177:       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
  178: #endif
  179:          return( GLOCK_ERROR_GETCWD );
  180:       }
  181:       strcpy( name, path );		/* we've got it */
  182:    } else {				/* strip direcotry from path */
  183:       s++;				/* after this, the filename */
  184:       l2 = strlen( s );			/* length of filename */
  185:       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
  186:       strcpy( name, s );		/* save file name */
  187:       strncpy( dirc, path, l1 - l2 );	/* now the directory */
  188:       dirc[l1-l2] = 0;			/* add zero */
  189:    }
  190:    l1 = strlen( dirc );			/* length of directory */
  191: #ifdef windows
  192:    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
  193: #else
  194:    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
  195: #endif
  196:    s = strrchr( name, '.' );		/* find last / */
  197:    s++;
  198:    strcpy(ext,s);			/* save extension */
  199:    l1= strlen( name);
  200:    l2= strlen( s)+1;
  201:    strncpy( finame, name, l1-l2);
  202:    finame[l1-l2]= 0;
  203:    return( 0 );				/* we're done */
  204: }
  205: 
  206: 
  207: /******************************************/
  208: 
  209: void replace(char *s, char*t)
  210: {
  211:   int i;
  212:   int lg=20;
  213:   i=0;
  214:   lg=strlen(t);
  215:   for(i=0; i<= lg; i++) {
  216:     (s[i] = t[i]);
  217:     if (t[i]== '\\') s[i]='/';
  218:   }
  219: }
  220: 
  221: int nbocc(char *s, char occ)
  222: {
  223:   int i,j=0;
  224:   int lg=20;
  225:   i=0;
  226:   lg=strlen(s);
  227:   for(i=0; i<= lg; i++) {
  228:   if  (s[i] == occ ) j++;
  229:   }
  230:   return j;
  231: }
  232: 
  233: void cutv(char *u,char *v, char*t, char occ)
  234: {
  235:   int i,lg,j,p=0;
  236:   i=0;
  237:   for(j=0; j<=strlen(t)-1; j++) {
  238:     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
  239:   }
  240: 
  241:   lg=strlen(t);
  242:   for(j=0; j<p; j++) {
  243:     (u[j] = t[j]);
  244:   }
  245:      u[p]='\0';
  246: 
  247:    for(j=0; j<= lg; j++) {
  248:     if (j>=(p+1))(v[j-p-1] = t[j]);
  249:   }
  250: }
  251: 
  252: /********************** nrerror ********************/
  253: 
  254: void nrerror(char error_text[])
  255: {
  256:   fprintf(stderr,"ERREUR ...\n");
  257:   fprintf(stderr,"%s\n",error_text);
  258:   exit(1);
  259: }
  260: /*********************** vector *******************/
  261: double *vector(int nl, int nh)
  262: {
  263:   double *v;
  264:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
  265:   if (!v) nrerror("allocation failure in vector");
  266:   return v-nl+NR_END;
  267: }
  268: 
  269: /************************ free vector ******************/
  270: void free_vector(double*v, int nl, int nh)
  271: {
  272:   free((FREE_ARG)(v+nl-NR_END));
  273: }
  274: 
  275: /************************ivector *******************************/
  276: int *ivector(long nl,long nh)
  277: {
  278:   int *v;
  279:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
  280:   if (!v) nrerror("allocation failure in ivector");
  281:   return v-nl+NR_END;
  282: }
  283: 
  284: /******************free ivector **************************/
  285: void free_ivector(int *v, long nl, long nh)
  286: {
  287:   free((FREE_ARG)(v+nl-NR_END));
  288: }
  289: 
  290: /******************* imatrix *******************************/
  291: int **imatrix(long nrl, long nrh, long ncl, long nch) 
  292:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
  293: { 
  294:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
  295:   int **m; 
  296:   
  297:   /* allocate pointers to rows */ 
  298:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
  299:   if (!m) nrerror("allocation failure 1 in matrix()"); 
  300:   m += NR_END; 
  301:   m -= nrl; 
  302:   
  303:   
  304:   /* allocate rows and set pointers to them */ 
  305:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
  306:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  307:   m[nrl] += NR_END; 
  308:   m[nrl] -= ncl; 
  309:   
  310:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
  311:   
  312:   /* return pointer to array of pointers to rows */ 
  313:   return m; 
  314: } 
  315: 
  316: /****************** free_imatrix *************************/
  317: void free_imatrix(m,nrl,nrh,ncl,nch)
  318:       int **m;
  319:       long nch,ncl,nrh,nrl; 
  320:      /* free an int matrix allocated by imatrix() */ 
  321: { 
  322:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
  323:   free((FREE_ARG) (m+nrl-NR_END)); 
  324: } 
  325: 
  326: /******************* matrix *******************************/
  327: double **matrix(long nrl, long nrh, long ncl, long nch)
  328: {
  329:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
  330:   double **m;
  331: 
  332:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  333:   if (!m) nrerror("allocation failure 1 in matrix()");
  334:   m += NR_END;
  335:   m -= nrl;
  336: 
  337:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  338:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  339:   m[nrl] += NR_END;
  340:   m[nrl] -= ncl;
  341: 
  342:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  343:   return m;
  344: }
  345: 
  346: /*************************free matrix ************************/
  347: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
  348: {
  349:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  350:   free((FREE_ARG)(m+nrl-NR_END));
  351: }
  352: 
  353: /******************* ma3x *******************************/
  354: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
  355: {
  356:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
  357:   double ***m;
  358: 
  359:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  360:   if (!m) nrerror("allocation failure 1 in matrix()");
  361:   m += NR_END;
  362:   m -= nrl;
  363: 
  364:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  365:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  366:   m[nrl] += NR_END;
  367:   m[nrl] -= ncl;
  368: 
  369:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  370: 
  371:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
  372:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
  373:   m[nrl][ncl] += NR_END;
  374:   m[nrl][ncl] -= nll;
  375:   for (j=ncl+1; j<=nch; j++) 
  376:     m[nrl][j]=m[nrl][j-1]+nlay;
  377:   
  378:   for (i=nrl+1; i<=nrh; i++) {
  379:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
  380:     for (j=ncl+1; j<=nch; j++) 
  381:       m[i][j]=m[i][j-1]+nlay;
  382:   }
  383:   return m;
  384: }
  385: 
  386: /*************************free ma3x ************************/
  387: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
  388: {
  389:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
  390:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  391:   free((FREE_ARG)(m+nrl-NR_END));
  392: }
  393: 
  394: /***************** f1dim *************************/
  395: extern int ncom; 
  396: extern double *pcom,*xicom;
  397: extern double (*nrfunc)(double []); 
  398:  
  399: double f1dim(double x) 
  400: { 
  401:   int j; 
  402:   double f;
  403:   double *xt; 
  404:  
  405:   xt=vector(1,ncom); 
  406:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
  407:   f=(*nrfunc)(xt); 
  408:   free_vector(xt,1,ncom); 
  409:   return f; 
  410: } 
  411: 
  412: /*****************brent *************************/
  413: double brent(double ax, double bx, double cx, double (*f)(double), double tol, 	double *xmin) 
  414: { 
  415:   int iter; 
  416:   double a,b,d,etemp;
  417:   double fu,fv,fw,fx;
  418:   double ftemp;
  419:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
  420:   double e=0.0; 
  421:  
  422:   a=(ax < cx ? ax : cx); 
  423:   b=(ax > cx ? ax : cx); 
  424:   x=w=v=bx; 
  425:   fw=fv=fx=(*f)(x); 
  426:   for (iter=1;iter<=ITMAX;iter++) { 
  427:     xm=0.5*(a+b); 
  428:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
  429:     /*		if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
  430:     printf(".");fflush(stdout);
  431: #ifdef DEBUG
  432:     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);
  433:     /*		if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
  434: #endif
  435:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
  436:       *xmin=x; 
  437:       return fx; 
  438:     } 
  439:     ftemp=fu;
  440:     if (fabs(e) > tol1) { 
  441:       r=(x-w)*(fx-fv); 
  442:       q=(x-v)*(fx-fw); 
  443:       p=(x-v)*q-(x-w)*r; 
  444:       q=2.0*(q-r); 
  445:       if (q > 0.0) p = -p; 
  446:       q=fabs(q); 
  447:       etemp=e; 
  448:       e=d; 
  449:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
  450: 	d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  451:       else { 
  452: 	d=p/q; 
  453: 	u=x+d; 
  454: 	if (u-a < tol2 || b-u < tol2) 
  455: 	  d=SIGN(tol1,xm-x); 
  456:       } 
  457:     } else { 
  458:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  459:     } 
  460:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
  461:     fu=(*f)(u); 
  462:     if (fu <= fx) { 
  463:       if (u >= x) a=x; else b=x; 
  464:       SHFT(v,w,x,u) 
  465: 	SHFT(fv,fw,fx,fu) 
  466: 	} else { 
  467: 	  if (u < x) a=u; else b=u; 
  468: 	  if (fu <= fw || w == x) { 
  469: 	    v=w; 
  470: 	    w=u; 
  471: 	    fv=fw; 
  472: 	    fw=fu; 
  473: 	  } else if (fu <= fv || v == x || v == w) { 
  474: 	    v=u; 
  475: 	    fv=fu; 
  476: 	  } 
  477: 	} 
  478:   } 
  479:   nrerror("Too many iterations in brent"); 
  480:   *xmin=x; 
  481:   return fx; 
  482: } 
  483: 
  484: /****************** mnbrak ***********************/
  485: 
  486: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
  487: 	    double (*func)(double)) 
  488: { 
  489:   double ulim,u,r,q, dum;
  490:   double fu; 
  491:  
  492:   *fa=(*func)(*ax); 
  493:   *fb=(*func)(*bx); 
  494:   if (*fb > *fa) { 
  495:     SHFT(dum,*ax,*bx,dum) 
  496:       SHFT(dum,*fb,*fa,dum) 
  497:       } 
  498:   *cx=(*bx)+GOLD*(*bx-*ax); 
  499:   *fc=(*func)(*cx); 
  500:   while (*fb > *fc) { 
  501:     r=(*bx-*ax)*(*fb-*fc); 
  502:     q=(*bx-*cx)*(*fb-*fa); 
  503:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
  504:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
  505:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
  506:     if ((*bx-u)*(u-*cx) > 0.0) { 
  507:       fu=(*func)(u); 
  508:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
  509:       fu=(*func)(u); 
  510:       if (fu < *fc) { 
  511: 	SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
  512: 	  SHFT(*fb,*fc,fu,(*func)(u)) 
  513: 	  } 
  514:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
  515:       u=ulim; 
  516:       fu=(*func)(u); 
  517:     } else { 
  518:       u=(*cx)+GOLD*(*cx-*bx); 
  519:       fu=(*func)(u); 
  520:     } 
  521:     SHFT(*ax,*bx,*cx,u) 
  522:       SHFT(*fa,*fb,*fc,fu) 
  523:       } 
  524: } 
  525: 
  526: /*************** linmin ************************/
  527: 
  528: int ncom; 
  529: double *pcom,*xicom;
  530: double (*nrfunc)(double []); 
  531:  
  532: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
  533: { 
  534:   double brent(double ax, double bx, double cx, 
  535: 	       double (*f)(double), double tol, double *xmin); 
  536:   double f1dim(double x); 
  537:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
  538: 	      double *fc, double (*func)(double)); 
  539:   int j; 
  540:   double xx,xmin,bx,ax; 
  541:   double fx,fb,fa;
  542:  
  543:   ncom=n; 
  544:   pcom=vector(1,n); 
  545:   xicom=vector(1,n); 
  546:   nrfunc=func; 
  547:   for (j=1;j<=n;j++) { 
  548:     pcom[j]=p[j]; 
  549:     xicom[j]=xi[j]; 
  550:   } 
  551:   ax=0.0; 
  552:   xx=1.0; 
  553:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
  554:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
  555: #ifdef DEBUG
  556:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  557: #endif
  558:   for (j=1;j<=n;j++) { 
  559:     xi[j] *= xmin; 
  560:     p[j] += xi[j]; 
  561:   } 
  562:   free_vector(xicom,1,n); 
  563:   free_vector(pcom,1,n); 
  564: } 
  565: 
  566: /*************** powell ************************/
  567: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
  568: 	    double (*func)(double [])) 
  569: { 
  570:   void linmin(double p[], double xi[], int n, double *fret, 
  571: 	      double (*func)(double [])); 
  572:   int i,ibig,j; 
  573:   double del,t,*pt,*ptt,*xit;
  574:   double fp,fptt;
  575:   double *xits;
  576:   pt=vector(1,n); 
  577:   ptt=vector(1,n); 
  578:   xit=vector(1,n); 
  579:   xits=vector(1,n); 
  580:   *fret=(*func)(p); 
  581:   for (j=1;j<=n;j++) pt[j]=p[j]; 
  582:   for (*iter=1;;++(*iter)) { 
  583:     fp=(*fret); 
  584:     ibig=0; 
  585:     del=0.0; 
  586:     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
  587:     for (i=1;i<=n;i++) 
  588:       printf(" %d %.12f",i, p[i]);
  589:     printf("\n");
  590:     for (i=1;i<=n;i++) { 
  591:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
  592:       fptt=(*fret); 
  593: #ifdef DEBUG
  594:       printf("fret=%lf \n",*fret);
  595: #endif
  596:       printf("%d",i);fflush(stdout);
  597:       linmin(p,xit,n,fret,func); 
  598:       if (fabs(fptt-(*fret)) > del) { 
  599: 	del=fabs(fptt-(*fret)); 
  600: 	ibig=i; 
  601:       } 
  602: #ifdef DEBUG
  603:       printf("%d %.12e",i,(*fret));
  604:       for (j=1;j<=n;j++) {
  605: 	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
  606: 	printf(" x(%d)=%.12e",j,xit[j]);
  607:       }
  608:       for(j=1;j<=n;j++) 
  609: 	printf(" p=%.12e",p[j]);
  610:       printf("\n");
  611: #endif
  612:     } 
  613:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
  614: #ifdef DEBUG
  615:       int k[2],l;
  616:       k[0]=1;
  617:       k[1]=-1;
  618:       printf("Max: %.12e",(*func)(p));
  619:       for (j=1;j<=n;j++) 
  620: 	printf(" %.12e",p[j]);
  621:       printf("\n");
  622:       for(l=0;l<=1;l++) {
  623: 	for (j=1;j<=n;j++) {
  624: 	  ptt[j]=p[j]+(p[j]-pt[j])*k[l];
  625: 	  printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
  626: 	}
  627: 	printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
  628:       }
  629: #endif
  630: 
  631: 
  632:       free_vector(xit,1,n); 
  633:       free_vector(xits,1,n); 
  634:       free_vector(ptt,1,n); 
  635:       free_vector(pt,1,n); 
  636:       return; 
  637:     } 
  638:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  639:     for (j=1;j<=n;j++) { 
  640:       ptt[j]=2.0*p[j]-pt[j]; 
  641:       xit[j]=p[j]-pt[j]; 
  642:       pt[j]=p[j]; 
  643:     } 
  644:     fptt=(*func)(ptt); 
  645:     if (fptt < fp) { 
  646:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
  647:       if (t < 0.0) { 
  648: 	linmin(p,xit,n,fret,func); 
  649: 	for (j=1;j<=n;j++) { 
  650: 	  xi[j][ibig]=xi[j][n]; 
  651: 	  xi[j][n]=xit[j]; 
  652: 	}
  653: #ifdef DEBUG
  654: 	printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
  655: 	for(j=1;j<=n;j++)
  656: 	  printf(" %.12e",xit[j]);
  657: 	printf("\n");
  658: #endif
  659:       } 
  660:     } 
  661:   } 
  662: } 
  663: 
  664: /**** Prevalence limit ****************/
  665: 
  666: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  667: {
  668:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
  669:      matrix by transitions matrix until convergence is reached */
  670: 
  671:   int i, ii,j,k;
  672:   double min, max, maxmin, maxmax,sumnew=0.;
  673:   double **matprod2();
  674:   double **out, cov[NCOVMAX], **pmij();
  675:   double **newm;
  676:   double agefin, delaymax=50 ; /* Max number of years to converge */
  677: 
  678:   for (ii=1;ii<=nlstate+ndeath;ii++)
  679:     for (j=1;j<=nlstate+ndeath;j++){
  680:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  681:     }
  682: 
  683:    cov[1]=1.;
  684:  
  685:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  686:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
  687:     newm=savm;
  688:     /* Covariates have to be included here again */
  689:      cov[2]=agefin;
  690:   
  691:       for (k=1; k<=cptcovn;k++) {
  692: 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  693: 	/*	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]]);*/
  694:       }
  695:       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  696:       for (k=1; k<=cptcovprod;k++)
  697: 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  698: 
  699:       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
  700:       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
  701:       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
  702:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
  703: 
  704:     savm=oldm;
  705:     oldm=newm;
  706:     maxmax=0.;
  707:     for(j=1;j<=nlstate;j++){
  708:       min=1.;
  709:       max=0.;
  710:       for(i=1; i<=nlstate; i++) {
  711: 	sumnew=0;
  712: 	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
  713: 	prlim[i][j]= newm[i][j]/(1-sumnew);
  714: 	max=FMAX(max,prlim[i][j]);
  715: 	min=FMIN(min,prlim[i][j]);
  716:       }
  717:       maxmin=max-min;
  718:       maxmax=FMAX(maxmax,maxmin);
  719:     }
  720:     if(maxmax < ftolpl){
  721:       return prlim;
  722:     }
  723:   }
  724: }
  725: 
  726: /*************** transition probabilities ***************/ 
  727: 
  728: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  729: {
  730:   double s1, s2;
  731:   /*double t34;*/
  732:   int i,j,j1, nc, ii, jj;
  733: 
  734:     for(i=1; i<= nlstate; i++){
  735:     for(j=1; j<i;j++){
  736:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
  737: 	/*s2 += param[i][j][nc]*cov[nc];*/
  738: 	s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
  739: 	/*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
  740:       }
  741:       ps[i][j]=s2;
  742:       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
  743:     }
  744:     for(j=i+1; j<=nlstate+ndeath;j++){
  745:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
  746: 	s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
  747: 	/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
  748:       }
  749:       ps[i][j]=s2;
  750:     }
  751:   }
  752:     /*ps[3][2]=1;*/
  753: 
  754:   for(i=1; i<= nlstate; i++){
  755:      s1=0;
  756:     for(j=1; j<i; j++)
  757:       s1+=exp(ps[i][j]);
  758:     for(j=i+1; j<=nlstate+ndeath; j++)
  759:       s1+=exp(ps[i][j]);
  760:     ps[i][i]=1./(s1+1.);
  761:     for(j=1; j<i; j++)
  762:       ps[i][j]= exp(ps[i][j])*ps[i][i];
  763:     for(j=i+1; j<=nlstate+ndeath; j++)
  764:       ps[i][j]= exp(ps[i][j])*ps[i][i];
  765:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  766:   } /* end i */
  767: 
  768:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
  769:     for(jj=1; jj<= nlstate+ndeath; jj++){
  770:       ps[ii][jj]=0;
  771:       ps[ii][ii]=1;
  772:     }
  773:   }
  774: 
  775: 
  776:   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
  777:     for(jj=1; jj<= nlstate+ndeath; jj++){
  778:      printf("%lf ",ps[ii][jj]);
  779:    }
  780:     printf("\n ");
  781:     }
  782:     printf("\n ");printf("%lf ",cov[2]);*/
  783: /*
  784:   for(i=1; i<= npar; i++) printf("%f ",x[i]);
  785:   goto end;*/
  786:     return ps;
  787: }
  788: 
  789: /**************** Product of 2 matrices ******************/
  790: 
  791: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
  792: {
  793:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
  794:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
  795:   /* in, b, out are matrice of pointers which should have been initialized 
  796:      before: only the contents of out is modified. The function returns
  797:      a pointer to pointers identical to out */
  798:   long i, j, k;
  799:   for(i=nrl; i<= nrh; i++)
  800:     for(k=ncolol; k<=ncoloh; k++)
  801:       for(j=ncl,out[i][k]=0.; j<=nch; j++)
  802: 	out[i][k] +=in[i][j]*b[j][k];
  803: 
  804:   return out;
  805: }
  806: 
  807: 
  808: /************* Higher Matrix Product ***************/
  809: 
  810: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  811: {
  812:   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
  813:      duration (i.e. until
  814:      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
  815:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
  816:      (typically every 2 years instead of every month which is too big).
  817:      Model is determined by parameters x and covariates have to be 
  818:      included manually here. 
  819: 
  820:      */
  821: 
  822:   int i, j, d, h, k;
  823:   double **out, cov[NCOVMAX];
  824:   double **newm;
  825: 
  826:   /* Hstepm could be zero and should return the unit matrix */
  827:   for (i=1;i<=nlstate+ndeath;i++)
  828:     for (j=1;j<=nlstate+ndeath;j++){
  829:       oldm[i][j]=(i==j ? 1.0 : 0.0);
  830:       po[i][j][0]=(i==j ? 1.0 : 0.0);
  831:     }
  832:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  833:   for(h=1; h <=nhstepm; h++){
  834:     for(d=1; d <=hstepm; d++){
  835:       newm=savm;
  836:       /* Covariates have to be included here again */
  837:       cov[1]=1.;
  838:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
  839:       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  840:       for (k=1; k<=cptcovage;k++)
  841: 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  842:       for (k=1; k<=cptcovprod;k++)
  843: 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  844: 
  845: 
  846:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
  847:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
  848:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
  849: 		   pmij(pmmij,cov,ncovmodel,x,nlstate));
  850:       savm=oldm;
  851:       oldm=newm;
  852:     }
  853:     for(i=1; i<=nlstate+ndeath; i++)
  854:       for(j=1;j<=nlstate+ndeath;j++) {
  855: 	po[i][j][h]=newm[i][j];
  856: 	/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
  857: 	 */
  858:       }
  859:   } /* end h */
  860:   return po;
  861: }
  862: 
  863: 
  864: /*************** log-likelihood *************/
  865: double func( double *x)
  866: {
  867:   int i, ii, j, k, mi, d, kk;
  868:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
  869:   double **out;
  870:   double sw; /* Sum of weights */
  871:   double lli; /* Individual log likelihood */
  872:   long ipmx;
  873:   /*extern weight */
  874:   /* We are differentiating ll according to initial status */
  875:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
  876:   /*for(i=1;i<imx;i++) 
  877:     printf(" %d\n",s[4][i]);
  878:   */
  879:   cov[1]=1.;
  880: 
  881:   for(k=1; k<=nlstate; k++) ll[k]=0.;
  882:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  883:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  884:     for(mi=1; mi<= wav[i]-1; mi++){
  885:       for (ii=1;ii<=nlstate+ndeath;ii++)
  886: 	for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  887:       for(d=0; d<dh[mi][i]; d++){
  888: 	newm=savm;
  889: 	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  890: 	for (kk=1; kk<=cptcovage;kk++) {
  891: 	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  892: 	}
  893: 	
  894: 	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  895: 		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  896: 	savm=oldm;
  897: 	oldm=newm;
  898: 	
  899: 	
  900:       } /* end mult */
  901:       
  902:       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
  903:       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
  904:       ipmx +=1;
  905:       sw += weight[i];
  906:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  907:     } /* end of wave */
  908:   } /* end of individual */
  909: 
  910:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  911:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  912:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  913:   return -l;
  914: }
  915: 
  916: 
  917: /*********** Maximum Likelihood Estimation ***************/
  918: 
  919: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  920: {
  921:   int i,j, iter;
  922:   double **xi,*delti;
  923:   double fret;
  924:   xi=matrix(1,npar,1,npar);
  925:   for (i=1;i<=npar;i++)
  926:     for (j=1;j<=npar;j++)
  927:       xi[i][j]=(i==j ? 1.0 : 0.0);
  928:   printf("Powell\n");
  929:   powell(p,xi,npar,ftol,&iter,&fret,func);
  930: 
  931:    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
  932:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  933: 
  934: }
  935: 
  936: /**** Computes Hessian and covariance matrix ***/
  937: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  938: {
  939:   double  **a,**y,*x,pd;
  940:   double **hess;
  941:   int i, j,jk;
  942:   int *indx;
  943: 
  944:   double hessii(double p[], double delta, int theta, double delti[]);
  945:   double hessij(double p[], double delti[], int i, int j);
  946:   void lubksb(double **a, int npar, int *indx, double b[]) ;
  947:   void ludcmp(double **a, int npar, int *indx, double *d) ;
  948: 
  949:   hess=matrix(1,npar,1,npar);
  950: 
  951:   printf("\nCalculation of the hessian matrix. Wait...\n");
  952:   for (i=1;i<=npar;i++){
  953:     printf("%d",i);fflush(stdout);
  954:     hess[i][i]=hessii(p,ftolhess,i,delti);
  955:     /*printf(" %f ",p[i]);*/
  956:     /*printf(" %lf ",hess[i][i]);*/
  957:   }
  958:   
  959:   for (i=1;i<=npar;i++) {
  960:     for (j=1;j<=npar;j++)  {
  961:       if (j>i) { 
  962: 	printf(".%d%d",i,j);fflush(stdout);
  963: 	hess[i][j]=hessij(p,delti,i,j);
  964: 	hess[j][i]=hess[i][j];    
  965: 	/*printf(" %lf ",hess[i][j]);*/
  966:       }
  967:     }
  968:   }
  969:   printf("\n");
  970: 
  971:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
  972:   
  973:   a=matrix(1,npar,1,npar);
  974:   y=matrix(1,npar,1,npar);
  975:   x=vector(1,npar);
  976:   indx=ivector(1,npar);
  977:   for (i=1;i<=npar;i++)
  978:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  979:   ludcmp(a,npar,indx,&pd);
  980: 
  981:   for (j=1;j<=npar;j++) {
  982:     for (i=1;i<=npar;i++) x[i]=0;
  983:     x[j]=1;
  984:     lubksb(a,npar,indx,x);
  985:     for (i=1;i<=npar;i++){ 
  986:       matcov[i][j]=x[i];
  987:     }
  988:   }
  989: 
  990:   printf("\n#Hessian matrix#\n");
  991:   for (i=1;i<=npar;i++) { 
  992:     for (j=1;j<=npar;j++) { 
  993:       printf("%.3e ",hess[i][j]);
  994:     }
  995:     printf("\n");
  996:   }
  997: 
  998:   /* Recompute Inverse */
  999:   for (i=1;i<=npar;i++)
 1000:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 1001:   ludcmp(a,npar,indx,&pd);
 1002: 
 1003:   /*  printf("\n#Hessian matrix recomputed#\n");
 1004: 
 1005:   for (j=1;j<=npar;j++) {
 1006:     for (i=1;i<=npar;i++) x[i]=0;
 1007:     x[j]=1;
 1008:     lubksb(a,npar,indx,x);
 1009:     for (i=1;i<=npar;i++){ 
 1010:       y[i][j]=x[i];
 1011:       printf("%.3e ",y[i][j]);
 1012:     }
 1013:     printf("\n");
 1014:   }
 1015:   */
 1016: 
 1017:   free_matrix(a,1,npar,1,npar);
 1018:   free_matrix(y,1,npar,1,npar);
 1019:   free_vector(x,1,npar);
 1020:   free_ivector(indx,1,npar);
 1021:   free_matrix(hess,1,npar,1,npar);
 1022: 
 1023: 
 1024: }
 1025: 
 1026: /*************** hessian matrix ****************/
 1027: double hessii( double x[], double delta, int theta, double delti[])
 1028: {
 1029:   int i;
 1030:   int l=1, lmax=20;
 1031:   double k1,k2;
 1032:   double p2[NPARMAX+1];
 1033:   double res;
 1034:   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 1035:   double fx;
 1036:   int k=0,kmax=10;
 1037:   double l1;
 1038: 
 1039:   fx=func(x);
 1040:   for (i=1;i<=npar;i++) p2[i]=x[i];
 1041:   for(l=0 ; l <=lmax; l++){
 1042:     l1=pow(10,l);
 1043:     delts=delt;
 1044:     for(k=1 ; k <kmax; k=k+1){
 1045:       delt = delta*(l1*k);
 1046:       p2[theta]=x[theta] +delt;
 1047:       k1=func(p2)-fx;
 1048:       p2[theta]=x[theta]-delt;
 1049:       k2=func(p2)-fx;
 1050:       /*res= (k1-2.0*fx+k2)/delt/delt; */
 1051:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 1052:       
 1053: #ifdef DEBUG
 1054:       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);
 1055: #endif
 1056:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 1057:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 1058: 	k=kmax;
 1059:       }
 1060:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 1061: 	k=kmax; l=lmax*10.;
 1062:       }
 1063:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 1064: 	delts=delt;
 1065:       }
 1066:     }
 1067:   }
 1068:   delti[theta]=delts;
 1069:   return res; 
 1070:   
 1071: }
 1072: 
 1073: double hessij( double x[], double delti[], int thetai,int thetaj)
 1074: {
 1075:   int i;
 1076:   int l=1, l1, lmax=20;
 1077:   double k1,k2,k3,k4,res,fx;
 1078:   double p2[NPARMAX+1];
 1079:   int k;
 1080: 
 1081:   fx=func(x);
 1082:   for (k=1; k<=2; k++) {
 1083:     for (i=1;i<=npar;i++) p2[i]=x[i];
 1084:     p2[thetai]=x[thetai]+delti[thetai]/k;
 1085:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 1086:     k1=func(p2)-fx;
 1087:   
 1088:     p2[thetai]=x[thetai]+delti[thetai]/k;
 1089:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 1090:     k2=func(p2)-fx;
 1091:   
 1092:     p2[thetai]=x[thetai]-delti[thetai]/k;
 1093:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 1094:     k3=func(p2)-fx;
 1095:   
 1096:     p2[thetai]=x[thetai]-delti[thetai]/k;
 1097:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 1098:     k4=func(p2)-fx;
 1099:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 1100: #ifdef DEBUG
 1101:     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);
 1102: #endif
 1103:   }
 1104:   return res;
 1105: }
 1106: 
 1107: /************** Inverse of matrix **************/
 1108: void ludcmp(double **a, int n, int *indx, double *d) 
 1109: { 
 1110:   int i,imax,j,k; 
 1111:   double big,dum,sum,temp; 
 1112:   double *vv; 
 1113:  
 1114:   vv=vector(1,n); 
 1115:   *d=1.0; 
 1116:   for (i=1;i<=n;i++) { 
 1117:     big=0.0; 
 1118:     for (j=1;j<=n;j++) 
 1119:       if ((temp=fabs(a[i][j])) > big) big=temp; 
 1120:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 1121:     vv[i]=1.0/big; 
 1122:   } 
 1123:   for (j=1;j<=n;j++) { 
 1124:     for (i=1;i<j;i++) { 
 1125:       sum=a[i][j]; 
 1126:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 1127:       a[i][j]=sum; 
 1128:     } 
 1129:     big=0.0; 
 1130:     for (i=j;i<=n;i++) { 
 1131:       sum=a[i][j]; 
 1132:       for (k=1;k<j;k++) 
 1133: 	sum -= a[i][k]*a[k][j]; 
 1134:       a[i][j]=sum; 
 1135:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
 1136: 	big=dum; 
 1137: 	imax=i; 
 1138:       } 
 1139:     } 
 1140:     if (j != imax) { 
 1141:       for (k=1;k<=n;k++) { 
 1142: 	dum=a[imax][k]; 
 1143: 	a[imax][k]=a[j][k]; 
 1144: 	a[j][k]=dum; 
 1145:       } 
 1146:       *d = -(*d); 
 1147:       vv[imax]=vv[j]; 
 1148:     } 
 1149:     indx[j]=imax; 
 1150:     if (a[j][j] == 0.0) a[j][j]=TINY; 
 1151:     if (j != n) { 
 1152:       dum=1.0/(a[j][j]); 
 1153:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 1154:     } 
 1155:   } 
 1156:   free_vector(vv,1,n);  /* Doesn't work */
 1157: ;
 1158: } 
 1159: 
 1160: void lubksb(double **a, int n, int *indx, double b[]) 
 1161: { 
 1162:   int i,ii=0,ip,j; 
 1163:   double sum; 
 1164:  
 1165:   for (i=1;i<=n;i++) { 
 1166:     ip=indx[i]; 
 1167:     sum=b[ip]; 
 1168:     b[ip]=b[i]; 
 1169:     if (ii) 
 1170:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 1171:     else if (sum) ii=i; 
 1172:     b[i]=sum; 
 1173:   } 
 1174:   for (i=n;i>=1;i--) { 
 1175:     sum=b[i]; 
 1176:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 1177:     b[i]=sum/a[i][i]; 
 1178:   } 
 1179: } 
 1180: 
 1181: /************ Frequencies ********************/
 1182: 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)
 1183: {  /* Some frequencies */
 1184:   
 1185:   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 1186:   double ***freq; /* Frequencies */
 1187:   double *pp;
 1188:   double pos, k2, dateintsum=0,k2cpt=0;
 1189:   FILE *ficresp;
 1190:   char fileresp[FILENAMELENGTH];
 1191:   
 1192:   pp=vector(1,nlstate);
 1193:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 1194:   strcpy(fileresp,"p");
 1195:   strcat(fileresp,fileres);
 1196:   if((ficresp=fopen(fileresp,"w"))==NULL) {
 1197:     printf("Problem with prevalence resultfile: %s\n", fileresp);
 1198:     exit(0);
 1199:   }
 1200:   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 1201:   j1=0;
 1202:   
 1203:   j=cptcoveff;
 1204:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 1205:   
 1206:   for(k1=1; k1<=j;k1++){
 1207:     for(i1=1; i1<=ncodemax[k1];i1++){
 1208:       j1++;
 1209:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 1210: 	scanf("%d", i);*/
 1211:       for (i=-1; i<=nlstate+ndeath; i++)  
 1212: 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 1213: 	  for(m=agemin; m <= agemax+3; m++)
 1214: 	    freq[i][jk][m]=0;
 1215:       
 1216:       dateintsum=0;
 1217:       k2cpt=0;
 1218:       for (i=1; i<=imx; i++) {
 1219: 	bool=1;
 1220: 	if  (cptcovn>0) {
 1221: 	  for (z1=1; z1<=cptcoveff; z1++) 
 1222: 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 1223: 	      bool=0;
 1224: 	}
 1225: 	if (bool==1) {
 1226: 	  for(m=firstpass; m<=lastpass; m++){
 1227: 	    k2=anint[m][i]+(mint[m][i]/12.);
 1228: 	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
 1229: 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 1230: 	      if(agev[m][i]==1) agev[m][i]=agemax+2;
 1231: 	      if (m<lastpass) {
 1232: 		freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 1233: 		freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
 1234: 	      }
 1235: 	      
 1236: 	      if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
 1237: 		dateintsum=dateintsum+k2;
 1238: 		k2cpt++;
 1239: 	      }
 1240: 	    }
 1241: 	  }
 1242: 	}
 1243:       }
 1244:        
 1245:       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 1246: 
 1247:       if  (cptcovn>0) {
 1248: 	fprintf(ficresp, "\n#********** Variable "); 
 1249: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 1250: 	fprintf(ficresp, "**********\n#");
 1251:       }
 1252:       for(i=1; i<=nlstate;i++) 
 1253: 	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 1254:       fprintf(ficresp, "\n");
 1255:       
 1256:       for(i=(int)agemin; i <= (int)agemax+3; i++){
 1257: 	if(i==(int)agemax+3)
 1258: 	  printf("Total");
 1259: 	else
 1260: 	  printf("Age %d", i);
 1261: 	for(jk=1; jk <=nlstate ; jk++){
 1262: 	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 1263: 	    pp[jk] += freq[jk][m][i]; 
 1264: 	}
 1265: 	for(jk=1; jk <=nlstate ; jk++){
 1266: 	  for(m=-1, pos=0; m <=0 ; m++)
 1267: 	    pos += freq[jk][m][i];
 1268: 	  if(pp[jk]>=1.e-10)
 1269: 	    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 1270: 	  else
 1271: 	    printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 1272: 	}
 1273: 
 1274: 	for(jk=1; jk <=nlstate ; jk++){
 1275: 	  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 1276: 	    pp[jk] += freq[jk][m][i];
 1277: 	}
 1278: 
 1279: 	for(jk=1,pos=0; jk <=nlstate ; jk++)
 1280: 	  pos += pp[jk];
 1281: 	for(jk=1; jk <=nlstate ; jk++){
 1282: 	  if(pos>=1.e-5)
 1283: 	    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 1284: 	  else
 1285: 	    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 1286: 	  if( i <= (int) agemax){
 1287: 	    if(pos>=1.e-5){
 1288: 	      fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
 1289: 	      probs[i][jk][j1]= pp[jk]/pos;
 1290: 	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 1291: 	    }
 1292: 	    else
 1293: 	      fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
 1294: 	  }
 1295: 	}
 1296: 	
 1297: 	for(jk=-1; jk <=nlstate+ndeath; jk++)
 1298: 	  for(m=-1; m <=nlstate+ndeath; m++)
 1299: 	    if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 1300: 	if(i <= (int) agemax)
 1301: 	  fprintf(ficresp,"\n");
 1302: 	printf("\n");
 1303:       }
 1304:     }
 1305:   }
 1306:   dateintmean=dateintsum/k2cpt; 
 1307:  
 1308:   fclose(ficresp);
 1309:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 1310:   free_vector(pp,1,nlstate);
 1311:   
 1312:   /* End of Freq */
 1313: }
 1314: 
 1315: /************ Prevalence ********************/
 1316: 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)
 1317: {  /* Some frequencies */
 1318:  
 1319:   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 1320:   double ***freq; /* Frequencies */
 1321:   double *pp;
 1322:   double pos, k2;
 1323: 
 1324:   pp=vector(1,nlstate);
 1325:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 1326:   
 1327:   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 1328:   j1=0;
 1329:   
 1330:   j=cptcoveff;
 1331:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 1332:   
 1333:  for(k1=1; k1<=j;k1++){
 1334:     for(i1=1; i1<=ncodemax[k1];i1++){
 1335:       j1++;
 1336:  
 1337:       for (i=-1; i<=nlstate+ndeath; i++)  
 1338: 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 1339: 	  for(m=agemin; m <= agemax+3; m++)
 1340: 	    freq[i][jk][m]=0;
 1341:      
 1342:       for (i=1; i<=imx; i++) {
 1343: 	bool=1;
 1344: 	if  (cptcovn>0) {
 1345: 	  for (z1=1; z1<=cptcoveff; z1++) 
 1346: 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 1347: 	      bool=0;
 1348: 	} 
 1349: 	if (bool==1) { 
 1350: 	  for(m=firstpass; m<=lastpass; m++){
 1351: 	    k2=anint[m][i]+(mint[m][i]/12.);
 1352: 	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
 1353: 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 1354: 	      if(agev[m][i]==1) agev[m][i]=agemax+2;
 1355: 	      if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
 1356: 	      /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */ 
 1357: 	    }
 1358: 	  }
 1359: 	}
 1360:       }
 1361: 	for(i=(int)agemin; i <= (int)agemax+3; i++){ 
 1362: 	  for(jk=1; jk <=nlstate ; jk++){
 1363: 	    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 1364: 	      pp[jk] += freq[jk][m][i]; 
 1365: 	  }
 1366: 	  for(jk=1; jk <=nlstate ; jk++){
 1367: 	    for(m=-1, pos=0; m <=0 ; m++)
 1368: 	    pos += freq[jk][m][i];
 1369: 	}
 1370: 	
 1371: 	 for(jk=1; jk <=nlstate ; jk++){
 1372: 	   for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 1373: 	     pp[jk] += freq[jk][m][i];
 1374: 	 }
 1375: 	 
 1376: 	 for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
 1377: 
 1378: 	 for(jk=1; jk <=nlstate ; jk++){	   
 1379: 	   if( i <= (int) agemax){
 1380: 	     if(pos>=1.e-5){
 1381: 	       probs[i][jk][j1]= pp[jk]/pos;
 1382: 	     }
 1383: 	   }
 1384: 	 }
 1385: 	 
 1386: 	}
 1387:     }
 1388:   }
 1389:   
 1390:   
 1391:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 1392:   free_vector(pp,1,nlstate);
 1393:   
 1394: }  /* End of Freq */
 1395: 
 1396: /************* Waves Concatenation ***************/
 1397: 
 1398: void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 1399: {
 1400:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 1401:      Death is a valid wave (if date is known).
 1402:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 1403:      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
 1404:      and mw[mi+1][i]. dh depends on stepm.
 1405:      */
 1406: 
 1407:   int i, mi, m;
 1408:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 1409:      double sum=0., jmean=0.;*/
 1410: 
 1411:   int j, k=0,jk, ju, jl;
 1412:   double sum=0.;
 1413:   jmin=1e+5;
 1414:   jmax=-1;
 1415:   jmean=0.;
 1416:   for(i=1; i<=imx; i++){
 1417:     mi=0;
 1418:     m=firstpass;
 1419:     while(s[m][i] <= nlstate){
 1420:       if(s[m][i]>=1)
 1421: 	mw[++mi][i]=m;
 1422:       if(m >=lastpass)
 1423: 	break;
 1424:       else
 1425: 	m++;
 1426:     }/* end while */
 1427:     if (s[m][i] > nlstate){
 1428:       mi++;	/* Death is another wave */
 1429:       /* if(mi==0)  never been interviewed correctly before death */
 1430: 	 /* Only death is a correct wave */
 1431:       mw[mi][i]=m;
 1432:     }
 1433: 
 1434:     wav[i]=mi;
 1435:     if(mi==0)
 1436:       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
 1437:   }
 1438: 
 1439:   for(i=1; i<=imx; i++){
 1440:     for(mi=1; mi<wav[i];mi++){
 1441:       if (stepm <=0)
 1442: 	dh[mi][i]=1;
 1443:       else{
 1444: 	if (s[mw[mi+1][i]][i] > nlstate) {
 1445: 	  if (agedc[i] < 2*AGESUP) {
 1446: 	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 1447: 	  if(j==0) j=1;  /* Survives at least one month after exam */
 1448: 	  k=k+1;
 1449: 	  if (j >= jmax) jmax=j;
 1450: 	  if (j <= jmin) jmin=j;
 1451: 	  sum=sum+j;
 1452: 	  /*if (j<0) printf("j=%d num=%d \n",j,i); */
 1453: 	  }
 1454: 	}
 1455: 	else{
 1456: 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 1457: 	  k=k+1;
 1458: 	  if (j >= jmax) jmax=j;
 1459: 	  else if (j <= jmin)jmin=j;
 1460: 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 1461: 	  sum=sum+j;
 1462: 	}
 1463: 	jk= j/stepm;
 1464: 	jl= j -jk*stepm;
 1465: 	ju= j -(jk+1)*stepm;
 1466: 	if(jl <= -ju)
 1467: 	  dh[mi][i]=jk;
 1468: 	else
 1469: 	  dh[mi][i]=jk+1;
 1470: 	if(dh[mi][i]==0)
 1471: 	  dh[mi][i]=1; /* At least one step */
 1472:       }
 1473:     }
 1474:   }
 1475:   jmean=sum/k;
 1476:   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 1477:  }
 1478: /*********** Tricode ****************************/
 1479: void tricode(int *Tvar, int **nbcode, int imx)
 1480: {
 1481:   int Ndum[20],ij=1, k, j, i;
 1482:   int cptcode=0;
 1483:   cptcoveff=0; 
 1484:  
 1485:   for (k=0; k<19; k++) Ndum[k]=0;
 1486:   for (k=1; k<=7; k++) ncodemax[k]=0;
 1487: 
 1488:   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 1489:     for (i=1; i<=imx; i++) {
 1490:       ij=(int)(covar[Tvar[j]][i]);
 1491:       Ndum[ij]++; 
 1492:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 1493:       if (ij > cptcode) cptcode=ij; 
 1494:     }
 1495: 
 1496:     for (i=0; i<=cptcode; i++) {
 1497:       if(Ndum[i]!=0) ncodemax[j]++;
 1498:     }
 1499:     ij=1; 
 1500: 
 1501: 
 1502:     for (i=1; i<=ncodemax[j]; i++) {
 1503:       for (k=0; k<=19; k++) {
 1504: 	if (Ndum[k] != 0) {
 1505: 	  nbcode[Tvar[j]][ij]=k; 
 1506: 	  /*	 printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/
 1507: 	  ij++;
 1508: 	}
 1509: 	if (ij > ncodemax[j]) break; 
 1510:       }  
 1511:     } 
 1512:   }  
 1513: 
 1514:  for (k=0; k<19; k++) Ndum[k]=0;
 1515: 
 1516:  for (i=1; i<=ncovmodel-2; i++) {
 1517:       ij=Tvar[i];
 1518:       Ndum[ij]++; 
 1519:     }
 1520: 
 1521:  ij=1;
 1522:  for (i=1; i<=10; i++) {
 1523:    if((Ndum[i]!=0) && (i<=ncovcol)){
 1524:      Tvaraff[ij]=i; 
 1525:      ij++;
 1526:    }
 1527:  }
 1528:  
 1529:     cptcoveff=ij-1;
 1530: }
 1531: 
 1532: /*********** Health Expectancies ****************/
 1533: 
 1534: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)
 1535: {
 1536:   /* Health expectancies */
 1537:   int i, j, nhstepm, hstepm, h, nstepm;
 1538:   double age, agelim, hf;
 1539:   double ***p3mat;
 1540:   
 1541:   fprintf(ficreseij,"# Health expectancies\n");
 1542:   fprintf(ficreseij,"# Age");
 1543:   for(i=1; i<=nlstate;i++)
 1544:     for(j=1; j<=nlstate;j++)
 1545:       fprintf(ficreseij," %1d-%1d",i,j);
 1546:   fprintf(ficreseij,"\n");
 1547: 
 1548:   if(estepm < stepm){
 1549:     printf ("Problem %d lower than %d\n",estepm, stepm);
 1550:   }
 1551:   else  hstepm=estepm;   
 1552:   /* We compute the life expectancy from trapezoids spaced every estepm months
 1553:    * This is mainly to measure the difference between two models: for example
 1554:    * if stepm=24 months pijx are given only every 2 years and by summing them
 1555:    * we are calculating an estimate of the Life Expectancy assuming a linear 
 1556:    * progression inbetween and thus overestimating or underestimating according
 1557:    * to the curvature of the survival function. If, for the same date, we 
 1558:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
 1559:    * to compare the new estimate of Life expectancy with the same linear 
 1560:    * hypothesis. A more precise result, taking into account a more precise
 1561:    * curvature will be obtained if estepm is as small as stepm. */
 1562: 
 1563:   /* For example we decided to compute the life expectancy with the smallest unit */
 1564:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 1565:      nhstepm is the number of hstepm from age to agelim 
 1566:      nstepm is the number of stepm from age to agelin. 
 1567:      Look at hpijx to understand the reason of that which relies in memory size
 1568:      and note for a fixed period like estepm months */
 1569:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 1570:      survival function given by stepm (the optimization length). Unfortunately it
 1571:      means that if the survival funtion is printed only each two years of age and if
 1572:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 1573:      results. So we changed our mind and took the option of the best precision.
 1574:   */
 1575:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 1576: 
 1577:   agelim=AGESUP;
 1578:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1579:     /* nhstepm age range expressed in number of stepm */
 1580:     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 1581:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 1582:     /* if (stepm >= YEARM) hstepm=1;*/
 1583:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 1584:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1585:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
 1586:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 1587:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 1588:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 1589:     for(i=1; i<=nlstate;i++)
 1590:       for(j=1; j<=nlstate;j++)
 1591: 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 1592: 	  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 1593: 	  /* 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]);*/
 1594: 	}
 1595:     fprintf(ficreseij,"%3.0f",age );
 1596:     for(i=1; i<=nlstate;i++)
 1597:       for(j=1; j<=nlstate;j++){
 1598: 	fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
 1599:       }
 1600:     fprintf(ficreseij,"\n");
 1601:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1602:   }
 1603: }
 1604: 
 1605: /************ Variance ******************/
 1606: void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)
 1607: {
 1608:   /* Variance of health expectancies */
 1609:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 1610:   double **newm;
 1611:   double **dnewm,**doldm;
 1612:   int i, j, nhstepm, hstepm, h, nstepm ;
 1613:   int k, cptcode;
 1614:   double *xp;
 1615:   double **gp, **gm;
 1616:   double ***gradg, ***trgradg;
 1617:   double ***p3mat;
 1618:   double age,agelim, hf;
 1619:   int theta;
 1620: 
 1621:    fprintf(ficresvij,"# Covariances of life expectancies\n");
 1622:   fprintf(ficresvij,"# Age");
 1623:   for(i=1; i<=nlstate;i++)
 1624:     for(j=1; j<=nlstate;j++)
 1625:       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 1626:   fprintf(ficresvij,"\n");
 1627: 
 1628:   xp=vector(1,npar);
 1629:   dnewm=matrix(1,nlstate,1,npar);
 1630:   doldm=matrix(1,nlstate,1,nlstate);
 1631:   
 1632:   if(estepm < stepm){
 1633:     printf ("Problem %d lower than %d\n",estepm, stepm);
 1634:   }
 1635:   else  hstepm=estepm;   
 1636:   /* For example we decided to compute the life expectancy with the smallest unit */
 1637:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 1638:      nhstepm is the number of hstepm from age to agelim 
 1639:      nstepm is the number of stepm from age to agelin. 
 1640:      Look at hpijx to understand the reason of that which relies in memory size
 1641:      and note for a fixed period like k years */
 1642:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 1643:      survival function given by stepm (the optimization length). Unfortunately it
 1644:      means that if the survival funtion is printed only each two years of age and if
 1645:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 1646:      results. So we changed our mind and took the option of the best precision.
 1647:   */
 1648:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 1649:   agelim = AGESUP;
 1650:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1651:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 1652:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 1653:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1654:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 1655:     gp=matrix(0,nhstepm,1,nlstate);
 1656:     gm=matrix(0,nhstepm,1,nlstate);
 1657: 
 1658:     for(theta=1; theta <=npar; theta++){
 1659:       for(i=1; i<=npar; i++){ /* Computes gradient */
 1660: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1661:       }
 1662:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1663:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1664: 
 1665:       if (popbased==1) {
 1666: 	for(i=1; i<=nlstate;i++)
 1667: 	  prlim[i][i]=probs[(int)age][i][ij];
 1668:       }
 1669:   
 1670:       for(j=1; j<= nlstate; j++){
 1671: 	for(h=0; h<=nhstepm; h++){
 1672: 	  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 1673: 	    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 1674: 	}
 1675:       }
 1676:     
 1677:       for(i=1; i<=npar; i++) /* Computes gradient */
 1678: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1679:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1680:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1681:  
 1682:       if (popbased==1) {
 1683: 	for(i=1; i<=nlstate;i++)
 1684: 	  prlim[i][i]=probs[(int)age][i][ij];
 1685:       }
 1686: 
 1687:       for(j=1; j<= nlstate; j++){
 1688: 	for(h=0; h<=nhstepm; h++){
 1689: 	  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 1690: 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 1691: 	}
 1692:       }
 1693: 
 1694:       for(j=1; j<= nlstate; j++)
 1695: 	for(h=0; h<=nhstepm; h++){
 1696: 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 1697: 	}
 1698:     } /* End theta */
 1699: 
 1700:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
 1701: 
 1702:     for(h=0; h<=nhstepm; h++)
 1703:       for(j=1; j<=nlstate;j++)
 1704: 	for(theta=1; theta <=npar; theta++)
 1705: 	  trgradg[h][j][theta]=gradg[h][theta][j];
 1706: 
 1707:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 1708:     for(i=1;i<=nlstate;i++)
 1709:       for(j=1;j<=nlstate;j++)
 1710: 	vareij[i][j][(int)age] =0.;
 1711: 
 1712:     for(h=0;h<=nhstepm;h++){
 1713:       for(k=0;k<=nhstepm;k++){
 1714: 	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 1715: 	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 1716: 	for(i=1;i<=nlstate;i++)
 1717: 	  for(j=1;j<=nlstate;j++)
 1718: 	    vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 1719:       }
 1720:     }
 1721: 
 1722:     fprintf(ficresvij,"%.0f ",age );
 1723:     for(i=1; i<=nlstate;i++)
 1724:       for(j=1; j<=nlstate;j++){
 1725: 	fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 1726:       }
 1727:     fprintf(ficresvij,"\n");
 1728:     free_matrix(gp,0,nhstepm,1,nlstate);
 1729:     free_matrix(gm,0,nhstepm,1,nlstate);
 1730:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 1731:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 1732:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1733:   } /* End age */
 1734:   
 1735:   free_vector(xp,1,npar);
 1736:   free_matrix(doldm,1,nlstate,1,npar);
 1737:   free_matrix(dnewm,1,nlstate,1,nlstate);
 1738: 
 1739: }
 1740: 
 1741: /************ Variance of prevlim ******************/
 1742: 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)
 1743: {
 1744:   /* Variance of prevalence limit */
 1745:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 1746:   double **newm;
 1747:   double **dnewm,**doldm;
 1748:   int i, j, nhstepm, hstepm;
 1749:   int k, cptcode;
 1750:   double *xp;
 1751:   double *gp, *gm;
 1752:   double **gradg, **trgradg;
 1753:   double age,agelim;
 1754:   int theta;
 1755:    
 1756:   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");
 1757:   fprintf(ficresvpl,"# Age");
 1758:   for(i=1; i<=nlstate;i++)
 1759:       fprintf(ficresvpl," %1d-%1d",i,i);
 1760:   fprintf(ficresvpl,"\n");
 1761: 
 1762:   xp=vector(1,npar);
 1763:   dnewm=matrix(1,nlstate,1,npar);
 1764:   doldm=matrix(1,nlstate,1,nlstate);
 1765:   
 1766:   hstepm=1*YEARM; /* Every year of age */
 1767:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 1768:   agelim = AGESUP;
 1769:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1770:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 1771:     if (stepm >= YEARM) hstepm=1;
 1772:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 1773:     gradg=matrix(1,npar,1,nlstate);
 1774:     gp=vector(1,nlstate);
 1775:     gm=vector(1,nlstate);
 1776: 
 1777:     for(theta=1; theta <=npar; theta++){
 1778:       for(i=1; i<=npar; i++){ /* Computes gradient */
 1779: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1780:       }
 1781:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1782:       for(i=1;i<=nlstate;i++)
 1783: 	gp[i] = prlim[i][i];
 1784:     
 1785:       for(i=1; i<=npar; i++) /* Computes gradient */
 1786: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1787:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1788:       for(i=1;i<=nlstate;i++)
 1789: 	gm[i] = prlim[i][i];
 1790: 
 1791:       for(i=1;i<=nlstate;i++)
 1792: 	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 1793:     } /* End theta */
 1794: 
 1795:     trgradg =matrix(1,nlstate,1,npar);
 1796: 
 1797:     for(j=1; j<=nlstate;j++)
 1798:       for(theta=1; theta <=npar; theta++)
 1799: 	trgradg[j][theta]=gradg[theta][j];
 1800: 
 1801:     for(i=1;i<=nlstate;i++)
 1802:       varpl[i][(int)age] =0.;
 1803:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 1804:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 1805:     for(i=1;i<=nlstate;i++)
 1806:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 1807: 
 1808:     fprintf(ficresvpl,"%.0f ",age );
 1809:     for(i=1; i<=nlstate;i++)
 1810:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 1811:     fprintf(ficresvpl,"\n");
 1812:     free_vector(gp,1,nlstate);
 1813:     free_vector(gm,1,nlstate);
 1814:     free_matrix(gradg,1,npar,1,nlstate);
 1815:     free_matrix(trgradg,1,nlstate,1,npar);
 1816:   } /* End age */
 1817: 
 1818:   free_vector(xp,1,npar);
 1819:   free_matrix(doldm,1,nlstate,1,npar);
 1820:   free_matrix(dnewm,1,nlstate,1,nlstate);
 1821: 
 1822: }
 1823: 
 1824: /************ Variance of one-step probabilities  ******************/
 1825: void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)
 1826: {
 1827:   int i, j;
 1828:   int k=0, cptcode;
 1829:   double **dnewm,**doldm;
 1830:   double *xp;
 1831:   double *gp, *gm;
 1832:   double **gradg, **trgradg;
 1833:   double age,agelim, cov[NCOVMAX];
 1834:   int theta;
 1835:   char fileresprob[FILENAMELENGTH];
 1836: 
 1837:   strcpy(fileresprob,"prob"); 
 1838:   strcat(fileresprob,fileres);
 1839:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 1840:     printf("Problem with resultfile: %s\n", fileresprob);
 1841:   }
 1842:   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);
 1843:   
 1844: 
 1845:   xp=vector(1,npar);
 1846:   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 1847:   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));
 1848:   
 1849:   cov[1]=1;
 1850:   for (age=bage; age<=fage; age ++){ 
 1851:     cov[2]=age;
 1852:     gradg=matrix(1,npar,1,9);
 1853:     trgradg=matrix(1,9,1,npar);
 1854:     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
 1855:     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
 1856:     
 1857:     for(theta=1; theta <=npar; theta++){
 1858:       for(i=1; i<=npar; i++)
 1859: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1860:      
 1861:       pmij(pmmij,cov,ncovmodel,xp,nlstate);
 1862:    
 1863:       k=0;
 1864:       for(i=1; i<= (nlstate+ndeath); i++){
 1865: 	for(j=1; j<=(nlstate+ndeath);j++){
 1866: 	   k=k+1;
 1867: 	  gp[k]=pmmij[i][j];
 1868: 	}
 1869:       }
 1870: 
 1871:       for(i=1; i<=npar; i++)
 1872: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1873:     
 1874: 
 1875:       pmij(pmmij,cov,ncovmodel,xp,nlstate);
 1876:       k=0;
 1877:       for(i=1; i<=(nlstate+ndeath); i++){
 1878: 	for(j=1; j<=(nlstate+ndeath);j++){
 1879: 	  k=k+1;
 1880: 	  gm[k]=pmmij[i][j];
 1881: 	}
 1882:       }
 1883:      
 1884:        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++) 
 1885: 	   gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
 1886:     }
 1887: 
 1888:      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
 1889:       for(theta=1; theta <=npar; theta++)
 1890:       trgradg[j][theta]=gradg[theta][j];
 1891:  
 1892:      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
 1893:      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);
 1894: 
 1895:      pmij(pmmij,cov,ncovmodel,x,nlstate);
 1896: 
 1897:      k=0;
 1898:      for(i=1; i<=(nlstate+ndeath); i++){
 1899:        for(j=1; j<=(nlstate+ndeath);j++){
 1900: 	 k=k+1;
 1901: 	 gm[k]=pmmij[i][j];
 1902: 	}
 1903:      }
 1904:      
 1905:      /*printf("\n%d ",(int)age);
 1906:      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
 1907:        
 1908: 
 1909:        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 1910:      }*/
 1911: 
 1912:   fprintf(ficresprob,"\n%d ",(int)age);
 1913: 
 1914:   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
 1915:     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
 1916: if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
 1917:   }
 1918: 
 1919:     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 1920:     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 1921:     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 1922:     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 1923: }
 1924:  free_vector(xp,1,npar);
 1925: fclose(ficresprob);
 1926: 
 1927: }
 1928: 
 1929: /******************* Printing html file ***********/
 1930: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 1931:  int lastpass, int stepm, int weightopt, char model[],\
 1932:  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
 1933:  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
 1934:  char version[], int popforecast, int estepm ){
 1935:   int jj1, k1, i1, cpt;
 1936:   FILE *fichtm;
 1937:   /*char optionfilehtm[FILENAMELENGTH];*/
 1938: 
 1939:   strcpy(optionfilehtm,optionfile);
 1940:   strcat(optionfilehtm,".htm");
 1941:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
 1942:     printf("Problem with %s \n",optionfilehtm), exit(0);
 1943:   }
 1944: 
 1945:  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
 1946: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
 1947: \n
 1948: Total number of observations=%d <br>\n
 1949: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
 1950: <hr  size=\"2\" color=\"#EC5E5E\"> 
 1951:  <ul><li>Outputs files<br>\n
 1952:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
 1953:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
 1954:  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
 1955:  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
 1956:  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
 1957:  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);
 1958: 
 1959:  fprintf(fichtm,"\n
 1960:  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
 1961:  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
 1962:  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
 1963:  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
 1964: 
 1965:  if(popforecast==1) fprintf(fichtm,"\n
 1966:  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
 1967:  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
 1968: 	<br>",fileres,fileres,fileres,fileres);
 1969:  else 
 1970:    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);
 1971: fprintf(fichtm," <li>Graphs</li><p>");
 1972: 
 1973:  m=cptcoveff;
 1974:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 1975: 
 1976:  jj1=0;
 1977:  for(k1=1; k1<=m;k1++){
 1978:    for(i1=1; i1<=ncodemax[k1];i1++){
 1979:        jj1++;
 1980:        if (cptcovn > 0) {
 1981: 	 fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 1982: 	 for (cpt=1; cpt<=cptcoveff;cpt++) 
 1983: 	   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 1984: 	 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 1985:        }
 1986:        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
 1987: <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 1988:        for(cpt=1; cpt<nlstate;cpt++){
 1989: 	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
 1990: <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
 1991:        }
 1992:     for(cpt=1; cpt<=nlstate;cpt++) {
 1993:        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
 1994: interval) in state (%d): v%s%d%d.gif <br>
 1995: <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
 1996:      }
 1997:      for(cpt=1; cpt<=nlstate;cpt++) {
 1998:         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
 1999: <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
 2000:      }
 2001:      fprintf(fichtm,"\n<br>- Total life expectancy by age and
 2002: health expectancies in states (1) and (2): e%s%d.gif<br>
 2003: <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
 2004: fprintf(fichtm,"\n</body>");
 2005:    }
 2006:    }
 2007: fclose(fichtm);
 2008: }
 2009: 
 2010: /******************* Gnuplot file **************/
 2011: void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 2012: 
 2013:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
 2014: 
 2015:   strcpy(optionfilegnuplot,optionfilefiname);
 2016:   strcat(optionfilegnuplot,".gp.txt");
 2017:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
 2018:     printf("Problem with file %s",optionfilegnuplot);
 2019:   }
 2020: 
 2021: #ifdef windows
 2022:     fprintf(ficgp,"cd \"%s\" \n",pathc);
 2023: #endif
 2024: m=pow(2,cptcoveff);
 2025:   
 2026:  /* 1eme*/
 2027:   for (cpt=1; cpt<= nlstate ; cpt ++) {
 2028:    for (k1=1; k1<= m ; k1 ++) {
 2029: 
 2030: #ifdef windows
 2031:     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 2032: #endif
 2033: #ifdef unix
 2034: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
 2035: #endif
 2036: 
 2037: for (i=1; i<= nlstate ; i ++) {
 2038:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2039:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2040: }
 2041:     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
 2042:     for (i=1; i<= nlstate ; i ++) {
 2043:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2044:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2045: } 
 2046:   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
 2047:      for (i=1; i<= nlstate ; i ++) {
 2048:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2049:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2050: }  
 2051:      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
 2052: #ifdef unix
 2053: fprintf(ficgp,"\nset ter gif small size 400,300");
 2054: #endif
 2055: fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
 2056:    }
 2057:   }
 2058:   /*2 eme*/
 2059: 
 2060:   for (k1=1; k1<= m ; k1 ++) { 
 2061:     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);
 2062:     
 2063:     for (i=1; i<= nlstate+1 ; i ++) {
 2064:       k=2*i;
 2065:       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
 2066:       for (j=1; j<= nlstate+1 ; j ++) {
 2067:   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2068:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2069: }   
 2070:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
 2071:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
 2072:     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
 2073:       for (j=1; j<= nlstate+1 ; j ++) {
 2074: 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2075: 	else fprintf(ficgp," \%%*lf (\%%*lf)");
 2076: }   
 2077:       fprintf(ficgp,"\" t\"\" w l 0,");
 2078:      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
 2079:       for (j=1; j<= nlstate+1 ; j ++) {
 2080:   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2081:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2082: }   
 2083:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
 2084:       else fprintf(ficgp,"\" t\"\" w l 0,");
 2085:     }
 2086:     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
 2087:   }
 2088:  
 2089:   /*3eme*/
 2090: 
 2091:   for (k1=1; k1<= m ; k1 ++) { 
 2092:     for (cpt=1; cpt<= nlstate ; cpt ++) {
 2093:       k=2+nlstate*(cpt-1);
 2094:       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
 2095:       for (i=1; i< nlstate ; i ++) {
 2096: 	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
 2097:       } 
 2098:       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
 2099:     }
 2100:     }
 2101:  
 2102:   /* CV preval stat */
 2103:     for (k1=1; k1<= m ; k1 ++) { 
 2104:     for (cpt=1; cpt<nlstate ; cpt ++) {
 2105:       k=3;
 2106:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
 2107: 
 2108:       for (i=1; i< nlstate ; i ++)
 2109: 	fprintf(ficgp,"+$%d",k+i+1);
 2110:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
 2111:       
 2112:       l=3+(nlstate+ndeath)*cpt;
 2113:       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
 2114:       for (i=1; i< nlstate ; i ++) {
 2115: 	l=3+(nlstate+ndeath)*cpt;
 2116: 	fprintf(ficgp,"+$%d",l+i+1);
 2117:       }
 2118:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
 2119:       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
 2120:     } 
 2121:   }  
 2122:   
 2123:   /* proba elementaires */
 2124:    for(i=1,jk=1; i <=nlstate; i++){
 2125:     for(k=1; k <=(nlstate+ndeath); k++){
 2126:       if (k != i) {
 2127: 	for(j=1; j <=ncovmodel; j++){
 2128: 	
 2129: 	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 2130: 	  jk++; 
 2131: 	  fprintf(ficgp,"\n");
 2132: 	}
 2133:       }
 2134:     }
 2135:     }
 2136: 
 2137:     for(jk=1; jk <=m; jk++) {
 2138:   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 2139:    i=1;
 2140:    for(k2=1; k2<=nlstate; k2++) {
 2141:      k3=i;
 2142:      for(k=1; k<=(nlstate+ndeath); k++) {
 2143:        if (k != k2){
 2144:     	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
 2145: ij=1;
 2146: 	for(j=3; j <=ncovmodel; j++) {
 2147: 	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 2148: 	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 2149: 	    ij++;
 2150: 	  }
 2151: 	  else
 2152: 	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 2153: 	}
 2154: 	  fprintf(ficgp,")/(1");
 2155: 	
 2156: 	for(k1=1; k1 <=nlstate; k1++){   
 2157: 	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 2158: ij=1;
 2159: 	  for(j=3; j <=ncovmodel; j++){
 2160: 	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 2161: 	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 2162: 	    ij++;
 2163: 	  }
 2164: 	  else
 2165: 	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 2166: 	  }
 2167: 	  fprintf(ficgp,")");
 2168: 	}
 2169: 	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 2170: 	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 2171: 	i=i+ncovmodel;
 2172:        }
 2173:      }
 2174:    }
 2175:    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
 2176:    }
 2177:    
 2178:   fclose(ficgp);
 2179: }  /* end gnuplot */
 2180: 
 2181: 
 2182: /*************** Moving average **************/
 2183: void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
 2184: 
 2185:   int i, cpt, cptcod;
 2186:     for (agedeb=ageminpar; agedeb<=fage; agedeb++)
 2187:       for (i=1; i<=nlstate;i++)
 2188: 	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
 2189: 	  mobaverage[(int)agedeb][i][cptcod]=0.;
 2190:     
 2191:     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
 2192:       for (i=1; i<=nlstate;i++){
 2193: 	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2194: 	  for (cpt=0;cpt<=4;cpt++){
 2195: 	    mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
 2196: 	  }
 2197: 	  mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
 2198: 	}
 2199:       }
 2200:     }
 2201:     
 2202: }
 2203: 
 2204: 
 2205: /************** Forecasting ******************/
 2206: 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){
 2207:   
 2208:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 2209:   int *popage;
 2210:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 2211:   double *popeffectif,*popcount;
 2212:   double ***p3mat;
 2213:   char fileresf[FILENAMELENGTH];
 2214: 
 2215:  agelim=AGESUP;
 2216: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
 2217: 
 2218:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 2219:  
 2220:  
 2221:   strcpy(fileresf,"f"); 
 2222:   strcat(fileresf,fileres);
 2223:   if((ficresf=fopen(fileresf,"w"))==NULL) {
 2224:     printf("Problem with forecast resultfile: %s\n", fileresf);
 2225:   }
 2226:   printf("Computing forecasting: result on file '%s' \n", fileresf);
 2227: 
 2228:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 2229: 
 2230:   if (mobilav==1) {
 2231:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2232:     movingaverage(agedeb, fage, ageminpar, mobaverage);
 2233:   }
 2234: 
 2235:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 2236:   if (stepm<=12) stepsize=1;
 2237:   
 2238:   agelim=AGESUP;
 2239:   
 2240:   hstepm=1;
 2241:   hstepm=hstepm/stepm; 
 2242:   yp1=modf(dateintmean,&yp);
 2243:   anprojmean=yp;
 2244:   yp2=modf((yp1*12),&yp);
 2245:   mprojmean=yp;
 2246:   yp1=modf((yp2*30.5),&yp);
 2247:   jprojmean=yp;
 2248:   if(jprojmean==0) jprojmean=1;
 2249:   if(mprojmean==0) jprojmean=1;
 2250:   
 2251:   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
 2252:   
 2253:   for(cptcov=1;cptcov<=i2;cptcov++){
 2254:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2255:       k=k+1;
 2256:       fprintf(ficresf,"\n#******");
 2257:       for(j=1;j<=cptcoveff;j++) {
 2258: 	fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 2259:       }
 2260:       fprintf(ficresf,"******\n");
 2261:       fprintf(ficresf,"# StartingAge FinalAge");
 2262:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
 2263:       
 2264:       
 2265:       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
 2266: 	fprintf(ficresf,"\n");
 2267: 	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
 2268: 
 2269:      	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2270: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2271: 	  nhstepm = nhstepm/hstepm; 
 2272: 	  
 2273: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2274: 	  oldm=oldms;savm=savms;
 2275: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2276: 	
 2277: 	  for (h=0; h<=nhstepm; h++){
 2278: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2279: 	      fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
 2280: 	    } 
 2281: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2282: 	      kk1=0.;kk2=0;
 2283: 	      for(i=1; i<=nlstate;i++) {	      
 2284: 		if (mobilav==1) 
 2285: 		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 2286: 		else {
 2287: 		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 2288: 		}
 2289: 		
 2290: 	      }
 2291: 	      if (h==(int)(calagedate+12*cpt)){
 2292: 		fprintf(ficresf," %.3f", kk1);
 2293: 	     		
 2294: 	      }
 2295: 	    }
 2296: 	  }
 2297: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2298: 	}
 2299:       }
 2300:     }
 2301:   }
 2302:        
 2303:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2304: 
 2305:   fclose(ficresf);
 2306: }
 2307: /************** Forecasting ******************/
 2308: 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){
 2309:   
 2310:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 2311:   int *popage;
 2312:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 2313:   double *popeffectif,*popcount;
 2314:   double ***p3mat,***tabpop,***tabpopprev;
 2315:   char filerespop[FILENAMELENGTH];
 2316: 
 2317:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2318:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2319:   agelim=AGESUP;
 2320:   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
 2321:   
 2322:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 2323:   
 2324:   
 2325:   strcpy(filerespop,"pop"); 
 2326:   strcat(filerespop,fileres);
 2327:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
 2328:     printf("Problem with forecast resultfile: %s\n", filerespop);
 2329:   }
 2330:   printf("Computing forecasting: result on file '%s' \n", filerespop);
 2331: 
 2332:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 2333: 
 2334:   if (mobilav==1) {
 2335:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2336:     movingaverage(agedeb, fage, ageminpar, mobaverage);
 2337:   }
 2338: 
 2339:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 2340:   if (stepm<=12) stepsize=1;
 2341:   
 2342:   agelim=AGESUP;
 2343:   
 2344:   hstepm=1;
 2345:   hstepm=hstepm/stepm; 
 2346:   
 2347:   if (popforecast==1) {
 2348:     if((ficpop=fopen(popfile,"r"))==NULL) {
 2349:       printf("Problem with population file : %s\n",popfile);exit(0);
 2350:     } 
 2351:     popage=ivector(0,AGESUP);
 2352:     popeffectif=vector(0,AGESUP);
 2353:     popcount=vector(0,AGESUP);
 2354:     
 2355:     i=1;   
 2356:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
 2357:    
 2358:     imx=i;
 2359:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
 2360:   }
 2361: 
 2362:   for(cptcov=1;cptcov<=i2;cptcov++){
 2363:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2364:       k=k+1;
 2365:       fprintf(ficrespop,"\n#******");
 2366:       for(j=1;j<=cptcoveff;j++) {
 2367: 	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 2368:       }
 2369:       fprintf(ficrespop,"******\n");
 2370:       fprintf(ficrespop,"# Age");
 2371:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
 2372:       if (popforecast==1)  fprintf(ficrespop," [Population]");
 2373:       
 2374:       for (cpt=0; cpt<=0;cpt++) { 
 2375: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 2376: 	
 2377:      	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2378: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2379: 	  nhstepm = nhstepm/hstepm; 
 2380: 	  
 2381: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2382: 	  oldm=oldms;savm=savms;
 2383: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2384: 	
 2385: 	  for (h=0; h<=nhstepm; h++){
 2386: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2387: 	      fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 2388: 	    } 
 2389: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2390: 	      kk1=0.;kk2=0;
 2391: 	      for(i=1; i<=nlstate;i++) {	      
 2392: 		if (mobilav==1) 
 2393: 		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 2394: 		else {
 2395: 		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 2396: 		}
 2397: 	      }
 2398: 	      if (h==(int)(calagedate+12*cpt)){
 2399: 		tabpop[(int)(agedeb)][j][cptcod]=kk1;
 2400: 		  /*fprintf(ficrespop," %.3f", kk1);
 2401: 		    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
 2402: 	      }
 2403: 	    }
 2404: 	    for(i=1; i<=nlstate;i++){
 2405: 	      kk1=0.;
 2406: 		for(j=1; j<=nlstate;j++){
 2407: 		  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
 2408: 		}
 2409: 		  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
 2410: 	    }
 2411: 
 2412: 	    if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
 2413: 	      fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
 2414: 	  }
 2415: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2416: 	}
 2417:       }
 2418:  
 2419:   /******/
 2420: 
 2421:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
 2422: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 2423: 	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2424: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2425: 	  nhstepm = nhstepm/hstepm; 
 2426: 	  
 2427: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2428: 	  oldm=oldms;savm=savms;
 2429: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2430: 	  for (h=0; h<=nhstepm; h++){
 2431: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2432: 	      fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 2433: 	    } 
 2434: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2435: 	      kk1=0.;kk2=0;
 2436: 	      for(i=1; i<=nlstate;i++) {	      
 2437: 		kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	
 2438: 	      }
 2439: 	      if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	
 2440: 	    }
 2441: 	  }
 2442: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2443: 	}
 2444:       }
 2445:    } 
 2446:   }
 2447:  
 2448:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2449: 
 2450:   if (popforecast==1) {
 2451:     free_ivector(popage,0,AGESUP);
 2452:     free_vector(popeffectif,0,AGESUP);
 2453:     free_vector(popcount,0,AGESUP);
 2454:   }
 2455:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2456:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2457:   fclose(ficrespop);
 2458: }
 2459: 
 2460: /***********************************************/
 2461: /**************** Main Program *****************/
 2462: /***********************************************/
 2463: 
 2464: int main(int argc, char *argv[])
 2465: {
 2466: 
 2467:   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
 2468:   double agedeb, agefin,hf;
 2469:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 2470: 
 2471:   double fret;
 2472:   double **xi,tmp,delta;
 2473: 
 2474:   double dum; /* Dummy variable */
 2475:   double ***p3mat;
 2476:   int *indx;
 2477:   char line[MAXLINE], linepar[MAXLINE];
 2478:   char title[MAXLINE];
 2479:   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 2480:   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 2481:   
 2482:   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 2483: 
 2484:   char filerest[FILENAMELENGTH];
 2485:   char fileregp[FILENAMELENGTH];
 2486:   char popfile[FILENAMELENGTH];
 2487:   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
 2488:   int firstobs=1, lastobs=10;
 2489:   int sdeb, sfin; /* Status at beginning and end */
 2490:   int c,  h , cpt,l;
 2491:   int ju,jl, mi;
 2492:   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
 2493:   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
 2494:   int mobilav=0,popforecast=0;
 2495:   int hstepm, nhstepm;
 2496:   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
 2497: 
 2498:   double bage, fage, age, agelim, agebase;
 2499:   double ftolpl=FTOL;
 2500:   double **prlim;
 2501:   double *severity;
 2502:   double ***param; /* Matrix of parameters */
 2503:   double  *p;
 2504:   double **matcov; /* Matrix of covariance */
 2505:   double ***delti3; /* Scale */
 2506:   double *delti; /* Scale */
 2507:   double ***eij, ***vareij;
 2508:   double **varpl; /* Variances of prevalence limits by age */
 2509:   double *epj, vepp;
 2510:   double kk1, kk2;
 2511:   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
 2512:   
 2513: 
 2514:   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";
 2515:   char *alph[]={"a","a","b","c","d","e"}, str[4];
 2516: 
 2517: 
 2518:   char z[1]="c", occ;
 2519: #include <sys/time.h>
 2520: #include <time.h>
 2521:   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
 2522:  
 2523:   /* long total_usecs;
 2524:   struct timeval start_time, end_time;
 2525:   
 2526:   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
 2527:   getcwd(pathcd, size);
 2528: 
 2529:   printf("\n%s",version);
 2530:   if(argc <=1){
 2531:     printf("\nEnter the parameter file name: ");
 2532:     scanf("%s",pathtot);
 2533:   }
 2534:   else{
 2535:     strcpy(pathtot,argv[1]);
 2536:   }
 2537:   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
 2538:   /*cygwin_split_path(pathtot,path,optionfile);
 2539:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
 2540:   /* cutv(path,optionfile,pathtot,'\\');*/
 2541: 
 2542:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
 2543:    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
 2544:   chdir(path);
 2545:   replace(pathc,path);
 2546: 
 2547: /*-------- arguments in the command line --------*/
 2548: 
 2549:   strcpy(fileres,"r");
 2550:   strcat(fileres, optionfilefiname);
 2551:   strcat(fileres,".txt");    /* Other files have txt extension */
 2552: 
 2553:   /*---------arguments file --------*/
 2554: 
 2555:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
 2556:     printf("Problem with optionfile %s\n",optionfile);
 2557:     goto end;
 2558:   }
 2559: 
 2560:   strcpy(filereso,"o");
 2561:   strcat(filereso,fileres);
 2562:   if((ficparo=fopen(filereso,"w"))==NULL) {
 2563:     printf("Problem with Output resultfile: %s\n", filereso);goto end;
 2564:   }
 2565: 
 2566:   /* Reads comments: lines beginning with '#' */
 2567:   while((c=getc(ficpar))=='#' && c!= EOF){
 2568:     ungetc(c,ficpar);
 2569:     fgets(line, MAXLINE, ficpar);
 2570:     puts(line);
 2571:     fputs(line,ficparo);
 2572:   }
 2573:   ungetc(c,ficpar);
 2574: 
 2575:   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
 2576:   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);
 2577:   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);
 2578: while((c=getc(ficpar))=='#' && c!= EOF){
 2579:     ungetc(c,ficpar);
 2580:     fgets(line, MAXLINE, ficpar);
 2581:     puts(line);
 2582:     fputs(line,ficparo);
 2583:   }
 2584:   ungetc(c,ficpar);
 2585:   
 2586:    
 2587:   covar=matrix(0,NCOVMAX,1,n); 
 2588:   cptcovn=0; 
 2589:   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
 2590: 
 2591:   ncovmodel=2+cptcovn;
 2592:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
 2593:   
 2594:   /* Read guess parameters */
 2595:   /* Reads comments: lines beginning with '#' */
 2596:   while((c=getc(ficpar))=='#' && c!= EOF){
 2597:     ungetc(c,ficpar);
 2598:     fgets(line, MAXLINE, ficpar);
 2599:     puts(line);
 2600:     fputs(line,ficparo);
 2601:   }
 2602:   ungetc(c,ficpar);
 2603:   
 2604:   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 2605:     for(i=1; i <=nlstate; i++)
 2606:     for(j=1; j <=nlstate+ndeath-1; j++){
 2607:       fscanf(ficpar,"%1d%1d",&i1,&j1);
 2608:       fprintf(ficparo,"%1d%1d",i1,j1);
 2609:       printf("%1d%1d",i,j);
 2610:       for(k=1; k<=ncovmodel;k++){
 2611: 	fscanf(ficpar," %lf",&param[i][j][k]);
 2612: 	printf(" %lf",param[i][j][k]);
 2613: 	fprintf(ficparo," %lf",param[i][j][k]);
 2614:       }
 2615:       fscanf(ficpar,"\n");
 2616:       printf("\n");
 2617:       fprintf(ficparo,"\n");
 2618:     }
 2619:   
 2620:     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
 2621: 
 2622:   p=param[1][1];
 2623:   
 2624:   /* Reads comments: lines beginning with '#' */
 2625:   while((c=getc(ficpar))=='#' && c!= EOF){
 2626:     ungetc(c,ficpar);
 2627:     fgets(line, MAXLINE, ficpar);
 2628:     puts(line);
 2629:     fputs(line,ficparo);
 2630:   }
 2631:   ungetc(c,ficpar);
 2632: 
 2633:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 2634:   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
 2635:   for(i=1; i <=nlstate; i++){
 2636:     for(j=1; j <=nlstate+ndeath-1; j++){
 2637:       fscanf(ficpar,"%1d%1d",&i1,&j1);
 2638:       printf("%1d%1d",i,j);
 2639:       fprintf(ficparo,"%1d%1d",i1,j1);
 2640:       for(k=1; k<=ncovmodel;k++){
 2641: 	fscanf(ficpar,"%le",&delti3[i][j][k]);
 2642: 	printf(" %le",delti3[i][j][k]);
 2643: 	fprintf(ficparo," %le",delti3[i][j][k]);
 2644:       }
 2645:       fscanf(ficpar,"\n");
 2646:       printf("\n");
 2647:       fprintf(ficparo,"\n");
 2648:     }
 2649:   }
 2650:   delti=delti3[1][1];
 2651:   
 2652:   /* Reads comments: lines beginning with '#' */
 2653:   while((c=getc(ficpar))=='#' && c!= EOF){
 2654:     ungetc(c,ficpar);
 2655:     fgets(line, MAXLINE, ficpar);
 2656:     puts(line);
 2657:     fputs(line,ficparo);
 2658:   }
 2659:   ungetc(c,ficpar);
 2660:   
 2661:   matcov=matrix(1,npar,1,npar);
 2662:   for(i=1; i <=npar; i++){
 2663:     fscanf(ficpar,"%s",&str);
 2664:     printf("%s",str);
 2665:     fprintf(ficparo,"%s",str);
 2666:     for(j=1; j <=i; j++){
 2667:       fscanf(ficpar," %le",&matcov[i][j]);
 2668:       printf(" %.5le",matcov[i][j]);
 2669:       fprintf(ficparo," %.5le",matcov[i][j]);
 2670:     }
 2671:     fscanf(ficpar,"\n");
 2672:     printf("\n");
 2673:     fprintf(ficparo,"\n");
 2674:   }
 2675:   for(i=1; i <=npar; i++)
 2676:     for(j=i+1;j<=npar;j++)
 2677:       matcov[i][j]=matcov[j][i];
 2678:    
 2679:   printf("\n");
 2680: 
 2681: 
 2682:     /*-------- Rewriting paramater file ----------*/
 2683:      strcpy(rfileres,"r");    /* "Rparameterfile */
 2684:      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
 2685:      strcat(rfileres,".");    /* */
 2686:      strcat(rfileres,optionfilext);    /* Other files have txt extension */
 2687:     if((ficres =fopen(rfileres,"w"))==NULL) {
 2688:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
 2689:     }
 2690:     fprintf(ficres,"#%s\n",version);
 2691:     
 2692:     /*-------- data file ----------*/
 2693:     if((fic=fopen(datafile,"r"))==NULL)    {
 2694:       printf("Problem with datafile: %s\n", datafile);goto end;
 2695:     }
 2696: 
 2697:     n= lastobs;
 2698:     severity = vector(1,maxwav);
 2699:     outcome=imatrix(1,maxwav+1,1,n);
 2700:     num=ivector(1,n);
 2701:     moisnais=vector(1,n);
 2702:     annais=vector(1,n);
 2703:     moisdc=vector(1,n);
 2704:     andc=vector(1,n);
 2705:     agedc=vector(1,n);
 2706:     cod=ivector(1,n);
 2707:     weight=vector(1,n);
 2708:     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
 2709:     mint=matrix(1,maxwav,1,n);
 2710:     anint=matrix(1,maxwav,1,n);
 2711:     s=imatrix(1,maxwav+1,1,n);
 2712:     adl=imatrix(1,maxwav+1,1,n);    
 2713:     tab=ivector(1,NCOVMAX);
 2714:     ncodemax=ivector(1,8);
 2715: 
 2716:     i=1;
 2717:     while (fgets(line, MAXLINE, fic) != NULL)    {
 2718:       if ((i >= firstobs) && (i <=lastobs)) {
 2719: 	
 2720: 	for (j=maxwav;j>=1;j--){
 2721: 	  cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
 2722: 	  strcpy(line,stra);
 2723: 	  cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 2724: 	  cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 2725: 	}
 2726: 	
 2727: 	cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
 2728: 	cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
 2729: 
 2730: 	cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
 2731: 	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
 2732: 
 2733: 	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
 2734: 	for (j=ncovcol;j>=1;j--){
 2735: 	  cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 2736: 	} 
 2737: 	num[i]=atol(stra);
 2738: 	
 2739: 	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
 2740: 	  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;}*/
 2741: 
 2742: 	i=i+1;
 2743:       }
 2744:     } 
 2745:     /* printf("ii=%d", ij);
 2746:        scanf("%d",i);*/
 2747:   imx=i-1; /* Number of individuals */
 2748: 
 2749:   /* for (i=1; i<=imx; i++){
 2750:     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
 2751:     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
 2752:     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
 2753:     }*/
 2754:  
 2755:   /* for (i=1; i<=imx; i++){
 2756:      if (s[4][i]==9)  s[4][i]=-1; 
 2757:      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]));}
 2758:   */
 2759:  
 2760:   /* Calculation of the number of parameter from char model*/
 2761:   Tvar=ivector(1,15); 
 2762:   Tprod=ivector(1,15); 
 2763:   Tvaraff=ivector(1,15); 
 2764:   Tvard=imatrix(1,15,1,2);
 2765:   Tage=ivector(1,15);      
 2766:    
 2767:   if (strlen(model) >1){
 2768:     j=0, j1=0, k1=1, k2=1;
 2769:     j=nbocc(model,'+');
 2770:     j1=nbocc(model,'*');
 2771:     cptcovn=j+1;
 2772:     cptcovprod=j1;
 2773:     
 2774:     strcpy(modelsav,model); 
 2775:     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
 2776:       printf("Error. Non available option model=%s ",model);
 2777:       goto end;
 2778:     }
 2779:     
 2780:     for(i=(j+1); i>=1;i--){
 2781:       cutv(stra,strb,modelsav,'+');
 2782:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); 
 2783:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
 2784:       /*scanf("%d",i);*/
 2785:       if (strchr(strb,'*')) {
 2786: 	cutv(strd,strc,strb,'*');
 2787: 	if (strcmp(strc,"age")==0) {
 2788: 	  cptcovprod--;
 2789: 	  cutv(strb,stre,strd,'V');
 2790: 	  Tvar[i]=atoi(stre);
 2791: 	  cptcovage++;
 2792: 	    Tage[cptcovage]=i;
 2793: 	    /*printf("stre=%s ", stre);*/
 2794: 	}
 2795: 	else if (strcmp(strd,"age")==0) {
 2796: 	  cptcovprod--;
 2797: 	  cutv(strb,stre,strc,'V');
 2798: 	  Tvar[i]=atoi(stre);
 2799: 	  cptcovage++;
 2800: 	  Tage[cptcovage]=i;
 2801: 	}
 2802: 	else {
 2803: 	  cutv(strb,stre,strc,'V');
 2804: 	  Tvar[i]=ncovcol+k1;
 2805: 	  cutv(strb,strc,strd,'V'); 
 2806: 	  Tprod[k1]=i;
 2807: 	  Tvard[k1][1]=atoi(strc);
 2808: 	  Tvard[k1][2]=atoi(stre);
 2809: 	  Tvar[cptcovn+k2]=Tvard[k1][1];
 2810: 	  Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
 2811: 	  for (k=1; k<=lastobs;k++) 
 2812: 	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
 2813: 	  k1++;
 2814: 	  k2=k2+2;
 2815: 	}
 2816:       }
 2817:       else {
 2818: 	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
 2819:        /*  scanf("%d",i);*/
 2820:       cutv(strd,strc,strb,'V');
 2821:       Tvar[i]=atoi(strc);
 2822:       }
 2823:       strcpy(modelsav,stra);  
 2824:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
 2825: 	scanf("%d",i);*/
 2826:     }
 2827: }
 2828:   
 2829:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
 2830:   printf("cptcovprod=%d ", cptcovprod);
 2831:   scanf("%d ",i);*/
 2832:     fclose(fic);
 2833: 
 2834:     /*  if(mle==1){*/
 2835:     if (weightopt != 1) { /* Maximisation without weights*/
 2836:       for(i=1;i<=n;i++) weight[i]=1.0;
 2837:     }
 2838:     /*-calculation of age at interview from date of interview and age at death -*/
 2839:     agev=matrix(1,maxwav,1,imx);
 2840: 
 2841:     for (i=1; i<=imx; i++) {
 2842:       for(m=2; (m<= maxwav); m++) {
 2843:        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
 2844: 	 anint[m][i]=9999;
 2845: 	 s[m][i]=-1;
 2846:        }
 2847:      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
 2848:       }
 2849:     }
 2850: 
 2851:     for (i=1; i<=imx; i++)  {
 2852:       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
 2853:       for(m=1; (m<= maxwav); m++){
 2854: 	if(s[m][i] >0){
 2855: 	  if (s[m][i] >= nlstate+1) {
 2856: 	    if(agedc[i]>0)
 2857: 	      if(moisdc[i]!=99 && andc[i]!=9999)
 2858: 		agev[m][i]=agedc[i];
 2859: 	    /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 2860: 	   else {
 2861: 	      if (andc[i]!=9999){
 2862: 	      printf("Warning negative age at death: %d line:%d\n",num[i],i);
 2863: 	      agev[m][i]=-1;
 2864: 	      }
 2865: 	    }
 2866: 	  }
 2867: 	  else if(s[m][i] !=9){ /* Should no more exist */
 2868: 	    agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
 2869: 	    if(mint[m][i]==99 || anint[m][i]==9999)
 2870: 	      agev[m][i]=1;
 2871: 	    else if(agev[m][i] <agemin){ 
 2872: 	      agemin=agev[m][i];
 2873: 	      /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
 2874: 	    }
 2875: 	    else if(agev[m][i] >agemax){
 2876: 	      agemax=agev[m][i];
 2877: 	     /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
 2878: 	    }
 2879: 	    /*agev[m][i]=anint[m][i]-annais[i];*/
 2880: 	    /*	 agev[m][i] = age[i]+2*m;*/
 2881: 	  }
 2882: 	  else { /* =9 */
 2883: 	    agev[m][i]=1;
 2884: 	    s[m][i]=-1;
 2885: 	  }
 2886: 	}
 2887: 	else /*= 0 Unknown */
 2888: 	  agev[m][i]=1;
 2889:       }
 2890:     
 2891:     }
 2892:     for (i=1; i<=imx; i++)  {
 2893:       for(m=1; (m<= maxwav); m++){
 2894: 	if (s[m][i] > (nlstate+ndeath)) {
 2895: 	  printf("Error: Wrong value in nlstate or ndeath\n");	
 2896: 	  goto end;
 2897: 	}
 2898:       }
 2899:     }
 2900: 
 2901: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
 2902: 
 2903:     free_vector(severity,1,maxwav);
 2904:     free_imatrix(outcome,1,maxwav+1,1,n);
 2905:     free_vector(moisnais,1,n);
 2906:     free_vector(annais,1,n);
 2907:     /* free_matrix(mint,1,maxwav,1,n);
 2908:        free_matrix(anint,1,maxwav,1,n);*/
 2909:     free_vector(moisdc,1,n);
 2910:     free_vector(andc,1,n);
 2911: 
 2912:    
 2913:     wav=ivector(1,imx);
 2914:     dh=imatrix(1,lastpass-firstpass+1,1,imx);
 2915:     mw=imatrix(1,lastpass-firstpass+1,1,imx);
 2916:    
 2917:     /* Concatenates waves */
 2918:       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
 2919: 
 2920: 
 2921:       Tcode=ivector(1,100);
 2922:       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
 2923:       ncodemax[1]=1;
 2924:       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
 2925:       
 2926:    codtab=imatrix(1,100,1,10);
 2927:    h=0;
 2928:    m=pow(2,cptcoveff);
 2929:  
 2930:    for(k=1;k<=cptcoveff; k++){
 2931:      for(i=1; i <=(m/pow(2,k));i++){
 2932:        for(j=1; j <= ncodemax[k]; j++){
 2933: 	 for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
 2934: 	   h++;
 2935: 	   if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
 2936: 	   /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
 2937: 	 } 
 2938:        }
 2939:      }
 2940:    } 
 2941:    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
 2942:       codtab[1][2]=1;codtab[2][2]=2; */
 2943:    /* for(i=1; i <=m ;i++){ 
 2944:       for(k=1; k <=cptcovn; k++){
 2945:       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
 2946:       }
 2947:       printf("\n");
 2948:       }
 2949:       scanf("%d",i);*/
 2950:     
 2951:    /* Calculates basic frequencies. Computes observed prevalence at single age
 2952:        and prints on file fileres'p'. */
 2953: 
 2954:     
 2955:    
 2956:     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 2957:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 2958:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 2959:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 2960:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
 2961:      
 2962:     /* For Powell, parameters are in a vector p[] starting at p[1]
 2963:        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
 2964:     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
 2965: 
 2966:     if(mle==1){
 2967:     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
 2968:     }
 2969:     
 2970:     /*--------- results files --------------*/
 2971:     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);
 2972:   
 2973: 
 2974:    jk=1;
 2975:    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 2976:    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 2977:    for(i=1,jk=1; i <=nlstate; i++){
 2978:      for(k=1; k <=(nlstate+ndeath); k++){
 2979:        if (k != i) 
 2980: 	 {
 2981: 	   printf("%d%d ",i,k);
 2982: 	   fprintf(ficres,"%1d%1d ",i,k);
 2983: 	   for(j=1; j <=ncovmodel; j++){
 2984: 	     printf("%f ",p[jk]);
 2985: 	     fprintf(ficres,"%f ",p[jk]);
 2986: 	     jk++; 
 2987: 	   }
 2988: 	   printf("\n");
 2989: 	   fprintf(ficres,"\n");
 2990: 	 }
 2991:      }
 2992:    }
 2993:  if(mle==1){
 2994:     /* Computing hessian and covariance matrix */
 2995:     ftolhess=ftol; /* Usually correct */
 2996:     hesscov(matcov, p, npar, delti, ftolhess, func);
 2997:  }
 2998:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
 2999:     printf("# Scales (for hessian or gradient estimation)\n");
 3000:      for(i=1,jk=1; i <=nlstate; i++){
 3001:       for(j=1; j <=nlstate+ndeath; j++){
 3002: 	if (j!=i) {
 3003: 	  fprintf(ficres,"%1d%1d",i,j);
 3004: 	  printf("%1d%1d",i,j);
 3005: 	  for(k=1; k<=ncovmodel;k++){
 3006: 	    printf(" %.5e",delti[jk]);
 3007: 	    fprintf(ficres," %.5e",delti[jk]);
 3008: 	    jk++;
 3009: 	  }
 3010: 	  printf("\n");
 3011: 	  fprintf(ficres,"\n");
 3012: 	}
 3013:       }
 3014:      }
 3015:     
 3016:     k=1;
 3017:     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");
 3018:     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");
 3019:     for(i=1;i<=npar;i++){
 3020:       /*  if (k>nlstate) k=1;
 3021:       i1=(i-1)/(ncovmodel*nlstate)+1; 
 3022:       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
 3023:       printf("%s%d%d",alph[k],i1,tab[i]);*/
 3024:       fprintf(ficres,"%3d",i);
 3025:       printf("%3d",i);
 3026:       for(j=1; j<=i;j++){
 3027: 	fprintf(ficres," %.5e",matcov[i][j]);
 3028: 	printf(" %.5e",matcov[i][j]);
 3029:       }
 3030:       fprintf(ficres,"\n");
 3031:       printf("\n");
 3032:       k++;
 3033:     }
 3034:     
 3035:     while((c=getc(ficpar))=='#' && c!= EOF){
 3036:       ungetc(c,ficpar);
 3037:       fgets(line, MAXLINE, ficpar);
 3038:       puts(line);
 3039:       fputs(line,ficparo);
 3040:     }
 3041:     ungetc(c,ficpar);
 3042:     estepm=0;
 3043:     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
 3044:     if (estepm==0 || estepm < stepm) estepm=stepm;
 3045:     if (fage <= 2) {
 3046:       bage = ageminpar;
 3047:       fage = agemaxpar;
 3048:     }
 3049:     
 3050:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
 3051:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 3052:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 3053:  
 3054:     while((c=getc(ficpar))=='#' && c!= EOF){
 3055:     ungetc(c,ficpar);
 3056:     fgets(line, MAXLINE, ficpar);
 3057:     puts(line);
 3058:     fputs(line,ficparo);
 3059:   }
 3060:   ungetc(c,ficpar);
 3061:   
 3062:   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
 3063:   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3064:  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3065:      
 3066:   while((c=getc(ficpar))=='#' && c!= EOF){
 3067:     ungetc(c,ficpar);
 3068:     fgets(line, MAXLINE, ficpar);
 3069:     puts(line);
 3070:     fputs(line,ficparo);
 3071:   }
 3072:   ungetc(c,ficpar);
 3073:  
 3074: 
 3075:    dateprev1=anprev1+mprev1/12.+jprev1/365.;
 3076:    dateprev2=anprev2+mprev2/12.+jprev2/365.;
 3077: 
 3078:   fscanf(ficpar,"pop_based=%d\n",&popbased);
 3079:   fprintf(ficparo,"pop_based=%d\n",popbased);   
 3080:   fprintf(ficres,"pop_based=%d\n",popbased);   
 3081:   
 3082:   while((c=getc(ficpar))=='#' && c!= EOF){
 3083:     ungetc(c,ficpar);
 3084:     fgets(line, MAXLINE, ficpar);
 3085:     puts(line);
 3086:     fputs(line,ficparo);
 3087:   }
 3088:   ungetc(c,ficpar);
 3089: 
 3090:   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
 3091: fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
 3092: fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
 3093: 
 3094: 
 3095: while((c=getc(ficpar))=='#' && c!= EOF){
 3096:     ungetc(c,ficpar);
 3097:     fgets(line, MAXLINE, ficpar);
 3098:     puts(line);
 3099:     fputs(line,ficparo);
 3100:   }
 3101:   ungetc(c,ficpar);
 3102: 
 3103:   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
 3104:   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 3105:   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 3106: 
 3107:  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3108: 
 3109: /*------------ gnuplot -------------*/
 3110:  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
 3111:  
 3112: /*------------ free_vector  -------------*/
 3113:  chdir(path);
 3114:  
 3115:  free_ivector(wav,1,imx);
 3116:  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
 3117:  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
 3118:  free_ivector(num,1,n);
 3119:  free_vector(agedc,1,n);
 3120:  /*free_matrix(covar,1,NCOVMAX,1,n);*/
 3121:  fclose(ficparo);
 3122:  fclose(ficres);
 3123: 
 3124: /*--------- index.htm --------*/
 3125: 
 3126:   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);
 3127: 
 3128:   
 3129:   /*--------------- Prevalence limit --------------*/
 3130:   
 3131:   strcpy(filerespl,"pl");
 3132:   strcat(filerespl,fileres);
 3133:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
 3134:     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
 3135:   }
 3136:   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
 3137:   fprintf(ficrespl,"#Prevalence limit\n");
 3138:   fprintf(ficrespl,"#Age ");
 3139:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
 3140:   fprintf(ficrespl,"\n");
 3141:   
 3142:   prlim=matrix(1,nlstate,1,nlstate);
 3143:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3144:   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3145:   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3146:   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3147:   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
 3148:   k=0;
 3149:   agebase=ageminpar;
 3150:   agelim=agemaxpar;
 3151:   ftolpl=1.e-10;
 3152:   i1=cptcoveff;
 3153:   if (cptcovn < 1){i1=1;}
 3154: 
 3155:   for(cptcov=1;cptcov<=i1;cptcov++){
 3156:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3157: 	k=k+1;
 3158: 	/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
 3159: 	fprintf(ficrespl,"\n#******");
 3160: 	for(j=1;j<=cptcoveff;j++) 
 3161: 	  fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3162: 	fprintf(ficrespl,"******\n");
 3163: 	
 3164: 	for (age=agebase; age<=agelim; age++){
 3165: 	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
 3166: 	  fprintf(ficrespl,"%.0f",age );
 3167: 	  for(i=1; i<=nlstate;i++)
 3168: 	  fprintf(ficrespl," %.5f", prlim[i][i]);
 3169: 	  fprintf(ficrespl,"\n");
 3170: 	}
 3171:       }
 3172:     }
 3173:   fclose(ficrespl);
 3174: 
 3175:   /*------------- h Pij x at various ages ------------*/
 3176:   
 3177:   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
 3178:   if((ficrespij=fopen(filerespij,"w"))==NULL) {
 3179:     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
 3180:   }
 3181:   printf("Computing pij: result on file '%s' \n", filerespij);
 3182:   
 3183:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 3184:   /*if (stepm<=24) stepsize=2;*/
 3185: 
 3186:   agelim=AGESUP;
 3187:   hstepm=stepsize*YEARM; /* Every year of age */
 3188:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
 3189:   
 3190:   k=0;
 3191:   for(cptcov=1;cptcov<=i1;cptcov++){
 3192:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3193:       k=k+1;
 3194: 	fprintf(ficrespij,"\n#****** ");
 3195: 	for(j=1;j<=cptcoveff;j++) 
 3196: 	  fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3197: 	fprintf(ficrespij,"******\n");
 3198: 	
 3199: 	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
 3200: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 3201: 	  nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 3202: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3203: 	  oldm=oldms;savm=savms;
 3204: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 3205: 	  fprintf(ficrespij,"# Age");
 3206: 	  for(i=1; i<=nlstate;i++)
 3207: 	    for(j=1; j<=nlstate+ndeath;j++)
 3208: 	      fprintf(ficrespij," %1d-%1d",i,j);
 3209: 	  fprintf(ficrespij,"\n");
 3210: 	  for (h=0; h<=nhstepm; h++){
 3211: 	    fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
 3212: 	    for(i=1; i<=nlstate;i++)
 3213: 	      for(j=1; j<=nlstate+ndeath;j++)
 3214: 		fprintf(ficrespij," %.5f", p3mat[i][j][h]);
 3215: 	    fprintf(ficrespij,"\n");
 3216: 	  }
 3217: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3218: 	  fprintf(ficrespij,"\n");
 3219: 	}
 3220:     }
 3221:   }
 3222: 
 3223:   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/
 3224: 
 3225:   fclose(ficrespij);
 3226: 
 3227: 
 3228:   /*---------- Forecasting ------------------*/
 3229:   if((stepm == 1) && (strcmp(model,".")==0)){
 3230:     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
 3231:     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
 3232:     free_matrix(mint,1,maxwav,1,n);
 3233:     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
 3234:     free_vector(weight,1,n);}
 3235:   else{
 3236:     erreur=108;
 3237:     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);
 3238:   }
 3239:   
 3240: 
 3241:   /*---------- Health expectancies and variances ------------*/
 3242: 
 3243:   strcpy(filerest,"t");
 3244:   strcat(filerest,fileres);
 3245:   if((ficrest=fopen(filerest,"w"))==NULL) {
 3246:     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
 3247:   }
 3248:   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
 3249: 
 3250: 
 3251:   strcpy(filerese,"e");
 3252:   strcat(filerese,fileres);
 3253:   if((ficreseij=fopen(filerese,"w"))==NULL) {
 3254:     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
 3255:   }
 3256:   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
 3257: 
 3258:  strcpy(fileresv,"v");
 3259:   strcat(fileresv,fileres);
 3260:   if((ficresvij=fopen(fileresv,"w"))==NULL) {
 3261:     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
 3262:   }
 3263:   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 3264: 
 3265:   k=0;
 3266:   for(cptcov=1;cptcov<=i1;cptcov++){
 3267:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3268:       k=k+1;
 3269:       fprintf(ficrest,"\n#****** ");
 3270:       for(j=1;j<=cptcoveff;j++) 
 3271: 	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3272:       fprintf(ficrest,"******\n");
 3273: 
 3274:       fprintf(ficreseij,"\n#****** ");
 3275:       for(j=1;j<=cptcoveff;j++) 
 3276: 	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3277:       fprintf(ficreseij,"******\n");
 3278: 
 3279:       fprintf(ficresvij,"\n#****** ");
 3280:       for(j=1;j<=cptcoveff;j++) 
 3281: 	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3282:       fprintf(ficresvij,"******\n");
 3283: 
 3284:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 3285:       oldm=oldms;savm=savms;
 3286:       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);  
 3287:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 3288:       oldm=oldms;savm=savms;
 3289:        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
 3290:     
 3291: 
 3292:  
 3293:       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
 3294:       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
 3295:       fprintf(ficrest,"\n");
 3296: 
 3297:       epj=vector(1,nlstate+1);
 3298:       for(age=bage; age <=fage ;age++){
 3299: 	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
 3300: 	if (popbased==1) {
 3301: 	  for(i=1; i<=nlstate;i++)
 3302: 	    prlim[i][i]=probs[(int)age][i][k];
 3303: 	}
 3304: 	
 3305: 	fprintf(ficrest," %4.0f",age);
 3306: 	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 3307: 	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
 3308: 	    epj[j] += prlim[i][i]*eij[i][j][(int)age];
 3309: 	  }
 3310: 	  epj[nlstate+1] +=epj[j];
 3311: 	}
 3312: 	for(i=1, vepp=0.;i <=nlstate;i++)
 3313: 	  for(j=1;j <=nlstate;j++)
 3314: 	    vepp += vareij[i][j][(int)age];
 3315: 	fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));
 3316: 	for(j=1;j <=nlstate;j++){
 3317: 	  fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));
 3318: 	}
 3319: 	fprintf(ficrest,"\n");
 3320:       }
 3321:     }
 3322:   }
 3323: 
 3324:   fclose(ficreseij);
 3325:   fclose(ficresvij);
 3326:   fclose(ficrest);
 3327:   fclose(ficpar);
 3328:   free_vector(epj,1,nlstate+1);
 3329:   
 3330:   /*------- Variance limit prevalence------*/   
 3331: 
 3332:   strcpy(fileresvpl,"vpl");
 3333:   strcat(fileresvpl,fileres);
 3334:   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
 3335:     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
 3336:     exit(0);
 3337:   }
 3338:   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
 3339: 
 3340:   k=0;
 3341:   for(cptcov=1;cptcov<=i1;cptcov++){
 3342:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3343:       k=k+1;
 3344:       fprintf(ficresvpl,"\n#****** ");
 3345:       for(j=1;j<=cptcoveff;j++) 
 3346: 	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3347:       fprintf(ficresvpl,"******\n");
 3348:       
 3349:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
 3350:       oldm=oldms;savm=savms;
 3351:      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
 3352:     }
 3353:  }
 3354: 
 3355:   fclose(ficresvpl);
 3356: 
 3357:   /*---------- End : free ----------------*/
 3358:   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
 3359:   
 3360:   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 3361:   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 3362:   
 3363:   
 3364:   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
 3365:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3366:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3367:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3368:  
 3369:   free_matrix(matcov,1,npar,1,npar);
 3370:   free_vector(delti,1,npar);
 3371:   free_matrix(agev,1,maxwav,1,imx);
 3372:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 3373: 
 3374:   if(erreur >0)
 3375:     printf("End of Imach with error or warning %d\n",erreur);
 3376:   else   printf("End of Imach\n");
 3377:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
 3378:   
 3379:   /* 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);*/
 3380:   /*printf("Total time was %d uSec.\n", total_usecs);*/
 3381:   /*------ End -----------*/
 3382: 
 3383: 
 3384:  end:
 3385: #ifdef windows
 3386:   /* chdir(pathcd);*/
 3387: #endif 
 3388:  /*system("wgnuplot graph.plt");*/
 3389:  /*system("../gp37mgw/wgnuplot graph.plt");*/
 3390:  /*system("cd ../gp37mgw");*/
 3391:  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
 3392:  strcpy(plotcmd,GNUPLOTPROGRAM);
 3393:  strcat(plotcmd," ");
 3394:  strcat(plotcmd,optionfilegnuplot);
 3395:  system(plotcmd);
 3396: 
 3397: #ifdef windows
 3398:   while (z[0] != 'q') {
 3399:     /* chdir(path); */
 3400:     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
 3401:     scanf("%s",z);
 3402:     if (z[0] == 'c') system("./imach");
 3403:     else if (z[0] == 'e') system(optionfilehtm);
 3404:     else if (z[0] == 'g') system(plotcmd);
 3405:     else if (z[0] == 'q') exit(0);
 3406:   }
 3407: #endif 
 3408: }
 3409: 
 3410: 

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