File:  [Local Repository] / imach / src / imach.c
Revision 1.47: download - view: text, annotated - select for diffs
Mon Jun 10 13:12:01 2002 UTC (22 years ago) by brouard
Branches: MAIN
CVS tags: HEAD
Many changes:
(a) We look at covariance between step probabilities by drawing
confidence interval ellipsoids of two step probabilities pij versus
pkl.
It is done by diagonalizing the inverse of the convariance matrix.

(b) In order to write to the gnuplot file or even to the html file
without using to much memory we are now reopening ficgp and fichtm
with an "append" option each time we need them into the main program.
It is better than keeping matrices in memory until the end.

    1: /* $Id: imach.c,v 1.47 2002/06/10 13:12:01 brouard Exp $
    2:    Interpolated Markov Chain
    3: 
    4:   Short summary of the programme:
    5:   
    6:   This program computes Healthy Life Expectancies from
    7:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    8:   first survey ("cross") where individuals from different ages are
    9:   interviewed on their health status or degree of disability (in the
   10:   case of a health survey which is our main interest) -2- at least a
   11:   second wave of interviews ("longitudinal") which measure each change
   12:   (if any) in individual health status.  Health expectancies are
   13:   computed from the time spent in each health state according to a
   14:   model. More health states you consider, more time is necessary to reach the
   15:   Maximum Likelihood of the parameters involved in the model.  The
   16:   simplest model is the multinomial logistic model where pij is the
   17:   probability to be observed in state j at the second wave
   18:   conditional to be observed in state i at the first wave. Therefore
   19:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   20:   'age' is age and 'sex' is a covariate. If you want to have a more
   21:   complex model than "constant and age", you should modify the program
   22:   where the markup *Covariates have to be included here again* invites
   23:   you to do it.  More covariates you add, slower the
   24:   convergence.
   25: 
   26:   The advantage of this computer programme, compared to a simple
   27:   multinomial logistic model, is clear when the delay between waves is not
   28:   identical for each individual. Also, if a individual missed an
   29:   intermediate interview, the information is lost, but taken into
   30:   account using an interpolation or extrapolation.  
   31: 
   32:   hPijx is the probability to be observed in state i at age x+h
   33:   conditional to the observed state i at age x. The delay 'h' can be
   34:   split into an exact number (nh*stepm) of unobserved intermediate
   35:   states. This elementary transition (by month or quarter trimester,
   36:   semester or year) is model as a multinomial logistic.  The hPx
   37:   matrix is simply the matrix product of nh*stepm elementary matrices
   38:   and the contribution of each individual to the likelihood is simply
   39:   hPijx.
   40: 
   41:   Also this programme outputs the covariance matrix of the parameters but also
   42:   of the life expectancies. It also computes the prevalence limits. 
   43:   
   44:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   45:            Institut national d'études démographiques, Paris.
   46:   This software have been partly granted by Euro-REVES, a concerted action
   47:   from the European Union.
   48:   It is copyrighted identically to a GNU software product, ie programme and
   49:   software can be distributed freely for non commercial use. Latest version
   50:   can be accessed at http://euroreves.ined.fr/imach .
   51:   **********************************************************************/
   52:  
   53: #include <math.h>
   54: #include <stdio.h>
   55: #include <stdlib.h>
   56: #include <unistd.h>
   57: 
   58: #define MAXLINE 256
   59: #define GNUPLOTPROGRAM "gnuplot"
   60: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   61: #define FILENAMELENGTH 80
   62: /*#define DEBUG*/
   63: #define 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: #ifdef windows
   79: #define DIRSEPARATOR '\\'
   80: #else
   81: #define DIRSEPARATOR '/'
   82: #endif
   83: 
   84: char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";
   85: int erreur; /* Error number */
   86: int nvar;
   87: int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
   88: int npar=NPARMAX;
   89: int nlstate=2; /* Number of live states */
   90: int ndeath=1; /* Number of dead states */
   91: int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   92: int popbased=0;
   93: 
   94: int *wav; /* Number of waves for this individuual 0 is possible */
   95: int maxwav; /* Maxim number of waves */
   96: int jmin, jmax; /* min, max spacing between 2 waves */
   97: int mle, weightopt;
   98: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   99: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
  100: double jmean; /* Mean space between 2 waves */
  101: double **oldm, **newm, **savm; /* Working pointers to matrices */
  102: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
  103: FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
  104: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
  105: FILE *fichtm; /* Html File */
  106: FILE *ficreseij;
  107: char filerese[FILENAMELENGTH];
  108: FILE  *ficresvij;
  109: char fileresv[FILENAMELENGTH];
  110: FILE  *ficresvpl;
  111: char fileresvpl[FILENAMELENGTH];
  112: char title[MAXLINE];
  113: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
  114: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
  115: 
  116: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  117: 
  118: char filerest[FILENAMELENGTH];
  119: char fileregp[FILENAMELENGTH];
  120: char popfile[FILENAMELENGTH];
  121: 
  122: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
  123: 
  124: #define NR_END 1
  125: #define FREE_ARG char*
  126: #define FTOL 1.0e-10
  127: 
  128: #define NRANSI 
  129: #define ITMAX 200 
  130: 
  131: #define TOL 2.0e-4 
  132: 
  133: #define CGOLD 0.3819660 
  134: #define ZEPS 1.0e-10 
  135: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
  136: 
  137: #define GOLD 1.618034 
  138: #define GLIMIT 100.0 
  139: #define TINY 1.0e-20 
  140: 
  141: static double maxarg1,maxarg2;
  142: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  143: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
  144:   
  145: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
  146: #define rint(a) floor(a+0.5)
  147: 
  148: static double sqrarg;
  149: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
  150: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
  151: 
  152: int imx; 
  153: int stepm;
  154: /* Stepm, step in month: minimum step interpolation*/
  155: 
  156: int estepm;
  157: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
  158: 
  159: int m,nb;
  160: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
  161: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  162: double **pmmij, ***probs, ***mobaverage;
  163: double dateintmean=0;
  164: 
  165: double *weight;
  166: int **s; /* Status */
  167: double *agedc, **covar, idx;
  168: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
  169: 
  170: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
  171: double ftolhess; /* Tolerance for computing hessian */
  172: 
  173: /**************** split *************************/
  174: static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
  175: {
  176:    char	*s;				/* pointer */
  177:    int	l1, l2;				/* length counters */
  178: 
  179:    l1 = strlen( path );			/* length of path */
  180:    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
  181:    s = strrchr( path,  DIRSEPARATOR );		/* find last / */
  182:    if ( s == NULL ) {			/* no directory, so use current */
  183: #if	defined(__bsd__)		/* get current working directory */
  184:       extern char	*getwd( );
  185: 
  186:       if ( getwd( dirc ) == NULL ) {
  187: #else
  188:       extern char	*getcwd( );
  189: 
  190:       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
  191: #endif
  192:          return( GLOCK_ERROR_GETCWD );
  193:       }
  194:       strcpy( name, path );		/* we've got it */
  195:    } else {				/* strip direcotry from path */
  196:       s++;				/* after this, the filename */
  197:       l2 = strlen( s );			/* length of filename */
  198:       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
  199:       strcpy( name, s );		/* save file name */
  200:       strncpy( dirc, path, l1 - l2 );	/* now the directory */
  201:       dirc[l1-l2] = 0;			/* add zero */
  202:    }
  203:    l1 = strlen( dirc );			/* length of directory */
  204: #ifdef windows
  205:    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
  206: #else
  207:    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
  208: #endif
  209:    s = strrchr( name, '.' );		/* find last / */
  210:    s++;
  211:    strcpy(ext,s);			/* save extension */
  212:    l1= strlen( name);
  213:    l2= strlen( s)+1;
  214:    strncpy( finame, name, l1-l2);
  215:    finame[l1-l2]= 0;
  216:    return( 0 );				/* we're done */
  217: }
  218: 
  219: 
  220: /******************************************/
  221: 
  222: void replace(char *s, char*t)
  223: {
  224:   int i;
  225:   int lg=20;
  226:   i=0;
  227:   lg=strlen(t);
  228:   for(i=0; i<= lg; i++) {
  229:     (s[i] = t[i]);
  230:     if (t[i]== '\\') s[i]='/';
  231:   }
  232: }
  233: 
  234: int nbocc(char *s, char occ)
  235: {
  236:   int i,j=0;
  237:   int lg=20;
  238:   i=0;
  239:   lg=strlen(s);
  240:   for(i=0; i<= lg; i++) {
  241:   if  (s[i] == occ ) j++;
  242:   }
  243:   return j;
  244: }
  245: 
  246: void cutv(char *u,char *v, char*t, char occ)
  247: {
  248:   int i,lg,j,p=0;
  249:   i=0;
  250:   for(j=0; j<=strlen(t)-1; j++) {
  251:     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
  252:   }
  253: 
  254:   lg=strlen(t);
  255:   for(j=0; j<p; j++) {
  256:     (u[j] = t[j]);
  257:   }
  258:      u[p]='\0';
  259: 
  260:    for(j=0; j<= lg; j++) {
  261:     if (j>=(p+1))(v[j-p-1] = t[j]);
  262:   }
  263: }
  264: 
  265: /********************** nrerror ********************/
  266: 
  267: void nrerror(char error_text[])
  268: {
  269:   fprintf(stderr,"ERREUR ...\n");
  270:   fprintf(stderr,"%s\n",error_text);
  271:   exit(1);
  272: }
  273: /*********************** vector *******************/
  274: double *vector(int nl, int nh)
  275: {
  276:   double *v;
  277:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
  278:   if (!v) nrerror("allocation failure in vector");
  279:   return v-nl+NR_END;
  280: }
  281: 
  282: /************************ free vector ******************/
  283: void free_vector(double*v, int nl, int nh)
  284: {
  285:   free((FREE_ARG)(v+nl-NR_END));
  286: }
  287: 
  288: /************************ivector *******************************/
  289: int *ivector(long nl,long nh)
  290: {
  291:   int *v;
  292:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
  293:   if (!v) nrerror("allocation failure in ivector");
  294:   return v-nl+NR_END;
  295: }
  296: 
  297: /******************free ivector **************************/
  298: void free_ivector(int *v, long nl, long nh)
  299: {
  300:   free((FREE_ARG)(v+nl-NR_END));
  301: }
  302: 
  303: /******************* imatrix *******************************/
  304: int **imatrix(long nrl, long nrh, long ncl, long nch) 
  305:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
  306: { 
  307:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
  308:   int **m; 
  309:   
  310:   /* allocate pointers to rows */ 
  311:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
  312:   if (!m) nrerror("allocation failure 1 in matrix()"); 
  313:   m += NR_END; 
  314:   m -= nrl; 
  315:   
  316:   
  317:   /* allocate rows and set pointers to them */ 
  318:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
  319:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  320:   m[nrl] += NR_END; 
  321:   m[nrl] -= ncl; 
  322:   
  323:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
  324:   
  325:   /* return pointer to array of pointers to rows */ 
  326:   return m; 
  327: } 
  328: 
  329: /****************** free_imatrix *************************/
  330: void free_imatrix(m,nrl,nrh,ncl,nch)
  331:       int **m;
  332:       long nch,ncl,nrh,nrl; 
  333:      /* free an int matrix allocated by imatrix() */ 
  334: { 
  335:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
  336:   free((FREE_ARG) (m+nrl-NR_END)); 
  337: } 
  338: 
  339: /******************* matrix *******************************/
  340: double **matrix(long nrl, long nrh, long ncl, long nch)
  341: {
  342:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
  343:   double **m;
  344: 
  345:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  346:   if (!m) nrerror("allocation failure 1 in matrix()");
  347:   m += NR_END;
  348:   m -= nrl;
  349: 
  350:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  351:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  352:   m[nrl] += NR_END;
  353:   m[nrl] -= ncl;
  354: 
  355:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  356:   return m;
  357: }
  358: 
  359: /*************************free matrix ************************/
  360: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
  361: {
  362:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  363:   free((FREE_ARG)(m+nrl-NR_END));
  364: }
  365: 
  366: /******************* ma3x *******************************/
  367: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
  368: {
  369:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
  370:   double ***m;
  371: 
  372:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  373:   if (!m) nrerror("allocation failure 1 in matrix()");
  374:   m += NR_END;
  375:   m -= nrl;
  376: 
  377:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  378:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  379:   m[nrl] += NR_END;
  380:   m[nrl] -= ncl;
  381: 
  382:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  383: 
  384:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
  385:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
  386:   m[nrl][ncl] += NR_END;
  387:   m[nrl][ncl] -= nll;
  388:   for (j=ncl+1; j<=nch; j++) 
  389:     m[nrl][j]=m[nrl][j-1]+nlay;
  390:   
  391:   for (i=nrl+1; i<=nrh; i++) {
  392:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
  393:     for (j=ncl+1; j<=nch; j++) 
  394:       m[i][j]=m[i][j-1]+nlay;
  395:   }
  396:   return m;
  397: }
  398: 
  399: /*************************free ma3x ************************/
  400: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
  401: {
  402:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
  403:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
  404:   free((FREE_ARG)(m+nrl-NR_END));
  405: }
  406: 
  407: /***************** f1dim *************************/
  408: extern int ncom; 
  409: extern double *pcom,*xicom;
  410: extern double (*nrfunc)(double []); 
  411:  
  412: double f1dim(double x) 
  413: { 
  414:   int j; 
  415:   double f;
  416:   double *xt; 
  417:  
  418:   xt=vector(1,ncom); 
  419:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
  420:   f=(*nrfunc)(xt); 
  421:   free_vector(xt,1,ncom); 
  422:   return f; 
  423: } 
  424: 
  425: /*****************brent *************************/
  426: double brent(double ax, double bx, double cx, double (*f)(double), double tol, 	double *xmin) 
  427: { 
  428:   int iter; 
  429:   double a,b,d,etemp;
  430:   double fu,fv,fw,fx;
  431:   double ftemp;
  432:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
  433:   double e=0.0; 
  434:  
  435:   a=(ax < cx ? ax : cx); 
  436:   b=(ax > cx ? ax : cx); 
  437:   x=w=v=bx; 
  438:   fw=fv=fx=(*f)(x); 
  439:   for (iter=1;iter<=ITMAX;iter++) { 
  440:     xm=0.5*(a+b); 
  441:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
  442:     /*		if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
  443:     printf(".");fflush(stdout);
  444: #ifdef DEBUG
  445:     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);
  446:     /*		if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
  447: #endif
  448:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
  449:       *xmin=x; 
  450:       return fx; 
  451:     } 
  452:     ftemp=fu;
  453:     if (fabs(e) > tol1) { 
  454:       r=(x-w)*(fx-fv); 
  455:       q=(x-v)*(fx-fw); 
  456:       p=(x-v)*q-(x-w)*r; 
  457:       q=2.0*(q-r); 
  458:       if (q > 0.0) p = -p; 
  459:       q=fabs(q); 
  460:       etemp=e; 
  461:       e=d; 
  462:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
  463: 	d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  464:       else { 
  465: 	d=p/q; 
  466: 	u=x+d; 
  467: 	if (u-a < tol2 || b-u < tol2) 
  468: 	  d=SIGN(tol1,xm-x); 
  469:       } 
  470:     } else { 
  471:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  472:     } 
  473:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
  474:     fu=(*f)(u); 
  475:     if (fu <= fx) { 
  476:       if (u >= x) a=x; else b=x; 
  477:       SHFT(v,w,x,u) 
  478: 	SHFT(fv,fw,fx,fu) 
  479: 	} else { 
  480: 	  if (u < x) a=u; else b=u; 
  481: 	  if (fu <= fw || w == x) { 
  482: 	    v=w; 
  483: 	    w=u; 
  484: 	    fv=fw; 
  485: 	    fw=fu; 
  486: 	  } else if (fu <= fv || v == x || v == w) { 
  487: 	    v=u; 
  488: 	    fv=fu; 
  489: 	  } 
  490: 	} 
  491:   } 
  492:   nrerror("Too many iterations in brent"); 
  493:   *xmin=x; 
  494:   return fx; 
  495: } 
  496: 
  497: /****************** mnbrak ***********************/
  498: 
  499: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
  500: 	    double (*func)(double)) 
  501: { 
  502:   double ulim,u,r,q, dum;
  503:   double fu; 
  504:  
  505:   *fa=(*func)(*ax); 
  506:   *fb=(*func)(*bx); 
  507:   if (*fb > *fa) { 
  508:     SHFT(dum,*ax,*bx,dum) 
  509:       SHFT(dum,*fb,*fa,dum) 
  510:       } 
  511:   *cx=(*bx)+GOLD*(*bx-*ax); 
  512:   *fc=(*func)(*cx); 
  513:   while (*fb > *fc) { 
  514:     r=(*bx-*ax)*(*fb-*fc); 
  515:     q=(*bx-*cx)*(*fb-*fa); 
  516:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
  517:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
  518:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
  519:     if ((*bx-u)*(u-*cx) > 0.0) { 
  520:       fu=(*func)(u); 
  521:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
  522:       fu=(*func)(u); 
  523:       if (fu < *fc) { 
  524: 	SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
  525: 	  SHFT(*fb,*fc,fu,(*func)(u)) 
  526: 	  } 
  527:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
  528:       u=ulim; 
  529:       fu=(*func)(u); 
  530:     } else { 
  531:       u=(*cx)+GOLD*(*cx-*bx); 
  532:       fu=(*func)(u); 
  533:     } 
  534:     SHFT(*ax,*bx,*cx,u) 
  535:       SHFT(*fa,*fb,*fc,fu) 
  536:       } 
  537: } 
  538: 
  539: /*************** linmin ************************/
  540: 
  541: int ncom; 
  542: double *pcom,*xicom;
  543: double (*nrfunc)(double []); 
  544:  
  545: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
  546: { 
  547:   double brent(double ax, double bx, double cx, 
  548: 	       double (*f)(double), double tol, double *xmin); 
  549:   double f1dim(double x); 
  550:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
  551: 	      double *fc, double (*func)(double)); 
  552:   int j; 
  553:   double xx,xmin,bx,ax; 
  554:   double fx,fb,fa;
  555:  
  556:   ncom=n; 
  557:   pcom=vector(1,n); 
  558:   xicom=vector(1,n); 
  559:   nrfunc=func; 
  560:   for (j=1;j<=n;j++) { 
  561:     pcom[j]=p[j]; 
  562:     xicom[j]=xi[j]; 
  563:   } 
  564:   ax=0.0; 
  565:   xx=1.0; 
  566:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
  567:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
  568: #ifdef DEBUG
  569:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
  570: #endif
  571:   for (j=1;j<=n;j++) { 
  572:     xi[j] *= xmin; 
  573:     p[j] += xi[j]; 
  574:   } 
  575:   free_vector(xicom,1,n); 
  576:   free_vector(pcom,1,n); 
  577: } 
  578: 
  579: /*************** powell ************************/
  580: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
  581: 	    double (*func)(double [])) 
  582: { 
  583:   void linmin(double p[], double xi[], int n, double *fret, 
  584: 	      double (*func)(double [])); 
  585:   int i,ibig,j; 
  586:   double del,t,*pt,*ptt,*xit;
  587:   double fp,fptt;
  588:   double *xits;
  589:   pt=vector(1,n); 
  590:   ptt=vector(1,n); 
  591:   xit=vector(1,n); 
  592:   xits=vector(1,n); 
  593:   *fret=(*func)(p); 
  594:   for (j=1;j<=n;j++) pt[j]=p[j]; 
  595:   for (*iter=1;;++(*iter)) { 
  596:     fp=(*fret); 
  597:     ibig=0; 
  598:     del=0.0; 
  599:     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
  600:     for (i=1;i<=n;i++) 
  601:       printf(" %d %.12f",i, p[i]);
  602:     printf("\n");
  603:     for (i=1;i<=n;i++) { 
  604:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
  605:       fptt=(*fret); 
  606: #ifdef DEBUG
  607:       printf("fret=%lf \n",*fret);
  608: #endif
  609:       printf("%d",i);fflush(stdout);
  610:       linmin(p,xit,n,fret,func); 
  611:       if (fabs(fptt-(*fret)) > del) { 
  612: 	del=fabs(fptt-(*fret)); 
  613: 	ibig=i; 
  614:       } 
  615: #ifdef DEBUG
  616:       printf("%d %.12e",i,(*fret));
  617:       for (j=1;j<=n;j++) {
  618: 	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
  619: 	printf(" x(%d)=%.12e",j,xit[j]);
  620:       }
  621:       for(j=1;j<=n;j++) 
  622: 	printf(" p=%.12e",p[j]);
  623:       printf("\n");
  624: #endif
  625:     } 
  626:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
  627: #ifdef DEBUG
  628:       int k[2],l;
  629:       k[0]=1;
  630:       k[1]=-1;
  631:       printf("Max: %.12e",(*func)(p));
  632:       for (j=1;j<=n;j++) 
  633: 	printf(" %.12e",p[j]);
  634:       printf("\n");
  635:       for(l=0;l<=1;l++) {
  636: 	for (j=1;j<=n;j++) {
  637: 	  ptt[j]=p[j]+(p[j]-pt[j])*k[l];
  638: 	  printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
  639: 	}
  640: 	printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
  641:       }
  642: #endif
  643: 
  644: 
  645:       free_vector(xit,1,n); 
  646:       free_vector(xits,1,n); 
  647:       free_vector(ptt,1,n); 
  648:       free_vector(pt,1,n); 
  649:       return; 
  650:     } 
  651:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  652:     for (j=1;j<=n;j++) { 
  653:       ptt[j]=2.0*p[j]-pt[j]; 
  654:       xit[j]=p[j]-pt[j]; 
  655:       pt[j]=p[j]; 
  656:     } 
  657:     fptt=(*func)(ptt); 
  658:     if (fptt < fp) { 
  659:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
  660:       if (t < 0.0) { 
  661: 	linmin(p,xit,n,fret,func); 
  662: 	for (j=1;j<=n;j++) { 
  663: 	  xi[j][ibig]=xi[j][n]; 
  664: 	  xi[j][n]=xit[j]; 
  665: 	}
  666: #ifdef DEBUG
  667: 	printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
  668: 	for(j=1;j<=n;j++)
  669: 	  printf(" %.12e",xit[j]);
  670: 	printf("\n");
  671: #endif
  672:       } 
  673:     } 
  674:   } 
  675: } 
  676: 
  677: /**** Prevalence limit ****************/
  678: 
  679: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  680: {
  681:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
  682:      matrix by transitions matrix until convergence is reached */
  683: 
  684:   int i, ii,j,k;
  685:   double min, max, maxmin, maxmax,sumnew=0.;
  686:   double **matprod2();
  687:   double **out, cov[NCOVMAX], **pmij();
  688:   double **newm;
  689:   double agefin, delaymax=50 ; /* Max number of years to converge */
  690: 
  691:   for (ii=1;ii<=nlstate+ndeath;ii++)
  692:     for (j=1;j<=nlstate+ndeath;j++){
  693:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  694:     }
  695: 
  696:    cov[1]=1.;
  697:  
  698:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  699:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
  700:     newm=savm;
  701:     /* Covariates have to be included here again */
  702:      cov[2]=agefin;
  703:   
  704:       for (k=1; k<=cptcovn;k++) {
  705: 	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  706: 	/*	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]]);*/
  707:       }
  708:       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  709:       for (k=1; k<=cptcovprod;k++)
  710: 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  711: 
  712:       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
  713:       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
  714:       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
  715:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
  716: 
  717:     savm=oldm;
  718:     oldm=newm;
  719:     maxmax=0.;
  720:     for(j=1;j<=nlstate;j++){
  721:       min=1.;
  722:       max=0.;
  723:       for(i=1; i<=nlstate; i++) {
  724: 	sumnew=0;
  725: 	for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
  726: 	prlim[i][j]= newm[i][j]/(1-sumnew);
  727: 	max=FMAX(max,prlim[i][j]);
  728: 	min=FMIN(min,prlim[i][j]);
  729:       }
  730:       maxmin=max-min;
  731:       maxmax=FMAX(maxmax,maxmin);
  732:     }
  733:     if(maxmax < ftolpl){
  734:       return prlim;
  735:     }
  736:   }
  737: }
  738: 
  739: /*************** transition probabilities ***************/ 
  740: 
  741: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  742: {
  743:   double s1, s2;
  744:   /*double t34;*/
  745:   int i,j,j1, nc, ii, jj;
  746: 
  747:     for(i=1; i<= nlstate; i++){
  748:     for(j=1; j<i;j++){
  749:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
  750: 	/*s2 += param[i][j][nc]*cov[nc];*/
  751: 	s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
  752: 	/*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
  753:       }
  754:       ps[i][j]=s2;
  755:       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
  756:     }
  757:     for(j=i+1; j<=nlstate+ndeath;j++){
  758:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
  759: 	s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
  760: 	/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
  761:       }
  762:       ps[i][j]=s2;
  763:     }
  764:   }
  765:     /*ps[3][2]=1;*/
  766: 
  767:   for(i=1; i<= nlstate; i++){
  768:      s1=0;
  769:     for(j=1; j<i; j++)
  770:       s1+=exp(ps[i][j]);
  771:     for(j=i+1; j<=nlstate+ndeath; j++)
  772:       s1+=exp(ps[i][j]);
  773:     ps[i][i]=1./(s1+1.);
  774:     for(j=1; j<i; j++)
  775:       ps[i][j]= exp(ps[i][j])*ps[i][i];
  776:     for(j=i+1; j<=nlstate+ndeath; j++)
  777:       ps[i][j]= exp(ps[i][j])*ps[i][i];
  778:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  779:   } /* end i */
  780: 
  781:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
  782:     for(jj=1; jj<= nlstate+ndeath; jj++){
  783:       ps[ii][jj]=0;
  784:       ps[ii][ii]=1;
  785:     }
  786:   }
  787: 
  788: 
  789:   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
  790:     for(jj=1; jj<= nlstate+ndeath; jj++){
  791:      printf("%lf ",ps[ii][jj]);
  792:    }
  793:     printf("\n ");
  794:     }
  795:     printf("\n ");printf("%lf ",cov[2]);*/
  796: /*
  797:   for(i=1; i<= npar; i++) printf("%f ",x[i]);
  798:   goto end;*/
  799:     return ps;
  800: }
  801: 
  802: /**************** Product of 2 matrices ******************/
  803: 
  804: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
  805: {
  806:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
  807:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
  808:   /* in, b, out are matrice of pointers which should have been initialized 
  809:      before: only the contents of out is modified. The function returns
  810:      a pointer to pointers identical to out */
  811:   long i, j, k;
  812:   for(i=nrl; i<= nrh; i++)
  813:     for(k=ncolol; k<=ncoloh; k++)
  814:       for(j=ncl,out[i][k]=0.; j<=nch; j++)
  815: 	out[i][k] +=in[i][j]*b[j][k];
  816: 
  817:   return out;
  818: }
  819: 
  820: 
  821: /************* Higher Matrix Product ***************/
  822: 
  823: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  824: {
  825:   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
  826:      duration (i.e. until
  827:      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
  828:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
  829:      (typically every 2 years instead of every month which is too big).
  830:      Model is determined by parameters x and covariates have to be 
  831:      included manually here. 
  832: 
  833:      */
  834: 
  835:   int i, j, d, h, k;
  836:   double **out, cov[NCOVMAX];
  837:   double **newm;
  838: 
  839:   /* Hstepm could be zero and should return the unit matrix */
  840:   for (i=1;i<=nlstate+ndeath;i++)
  841:     for (j=1;j<=nlstate+ndeath;j++){
  842:       oldm[i][j]=(i==j ? 1.0 : 0.0);
  843:       po[i][j][0]=(i==j ? 1.0 : 0.0);
  844:     }
  845:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  846:   for(h=1; h <=nhstepm; h++){
  847:     for(d=1; d <=hstepm; d++){
  848:       newm=savm;
  849:       /* Covariates have to be included here again */
  850:       cov[1]=1.;
  851:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
  852:       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  853:       for (k=1; k<=cptcovage;k++)
  854: 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  855:       for (k=1; k<=cptcovprod;k++)
  856: 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  857: 
  858: 
  859:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
  860:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
  861:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
  862: 		   pmij(pmmij,cov,ncovmodel,x,nlstate));
  863:       savm=oldm;
  864:       oldm=newm;
  865:     }
  866:     for(i=1; i<=nlstate+ndeath; i++)
  867:       for(j=1;j<=nlstate+ndeath;j++) {
  868: 	po[i][j][h]=newm[i][j];
  869: 	/*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
  870: 	 */
  871:       }
  872:   } /* end h */
  873:   return po;
  874: }
  875: 
  876: 
  877: /*************** log-likelihood *************/
  878: double func( double *x)
  879: {
  880:   int i, ii, j, k, mi, d, kk;
  881:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
  882:   double **out;
  883:   double sw; /* Sum of weights */
  884:   double lli; /* Individual log likelihood */
  885:   long ipmx;
  886:   /*extern weight */
  887:   /* We are differentiating ll according to initial status */
  888:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
  889:   /*for(i=1;i<imx;i++) 
  890:     printf(" %d\n",s[4][i]);
  891:   */
  892:   cov[1]=1.;
  893: 
  894:   for(k=1; k<=nlstate; k++) ll[k]=0.;
  895:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  896:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  897:     for(mi=1; mi<= wav[i]-1; mi++){
  898:       for (ii=1;ii<=nlstate+ndeath;ii++)
  899: 	for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  900:       for(d=0; d<dh[mi][i]; d++){
  901: 	newm=savm;
  902: 	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  903: 	for (kk=1; kk<=cptcovage;kk++) {
  904: 	  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  905: 	}
  906: 	
  907: 	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  908: 		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  909: 	savm=oldm;
  910: 	oldm=newm;
  911: 	
  912: 	
  913:       } /* end mult */
  914:       
  915:       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
  916:       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
  917:       ipmx +=1;
  918:       sw += weight[i];
  919:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  920:     } /* end of wave */
  921:   } /* end of individual */
  922: 
  923:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  924:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  925:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  926:   return -l;
  927: }
  928: 
  929: 
  930: /*********** Maximum Likelihood Estimation ***************/
  931: 
  932: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  933: {
  934:   int i,j, iter;
  935:   double **xi,*delti;
  936:   double fret;
  937:   xi=matrix(1,npar,1,npar);
  938:   for (i=1;i<=npar;i++)
  939:     for (j=1;j<=npar;j++)
  940:       xi[i][j]=(i==j ? 1.0 : 0.0);
  941:   printf("Powell\n");
  942:   powell(p,xi,npar,ftol,&iter,&fret,func);
  943: 
  944:    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
  945:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  946: 
  947: }
  948: 
  949: /**** Computes Hessian and covariance matrix ***/
  950: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  951: {
  952:   double  **a,**y,*x,pd;
  953:   double **hess;
  954:   int i, j,jk;
  955:   int *indx;
  956: 
  957:   double hessii(double p[], double delta, int theta, double delti[]);
  958:   double hessij(double p[], double delti[], int i, int j);
  959:   void lubksb(double **a, int npar, int *indx, double b[]) ;
  960:   void ludcmp(double **a, int npar, int *indx, double *d) ;
  961: 
  962:   hess=matrix(1,npar,1,npar);
  963: 
  964:   printf("\nCalculation of the hessian matrix. Wait...\n");
  965:   for (i=1;i<=npar;i++){
  966:     printf("%d",i);fflush(stdout);
  967:     hess[i][i]=hessii(p,ftolhess,i,delti);
  968:     /*printf(" %f ",p[i]);*/
  969:     /*printf(" %lf ",hess[i][i]);*/
  970:   }
  971:   
  972:   for (i=1;i<=npar;i++) {
  973:     for (j=1;j<=npar;j++)  {
  974:       if (j>i) { 
  975: 	printf(".%d%d",i,j);fflush(stdout);
  976: 	hess[i][j]=hessij(p,delti,i,j);
  977: 	hess[j][i]=hess[i][j];    
  978: 	/*printf(" %lf ",hess[i][j]);*/
  979:       }
  980:     }
  981:   }
  982:   printf("\n");
  983: 
  984:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
  985:   
  986:   a=matrix(1,npar,1,npar);
  987:   y=matrix(1,npar,1,npar);
  988:   x=vector(1,npar);
  989:   indx=ivector(1,npar);
  990:   for (i=1;i<=npar;i++)
  991:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  992:   ludcmp(a,npar,indx,&pd);
  993: 
  994:   for (j=1;j<=npar;j++) {
  995:     for (i=1;i<=npar;i++) x[i]=0;
  996:     x[j]=1;
  997:     lubksb(a,npar,indx,x);
  998:     for (i=1;i<=npar;i++){ 
  999:       matcov[i][j]=x[i];
 1000:     }
 1001:   }
 1002: 
 1003:   printf("\n#Hessian matrix#\n");
 1004:   for (i=1;i<=npar;i++) { 
 1005:     for (j=1;j<=npar;j++) { 
 1006:       printf("%.3e ",hess[i][j]);
 1007:     }
 1008:     printf("\n");
 1009:   }
 1010: 
 1011:   /* Recompute Inverse */
 1012:   for (i=1;i<=npar;i++)
 1013:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 1014:   ludcmp(a,npar,indx,&pd);
 1015: 
 1016:   /*  printf("\n#Hessian matrix recomputed#\n");
 1017: 
 1018:   for (j=1;j<=npar;j++) {
 1019:     for (i=1;i<=npar;i++) x[i]=0;
 1020:     x[j]=1;
 1021:     lubksb(a,npar,indx,x);
 1022:     for (i=1;i<=npar;i++){ 
 1023:       y[i][j]=x[i];
 1024:       printf("%.3e ",y[i][j]);
 1025:     }
 1026:     printf("\n");
 1027:   }
 1028:   */
 1029: 
 1030:   free_matrix(a,1,npar,1,npar);
 1031:   free_matrix(y,1,npar,1,npar);
 1032:   free_vector(x,1,npar);
 1033:   free_ivector(indx,1,npar);
 1034:   free_matrix(hess,1,npar,1,npar);
 1035: 
 1036: 
 1037: }
 1038: 
 1039: /*************** hessian matrix ****************/
 1040: double hessii( double x[], double delta, int theta, double delti[])
 1041: {
 1042:   int i;
 1043:   int l=1, lmax=20;
 1044:   double k1,k2;
 1045:   double p2[NPARMAX+1];
 1046:   double res;
 1047:   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 1048:   double fx;
 1049:   int k=0,kmax=10;
 1050:   double l1;
 1051: 
 1052:   fx=func(x);
 1053:   for (i=1;i<=npar;i++) p2[i]=x[i];
 1054:   for(l=0 ; l <=lmax; l++){
 1055:     l1=pow(10,l);
 1056:     delts=delt;
 1057:     for(k=1 ; k <kmax; k=k+1){
 1058:       delt = delta*(l1*k);
 1059:       p2[theta]=x[theta] +delt;
 1060:       k1=func(p2)-fx;
 1061:       p2[theta]=x[theta]-delt;
 1062:       k2=func(p2)-fx;
 1063:       /*res= (k1-2.0*fx+k2)/delt/delt; */
 1064:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 1065:       
 1066: #ifdef DEBUG
 1067:       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);
 1068: #endif
 1069:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 1070:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 1071: 	k=kmax;
 1072:       }
 1073:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 1074: 	k=kmax; l=lmax*10.;
 1075:       }
 1076:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 1077: 	delts=delt;
 1078:       }
 1079:     }
 1080:   }
 1081:   delti[theta]=delts;
 1082:   return res; 
 1083:   
 1084: }
 1085: 
 1086: double hessij( double x[], double delti[], int thetai,int thetaj)
 1087: {
 1088:   int i;
 1089:   int l=1, l1, lmax=20;
 1090:   double k1,k2,k3,k4,res,fx;
 1091:   double p2[NPARMAX+1];
 1092:   int k;
 1093: 
 1094:   fx=func(x);
 1095:   for (k=1; k<=2; k++) {
 1096:     for (i=1;i<=npar;i++) p2[i]=x[i];
 1097:     p2[thetai]=x[thetai]+delti[thetai]/k;
 1098:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 1099:     k1=func(p2)-fx;
 1100:   
 1101:     p2[thetai]=x[thetai]+delti[thetai]/k;
 1102:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 1103:     k2=func(p2)-fx;
 1104:   
 1105:     p2[thetai]=x[thetai]-delti[thetai]/k;
 1106:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 1107:     k3=func(p2)-fx;
 1108:   
 1109:     p2[thetai]=x[thetai]-delti[thetai]/k;
 1110:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 1111:     k4=func(p2)-fx;
 1112:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 1113: #ifdef DEBUG
 1114:     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);
 1115: #endif
 1116:   }
 1117:   return res;
 1118: }
 1119: 
 1120: /************** Inverse of matrix **************/
 1121: void ludcmp(double **a, int n, int *indx, double *d) 
 1122: { 
 1123:   int i,imax,j,k; 
 1124:   double big,dum,sum,temp; 
 1125:   double *vv; 
 1126:  
 1127:   vv=vector(1,n); 
 1128:   *d=1.0; 
 1129:   for (i=1;i<=n;i++) { 
 1130:     big=0.0; 
 1131:     for (j=1;j<=n;j++) 
 1132:       if ((temp=fabs(a[i][j])) > big) big=temp; 
 1133:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 1134:     vv[i]=1.0/big; 
 1135:   } 
 1136:   for (j=1;j<=n;j++) { 
 1137:     for (i=1;i<j;i++) { 
 1138:       sum=a[i][j]; 
 1139:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 1140:       a[i][j]=sum; 
 1141:     } 
 1142:     big=0.0; 
 1143:     for (i=j;i<=n;i++) { 
 1144:       sum=a[i][j]; 
 1145:       for (k=1;k<j;k++) 
 1146: 	sum -= a[i][k]*a[k][j]; 
 1147:       a[i][j]=sum; 
 1148:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
 1149: 	big=dum; 
 1150: 	imax=i; 
 1151:       } 
 1152:     } 
 1153:     if (j != imax) { 
 1154:       for (k=1;k<=n;k++) { 
 1155: 	dum=a[imax][k]; 
 1156: 	a[imax][k]=a[j][k]; 
 1157: 	a[j][k]=dum; 
 1158:       } 
 1159:       *d = -(*d); 
 1160:       vv[imax]=vv[j]; 
 1161:     } 
 1162:     indx[j]=imax; 
 1163:     if (a[j][j] == 0.0) a[j][j]=TINY; 
 1164:     if (j != n) { 
 1165:       dum=1.0/(a[j][j]); 
 1166:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 1167:     } 
 1168:   } 
 1169:   free_vector(vv,1,n);  /* Doesn't work */
 1170: ;
 1171: } 
 1172: 
 1173: void lubksb(double **a, int n, int *indx, double b[]) 
 1174: { 
 1175:   int i,ii=0,ip,j; 
 1176:   double sum; 
 1177:  
 1178:   for (i=1;i<=n;i++) { 
 1179:     ip=indx[i]; 
 1180:     sum=b[ip]; 
 1181:     b[ip]=b[i]; 
 1182:     if (ii) 
 1183:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 1184:     else if (sum) ii=i; 
 1185:     b[i]=sum; 
 1186:   } 
 1187:   for (i=n;i>=1;i--) { 
 1188:     sum=b[i]; 
 1189:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 1190:     b[i]=sum/a[i][i]; 
 1191:   } 
 1192: } 
 1193: 
 1194: /************ Frequencies ********************/
 1195: 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)
 1196: {  /* Some frequencies */
 1197:   
 1198:   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 1199:   double ***freq; /* Frequencies */
 1200:   double *pp;
 1201:   double pos, k2, dateintsum=0,k2cpt=0;
 1202:   FILE *ficresp;
 1203:   char fileresp[FILENAMELENGTH];
 1204:   
 1205:   pp=vector(1,nlstate);
 1206:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 1207:   strcpy(fileresp,"p");
 1208:   strcat(fileresp,fileres);
 1209:   if((ficresp=fopen(fileresp,"w"))==NULL) {
 1210:     printf("Problem with prevalence resultfile: %s\n", fileresp);
 1211:     exit(0);
 1212:   }
 1213:   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 1214:   j1=0;
 1215:   
 1216:   j=cptcoveff;
 1217:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 1218:   
 1219:   for(k1=1; k1<=j;k1++){
 1220:     for(i1=1; i1<=ncodemax[k1];i1++){
 1221:       j1++;
 1222:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 1223: 	scanf("%d", i);*/
 1224:       for (i=-1; i<=nlstate+ndeath; i++)  
 1225: 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 1226: 	  for(m=agemin; m <= agemax+3; m++)
 1227: 	    freq[i][jk][m]=0;
 1228:       
 1229:       dateintsum=0;
 1230:       k2cpt=0;
 1231:       for (i=1; i<=imx; i++) {
 1232: 	bool=1;
 1233: 	if  (cptcovn>0) {
 1234: 	  for (z1=1; z1<=cptcoveff; z1++) 
 1235: 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 1236: 	      bool=0;
 1237: 	}
 1238: 	if (bool==1) {
 1239: 	  for(m=firstpass; m<=lastpass; m++){
 1240: 	    k2=anint[m][i]+(mint[m][i]/12.);
 1241: 	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
 1242: 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 1243: 	      if(agev[m][i]==1) agev[m][i]=agemax+2;
 1244: 	      if (m<lastpass) {
 1245: 		freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 1246: 		freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
 1247: 	      }
 1248: 	      
 1249: 	      if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
 1250: 		dateintsum=dateintsum+k2;
 1251: 		k2cpt++;
 1252: 	      }
 1253: 	    }
 1254: 	  }
 1255: 	}
 1256:       }
 1257:        
 1258:       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 1259: 
 1260:       if  (cptcovn>0) {
 1261: 	fprintf(ficresp, "\n#********** Variable "); 
 1262: 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 1263: 	fprintf(ficresp, "**********\n#");
 1264:       }
 1265:       for(i=1; i<=nlstate;i++) 
 1266: 	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 1267:       fprintf(ficresp, "\n");
 1268:       
 1269:       for(i=(int)agemin; i <= (int)agemax+3; i++){
 1270: 	if(i==(int)agemax+3)
 1271: 	  printf("Total");
 1272: 	else
 1273: 	  printf("Age %d", i);
 1274: 	for(jk=1; jk <=nlstate ; jk++){
 1275: 	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 1276: 	    pp[jk] += freq[jk][m][i]; 
 1277: 	}
 1278: 	for(jk=1; jk <=nlstate ; jk++){
 1279: 	  for(m=-1, pos=0; m <=0 ; m++)
 1280: 	    pos += freq[jk][m][i];
 1281: 	  if(pp[jk]>=1.e-10)
 1282: 	    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 1283: 	  else
 1284: 	    printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 1285: 	}
 1286: 
 1287: 	for(jk=1; jk <=nlstate ; jk++){
 1288: 	  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 1289: 	    pp[jk] += freq[jk][m][i];
 1290: 	}
 1291: 
 1292: 	for(jk=1,pos=0; jk <=nlstate ; jk++)
 1293: 	  pos += pp[jk];
 1294: 	for(jk=1; jk <=nlstate ; jk++){
 1295: 	  if(pos>=1.e-5)
 1296: 	    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 1297: 	  else
 1298: 	    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 1299: 	  if( i <= (int) agemax){
 1300: 	    if(pos>=1.e-5){
 1301: 	      fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
 1302: 	      probs[i][jk][j1]= pp[jk]/pos;
 1303: 	      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 1304: 	    }
 1305: 	    else
 1306: 	      fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
 1307: 	  }
 1308: 	}
 1309: 	
 1310: 	for(jk=-1; jk <=nlstate+ndeath; jk++)
 1311: 	  for(m=-1; m <=nlstate+ndeath; m++)
 1312: 	    if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 1313: 	if(i <= (int) agemax)
 1314: 	  fprintf(ficresp,"\n");
 1315: 	printf("\n");
 1316:       }
 1317:     }
 1318:   }
 1319:   dateintmean=dateintsum/k2cpt; 
 1320:  
 1321:   fclose(ficresp);
 1322:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 1323:   free_vector(pp,1,nlstate);
 1324:   
 1325:   /* End of Freq */
 1326: }
 1327: 
 1328: /************ Prevalence ********************/
 1329: 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)
 1330: {  /* Some frequencies */
 1331:  
 1332:   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 1333:   double ***freq; /* Frequencies */
 1334:   double *pp;
 1335:   double pos, k2;
 1336: 
 1337:   pp=vector(1,nlstate);
 1338:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
 1339:   
 1340:   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
 1341:   j1=0;
 1342:   
 1343:   j=cptcoveff;
 1344:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 1345:   
 1346:   for(k1=1; k1<=j;k1++){
 1347:     for(i1=1; i1<=ncodemax[k1];i1++){
 1348:       j1++;
 1349:       
 1350:       for (i=-1; i<=nlstate+ndeath; i++)  
 1351: 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 1352: 	  for(m=agemin; m <= agemax+3; m++)
 1353: 	    freq[i][jk][m]=0;
 1354:      
 1355:       for (i=1; i<=imx; i++) {
 1356: 	bool=1;
 1357: 	if  (cptcovn>0) {
 1358: 	  for (z1=1; z1<=cptcoveff; z1++) 
 1359: 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 1360: 	      bool=0;
 1361: 	} 
 1362: 	if (bool==1) { 
 1363: 	  for(m=firstpass; m<=lastpass; m++){
 1364: 	    k2=anint[m][i]+(mint[m][i]/12.);
 1365: 	    if ((k2>=dateprev1) && (k2<=dateprev2)) {
 1366: 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 1367: 	      if(agev[m][i]==1) agev[m][i]=agemax+2;
 1368: 	      if (m<lastpass) {
 1369: 	      	if (calagedate>0) 
 1370: 		  freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
 1371: 		else
 1372: 		  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 1373: 		freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
 1374: 	      }
 1375: 	    }
 1376: 	  }
 1377: 	}
 1378:       }
 1379:       for(i=(int)agemin; i <= (int)agemax+3; i++){ 
 1380: 	for(jk=1; jk <=nlstate ; jk++){
 1381: 	  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 1382: 	    pp[jk] += freq[jk][m][i]; 
 1383: 	}
 1384: 	for(jk=1; jk <=nlstate ; jk++){
 1385: 	  for(m=-1, pos=0; m <=0 ; m++)
 1386: 	    pos += freq[jk][m][i];
 1387: 	}
 1388: 	
 1389: 	for(jk=1; jk <=nlstate ; jk++){
 1390: 	  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 1391: 	    pp[jk] += freq[jk][m][i];
 1392: 	}
 1393: 	
 1394: 	for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
 1395: 	
 1396: 	for(jk=1; jk <=nlstate ; jk++){	   
 1397: 	  if( i <= (int) agemax){
 1398: 	    if(pos>=1.e-5){
 1399: 	      probs[i][jk][j1]= pp[jk]/pos;
 1400: 	    }
 1401: 	  }
 1402: 	}
 1403: 	
 1404:       }
 1405:     }
 1406:   }
 1407: 
 1408:   
 1409:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
 1410:   free_vector(pp,1,nlstate);
 1411:   
 1412: }  /* End of Freq */
 1413: 
 1414: /************* Waves Concatenation ***************/
 1415: 
 1416: void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 1417: {
 1418:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 1419:      Death is a valid wave (if date is known).
 1420:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 1421:      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
 1422:      and mw[mi+1][i]. dh depends on stepm.
 1423:      */
 1424: 
 1425:   int i, mi, m;
 1426:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 1427:      double sum=0., jmean=0.;*/
 1428: 
 1429:   int j, k=0,jk, ju, jl;
 1430:   double sum=0.;
 1431:   jmin=1e+5;
 1432:   jmax=-1;
 1433:   jmean=0.;
 1434:   for(i=1; i<=imx; i++){
 1435:     mi=0;
 1436:     m=firstpass;
 1437:     while(s[m][i] <= nlstate){
 1438:       if(s[m][i]>=1)
 1439: 	mw[++mi][i]=m;
 1440:       if(m >=lastpass)
 1441: 	break;
 1442:       else
 1443: 	m++;
 1444:     }/* end while */
 1445:     if (s[m][i] > nlstate){
 1446:       mi++;	/* Death is another wave */
 1447:       /* if(mi==0)  never been interviewed correctly before death */
 1448: 	 /* Only death is a correct wave */
 1449:       mw[mi][i]=m;
 1450:     }
 1451: 
 1452:     wav[i]=mi;
 1453:     if(mi==0)
 1454:       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);
 1455:   }
 1456: 
 1457:   for(i=1; i<=imx; i++){
 1458:     for(mi=1; mi<wav[i];mi++){
 1459:       if (stepm <=0)
 1460: 	dh[mi][i]=1;
 1461:       else{
 1462: 	if (s[mw[mi+1][i]][i] > nlstate) {
 1463: 	  if (agedc[i] < 2*AGESUP) {
 1464: 	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 1465: 	  if(j==0) j=1;  /* Survives at least one month after exam */
 1466: 	  k=k+1;
 1467: 	  if (j >= jmax) jmax=j;
 1468: 	  if (j <= jmin) jmin=j;
 1469: 	  sum=sum+j;
 1470: 	  /*if (j<0) printf("j=%d num=%d \n",j,i); */
 1471: 	  }
 1472: 	}
 1473: 	else{
 1474: 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 1475: 	  k=k+1;
 1476: 	  if (j >= jmax) jmax=j;
 1477: 	  else if (j <= jmin)jmin=j;
 1478: 	  /*	    if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 1479: 	  sum=sum+j;
 1480: 	}
 1481: 	jk= j/stepm;
 1482: 	jl= j -jk*stepm;
 1483: 	ju= j -(jk+1)*stepm;
 1484: 	if(jl <= -ju)
 1485: 	  dh[mi][i]=jk;
 1486: 	else
 1487: 	  dh[mi][i]=jk+1;
 1488: 	if(dh[mi][i]==0)
 1489: 	  dh[mi][i]=1; /* At least one step */
 1490:       }
 1491:     }
 1492:   }
 1493:   jmean=sum/k;
 1494:   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 1495:  }
 1496: /*********** Tricode ****************************/
 1497: void tricode(int *Tvar, int **nbcode, int imx)
 1498: {
 1499:   int Ndum[20],ij=1, k, j, i;
 1500:   int cptcode=0;
 1501:   cptcoveff=0; 
 1502:  
 1503:   for (k=0; k<19; k++) Ndum[k]=0;
 1504:   for (k=1; k<=7; k++) ncodemax[k]=0;
 1505: 
 1506:   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 1507:     for (i=1; i<=imx; i++) {
 1508:       ij=(int)(covar[Tvar[j]][i]);
 1509:       Ndum[ij]++; 
 1510:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 1511:       if (ij > cptcode) cptcode=ij; 
 1512:     }
 1513: 
 1514:     for (i=0; i<=cptcode; i++) {
 1515:       if(Ndum[i]!=0) ncodemax[j]++;
 1516:     }
 1517:     ij=1; 
 1518: 
 1519: 
 1520:     for (i=1; i<=ncodemax[j]; i++) {
 1521:       for (k=0; k<=19; k++) {
 1522: 	if (Ndum[k] != 0) {
 1523: 	  nbcode[Tvar[j]][ij]=k; 
 1524: 	  
 1525: 	  ij++;
 1526: 	}
 1527: 	if (ij > ncodemax[j]) break; 
 1528:       }  
 1529:     } 
 1530:   }  
 1531: 
 1532:  for (k=0; k<19; k++) Ndum[k]=0;
 1533: 
 1534:  for (i=1; i<=ncovmodel-2; i++) {
 1535:       ij=Tvar[i];
 1536:       Ndum[ij]++; 
 1537:     }
 1538: 
 1539:  ij=1;
 1540:  for (i=1; i<=10; i++) {
 1541:    if((Ndum[i]!=0) && (i<=ncovcol)){
 1542:      Tvaraff[ij]=i; 
 1543:      ij++;
 1544:    }
 1545:  }
 1546:  
 1547:     cptcoveff=ij-1;
 1548: }
 1549: 
 1550: /*********** Health Expectancies ****************/
 1551: 
 1552: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
 1553: 
 1554: {
 1555:   /* Health expectancies */
 1556:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
 1557:   double age, agelim, hf;
 1558:   double ***p3mat,***varhe;
 1559:   double **dnewm,**doldm;
 1560:   double *xp;
 1561:   double **gp, **gm;
 1562:   double ***gradg, ***trgradg;
 1563:   int theta;
 1564: 
 1565:   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
 1566:   xp=vector(1,npar);
 1567:   dnewm=matrix(1,nlstate*2,1,npar);
 1568:   doldm=matrix(1,nlstate*2,1,nlstate*2);
 1569:   
 1570:   fprintf(ficreseij,"# Health expectancies\n");
 1571:   fprintf(ficreseij,"# Age");
 1572:   for(i=1; i<=nlstate;i++)
 1573:     for(j=1; j<=nlstate;j++)
 1574:       fprintf(ficreseij," %1d-%1d (SE)",i,j);
 1575:   fprintf(ficreseij,"\n");
 1576: 
 1577:   if(estepm < stepm){
 1578:     printf ("Problem %d lower than %d\n",estepm, stepm);
 1579:   }
 1580:   else  hstepm=estepm;   
 1581:   /* We compute the life expectancy from trapezoids spaced every estepm months
 1582:    * This is mainly to measure the difference between two models: for example
 1583:    * if stepm=24 months pijx are given only every 2 years and by summing them
 1584:    * we are calculating an estimate of the Life Expectancy assuming a linear 
 1585:    * progression inbetween and thus overestimating or underestimating according
 1586:    * to the curvature of the survival function. If, for the same date, we 
 1587:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
 1588:    * to compare the new estimate of Life expectancy with the same linear 
 1589:    * hypothesis. A more precise result, taking into account a more precise
 1590:    * curvature will be obtained if estepm is as small as stepm. */
 1591: 
 1592:   /* For example we decided to compute the life expectancy with the smallest unit */
 1593:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 1594:      nhstepm is the number of hstepm from age to agelim 
 1595:      nstepm is the number of stepm from age to agelin. 
 1596:      Look at hpijx to understand the reason of that which relies in memory size
 1597:      and note for a fixed period like estepm months */
 1598:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 1599:      survival function given by stepm (the optimization length). Unfortunately it
 1600:      means that if the survival funtion is printed only each two years of age and if
 1601:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 1602:      results. So we changed our mind and took the option of the best precision.
 1603:   */
 1604:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 1605: 
 1606:   agelim=AGESUP;
 1607:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1608:     /* nhstepm age range expressed in number of stepm */
 1609:     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 1610:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 1611:     /* if (stepm >= YEARM) hstepm=1;*/
 1612:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 1613:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1614:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
 1615:     gp=matrix(0,nhstepm,1,nlstate*2);
 1616:     gm=matrix(0,nhstepm,1,nlstate*2);
 1617: 
 1618:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
 1619:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 1620:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 1621:  
 1622: 
 1623:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 1624: 
 1625:     /* Computing Variances of health expectancies */
 1626: 
 1627:      for(theta=1; theta <=npar; theta++){
 1628:       for(i=1; i<=npar; i++){ 
 1629: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1630:       }
 1631:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1632:   
 1633:       cptj=0;
 1634:       for(j=1; j<= nlstate; j++){
 1635: 	for(i=1; i<=nlstate; i++){
 1636: 	  cptj=cptj+1;
 1637: 	  for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
 1638: 	    gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 1639: 	  }
 1640: 	}
 1641:       }
 1642:      
 1643:      
 1644:       for(i=1; i<=npar; i++) 
 1645: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1646:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1647:       
 1648:       cptj=0;
 1649:       for(j=1; j<= nlstate; j++){
 1650: 	for(i=1;i<=nlstate;i++){
 1651: 	  cptj=cptj+1;
 1652: 	  for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 1653: 	    gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 1654: 	  }
 1655: 	}
 1656:       }
 1657:       for(j=1; j<= nlstate*2; j++)
 1658: 	for(h=0; h<=nhstepm-1; h++){
 1659: 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 1660: 	}
 1661:      } 
 1662:    
 1663: /* End theta */
 1664: 
 1665:      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
 1666: 
 1667:      for(h=0; h<=nhstepm-1; h++)
 1668:       for(j=1; j<=nlstate*2;j++)
 1669: 	for(theta=1; theta <=npar; theta++)
 1670: 	  trgradg[h][j][theta]=gradg[h][theta][j];
 1671:      
 1672: 
 1673:      for(i=1;i<=nlstate*2;i++)
 1674:       for(j=1;j<=nlstate*2;j++)
 1675: 	varhe[i][j][(int)age] =0.;
 1676: 
 1677:      printf("%d|",(int)age);fflush(stdout);
 1678:      for(h=0;h<=nhstepm-1;h++){
 1679:       for(k=0;k<=nhstepm-1;k++){
 1680: 	matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
 1681: 	matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
 1682: 	for(i=1;i<=nlstate*2;i++)
 1683: 	  for(j=1;j<=nlstate*2;j++)
 1684: 	    varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 1685:       }
 1686:     }
 1687:     /* Computing expectancies */
 1688:     for(i=1; i<=nlstate;i++)
 1689:       for(j=1; j<=nlstate;j++)
 1690: 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 1691: 	  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 1692: 	  
 1693: /* 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]);*/
 1694: 
 1695: 	}
 1696: 
 1697:     fprintf(ficreseij,"%3.0f",age );
 1698:     cptj=0;
 1699:     for(i=1; i<=nlstate;i++)
 1700:       for(j=1; j<=nlstate;j++){
 1701: 	cptj++;
 1702: 	fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 1703:       }
 1704:     fprintf(ficreseij,"\n");
 1705:    
 1706:     free_matrix(gm,0,nhstepm,1,nlstate*2);
 1707:     free_matrix(gp,0,nhstepm,1,nlstate*2);
 1708:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
 1709:     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
 1710:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1711:   }
 1712:   printf("\n");
 1713: 
 1714:   free_vector(xp,1,npar);
 1715:   free_matrix(dnewm,1,nlstate*2,1,npar);
 1716:   free_matrix(doldm,1,nlstate*2,1,nlstate*2);
 1717:   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
 1718: }
 1719: 
 1720: /************ Variance ******************/
 1721: 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)
 1722: {
 1723:   /* Variance of health expectancies */
 1724:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 1725:   double **newm;
 1726:   double **dnewm,**doldm;
 1727:   int i, j, nhstepm, hstepm, h, nstepm ;
 1728:   int k, cptcode;
 1729:   double *xp;
 1730:   double **gp, **gm;
 1731:   double ***gradg, ***trgradg;
 1732:   double ***p3mat;
 1733:   double age,agelim, hf;
 1734:   int theta;
 1735: 
 1736:   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
 1737:   fprintf(ficresvij,"# Age");
 1738:   for(i=1; i<=nlstate;i++)
 1739:     for(j=1; j<=nlstate;j++)
 1740:       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 1741:   fprintf(ficresvij,"\n");
 1742: 
 1743:   xp=vector(1,npar);
 1744:   dnewm=matrix(1,nlstate,1,npar);
 1745:   doldm=matrix(1,nlstate,1,nlstate);
 1746:   
 1747:   if(estepm < stepm){
 1748:     printf ("Problem %d lower than %d\n",estepm, stepm);
 1749:   }
 1750:   else  hstepm=estepm;   
 1751:   /* For example we decided to compute the life expectancy with the smallest unit */
 1752:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 1753:      nhstepm is the number of hstepm from age to agelim 
 1754:      nstepm is the number of stepm from age to agelin. 
 1755:      Look at hpijx to understand the reason of that which relies in memory size
 1756:      and note for a fixed period like k years */
 1757:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 1758:      survival function given by stepm (the optimization length). Unfortunately it
 1759:      means that if the survival funtion is printed only each two years of age and if
 1760:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 1761:      results. So we changed our mind and took the option of the best precision.
 1762:   */
 1763:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 1764:   agelim = AGESUP;
 1765:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1766:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 1767:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 1768:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1769:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 1770:     gp=matrix(0,nhstepm,1,nlstate);
 1771:     gm=matrix(0,nhstepm,1,nlstate);
 1772: 
 1773:     for(theta=1; theta <=npar; theta++){
 1774:       for(i=1; i<=npar; i++){ /* Computes gradient */
 1775: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1776:       }
 1777:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1778:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1779: 
 1780:       if (popbased==1) {
 1781: 	for(i=1; i<=nlstate;i++)
 1782: 	  prlim[i][i]=probs[(int)age][i][ij];
 1783:       }
 1784:   
 1785:       for(j=1; j<= nlstate; j++){
 1786: 	for(h=0; h<=nhstepm; h++){
 1787: 	  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 1788: 	    gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 1789: 	}
 1790:       }
 1791:     
 1792:       for(i=1; i<=npar; i++) /* Computes gradient */
 1793: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1794:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 1795:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1796:  
 1797:       if (popbased==1) {
 1798: 	for(i=1; i<=nlstate;i++)
 1799: 	  prlim[i][i]=probs[(int)age][i][ij];
 1800:       }
 1801: 
 1802:       for(j=1; j<= nlstate; j++){
 1803: 	for(h=0; h<=nhstepm; h++){
 1804: 	  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 1805: 	    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 1806: 	}
 1807:       }
 1808: 
 1809:       for(j=1; j<= nlstate; j++)
 1810: 	for(h=0; h<=nhstepm; h++){
 1811: 	  gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 1812: 	}
 1813:     } /* End theta */
 1814: 
 1815:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
 1816: 
 1817:     for(h=0; h<=nhstepm; h++)
 1818:       for(j=1; j<=nlstate;j++)
 1819: 	for(theta=1; theta <=npar; theta++)
 1820: 	  trgradg[h][j][theta]=gradg[h][theta][j];
 1821: 
 1822:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 1823:     for(i=1;i<=nlstate;i++)
 1824:       for(j=1;j<=nlstate;j++)
 1825: 	vareij[i][j][(int)age] =0.;
 1826: 
 1827:     for(h=0;h<=nhstepm;h++){
 1828:       for(k=0;k<=nhstepm;k++){
 1829: 	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 1830: 	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 1831: 	for(i=1;i<=nlstate;i++)
 1832: 	  for(j=1;j<=nlstate;j++)
 1833: 	    vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 1834:       }
 1835:     }
 1836: 
 1837:     fprintf(ficresvij,"%.0f ",age );
 1838:     for(i=1; i<=nlstate;i++)
 1839:       for(j=1; j<=nlstate;j++){
 1840: 	fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 1841:       }
 1842:     fprintf(ficresvij,"\n");
 1843:     free_matrix(gp,0,nhstepm,1,nlstate);
 1844:     free_matrix(gm,0,nhstepm,1,nlstate);
 1845:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 1846:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 1847:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 1848:   } /* End age */
 1849:   
 1850:   free_vector(xp,1,npar);
 1851:   free_matrix(doldm,1,nlstate,1,npar);
 1852:   free_matrix(dnewm,1,nlstate,1,nlstate);
 1853: 
 1854: }
 1855: 
 1856: /************ Variance of prevlim ******************/
 1857: 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)
 1858: {
 1859:   /* Variance of prevalence limit */
 1860:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 1861:   double **newm;
 1862:   double **dnewm,**doldm;
 1863:   int i, j, nhstepm, hstepm;
 1864:   int k, cptcode;
 1865:   double *xp;
 1866:   double *gp, *gm;
 1867:   double **gradg, **trgradg;
 1868:   double age,agelim;
 1869:   int theta;
 1870:    
 1871:   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
 1872:   fprintf(ficresvpl,"# Age");
 1873:   for(i=1; i<=nlstate;i++)
 1874:       fprintf(ficresvpl," %1d-%1d",i,i);
 1875:   fprintf(ficresvpl,"\n");
 1876: 
 1877:   xp=vector(1,npar);
 1878:   dnewm=matrix(1,nlstate,1,npar);
 1879:   doldm=matrix(1,nlstate,1,nlstate);
 1880:   
 1881:   hstepm=1*YEARM; /* Every year of age */
 1882:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 1883:   agelim = AGESUP;
 1884:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 1885:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 1886:     if (stepm >= YEARM) hstepm=1;
 1887:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 1888:     gradg=matrix(1,npar,1,nlstate);
 1889:     gp=vector(1,nlstate);
 1890:     gm=vector(1,nlstate);
 1891: 
 1892:     for(theta=1; theta <=npar; theta++){
 1893:       for(i=1; i<=npar; i++){ /* Computes gradient */
 1894: 	xp[i] = x[i] + (i==theta ?delti[theta]:0);
 1895:       }
 1896:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1897:       for(i=1;i<=nlstate;i++)
 1898: 	gp[i] = prlim[i][i];
 1899:     
 1900:       for(i=1; i<=npar; i++) /* Computes gradient */
 1901: 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
 1902:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 1903:       for(i=1;i<=nlstate;i++)
 1904: 	gm[i] = prlim[i][i];
 1905: 
 1906:       for(i=1;i<=nlstate;i++)
 1907: 	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 1908:     } /* End theta */
 1909: 
 1910:     trgradg =matrix(1,nlstate,1,npar);
 1911: 
 1912:     for(j=1; j<=nlstate;j++)
 1913:       for(theta=1; theta <=npar; theta++)
 1914: 	trgradg[j][theta]=gradg[theta][j];
 1915: 
 1916:     for(i=1;i<=nlstate;i++)
 1917:       varpl[i][(int)age] =0.;
 1918:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 1919:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 1920:     for(i=1;i<=nlstate;i++)
 1921:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 1922: 
 1923:     fprintf(ficresvpl,"%.0f ",age );
 1924:     for(i=1; i<=nlstate;i++)
 1925:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 1926:     fprintf(ficresvpl,"\n");
 1927:     free_vector(gp,1,nlstate);
 1928:     free_vector(gm,1,nlstate);
 1929:     free_matrix(gradg,1,npar,1,nlstate);
 1930:     free_matrix(trgradg,1,nlstate,1,npar);
 1931:   } /* End age */
 1932: 
 1933:   free_vector(xp,1,npar);
 1934:   free_matrix(doldm,1,nlstate,1,npar);
 1935:   free_matrix(dnewm,1,nlstate,1,nlstate);
 1936: 
 1937: }
 1938: 
 1939: /************ Variance of one-step probabilities  ******************/
 1940: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 1941: {
 1942:   int i, j,  i1, k1, l1;
 1943:   int k2, l2, j1,  z1;
 1944:   int k=0,l, cptcode;
 1945:   int first=1;
 1946:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
 1947:   double **dnewm,**doldm;
 1948:   double *xp;
 1949:   double *gp, *gm;
 1950:   double **gradg, **trgradg;
 1951:   double **mu;
 1952:   double age,agelim, cov[NCOVMAX];
 1953:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 1954:   int theta;
 1955:   char fileresprob[FILENAMELENGTH];
 1956:   char fileresprobcov[FILENAMELENGTH];
 1957:   char fileresprobcor[FILENAMELENGTH];
 1958: 
 1959:   double ***varpij;
 1960: 
 1961:   strcpy(fileresprob,"prob"); 
 1962:   strcat(fileresprob,fileres);
 1963:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 1964:     printf("Problem with resultfile: %s\n", fileresprob);
 1965:   }
 1966:   strcpy(fileresprobcov,"probcov"); 
 1967:   strcat(fileresprobcov,fileres);
 1968:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 1969:     printf("Problem with resultfile: %s\n", fileresprobcov);
 1970:   }
 1971:   strcpy(fileresprobcor,"probcor"); 
 1972:   strcat(fileresprobcor,fileres);
 1973:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 1974:     printf("Problem with resultfile: %s\n", fileresprobcor);
 1975:   }
 1976:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 1977:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 1978:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 1979:   
 1980:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 1981:   fprintf(ficresprob,"# Age");
 1982:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 1983:   fprintf(ficresprobcov,"# Age");
 1984:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 1985:   fprintf(ficresprobcov,"# Age");
 1986: 
 1987: 
 1988:   for(i=1; i<=nlstate;i++)
 1989:     for(j=1; j<=(nlstate+ndeath);j++){
 1990:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 1991:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
 1992:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
 1993:     }  
 1994:   fprintf(ficresprob,"\n");
 1995:   fprintf(ficresprobcov,"\n");
 1996:   fprintf(ficresprobcor,"\n");
 1997:   xp=vector(1,npar);
 1998:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 1999:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 2000:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
 2001:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
 2002:   first=1;
 2003:   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 2004:     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
 2005:     exit(0);
 2006:   }
 2007:   else{
 2008:     fprintf(ficgp,"\n# Routine varprob");
 2009:   }
 2010:   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
 2011:     printf("Problem with html file: %s\n", optionfilehtm);
 2012:     exit(0);
 2013:   }
 2014:   else{
 2015:     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
 2016:     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 2017:     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 2018: 
 2019:   }
 2020:   cov[1]=1;
 2021:   j=cptcoveff;
 2022:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 2023:   j1=0;
 2024:   for(k1=1; k1<=1;k1++){
 2025:     for(i1=1; i1<=ncodemax[k1];i1++){ 
 2026:     j1++;
 2027: 
 2028:     if  (cptcovn>0) {
 2029:       fprintf(ficresprob, "\n#********** Variable "); 
 2030:       fprintf(ficresprobcov, "\n#********** Variable "); 
 2031:       fprintf(ficgp, "\n#********** Variable "); 
 2032:       fprintf(fichtm, "\n<h4>********** Variable</h4>\n "); 
 2033:       fprintf(ficresprobcor, "\n#********** Variable "); 
 2034:       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2035:       fprintf(ficresprob, "**********\n#");
 2036:       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2037:       fprintf(ficresprobcov, "**********\n#");
 2038:       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2039:       fprintf(ficgp, "**********\n#");
 2040:       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2041:       fprintf(ficgp, "**********\n#");
 2042:       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 2043:       fprintf(fichtm, "**********\n#");
 2044:     }
 2045:     
 2046:       for (age=bage; age<=fage; age ++){ 
 2047: 	cov[2]=age;
 2048: 	for (k=1; k<=cptcovn;k++) {
 2049: 	  cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
 2050: 	}
 2051: 	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 2052: 	for (k=1; k<=cptcovprod;k++)
 2053: 	  cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 2054: 	
 2055: 	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 2056: 	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
 2057: 	gp=vector(1,(nlstate)*(nlstate+ndeath));
 2058: 	gm=vector(1,(nlstate)*(nlstate+ndeath));
 2059:     
 2060: 	for(theta=1; theta <=npar; theta++){
 2061: 	  for(i=1; i<=npar; i++)
 2062: 	    xp[i] = x[i] + (i==theta ?delti[theta]:0);
 2063: 	  
 2064: 	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
 2065: 	  
 2066: 	  k=0;
 2067: 	  for(i=1; i<= (nlstate); i++){
 2068: 	    for(j=1; j<=(nlstate+ndeath);j++){
 2069: 	      k=k+1;
 2070: 	      gp[k]=pmmij[i][j];
 2071: 	    }
 2072: 	  }
 2073: 	  
 2074: 	  for(i=1; i<=npar; i++)
 2075: 	    xp[i] = x[i] - (i==theta ?delti[theta]:0);
 2076:     
 2077: 	  pmij(pmmij,cov,ncovmodel,xp,nlstate);
 2078: 	  k=0;
 2079: 	  for(i=1; i<=(nlstate); i++){
 2080: 	    for(j=1; j<=(nlstate+ndeath);j++){
 2081: 	      k=k+1;
 2082: 	      gm[k]=pmmij[i][j];
 2083: 	    }
 2084: 	  }
 2085:      
 2086: 	  for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 2087: 	    gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
 2088: 	}
 2089: 
 2090: 	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
 2091: 	  for(theta=1; theta <=npar; theta++)
 2092: 	    trgradg[j][theta]=gradg[theta][j];
 2093: 	
 2094: 	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 2095: 	matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
 2096: 	
 2097: 	pmij(pmmij,cov,ncovmodel,x,nlstate);
 2098: 	
 2099: 	k=0;
 2100: 	for(i=1; i<=(nlstate); i++){
 2101: 	  for(j=1; j<=(nlstate+ndeath);j++){
 2102: 	    k=k+1;
 2103: 	    mu[k][(int) age]=pmmij[i][j];
 2104: 	  }
 2105: 	}
 2106:      	for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 2107: 	  for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
 2108: 	    varpij[i][j][(int)age] = doldm[i][j];
 2109: 
 2110: 	/*printf("\n%d ",(int)age);
 2111:      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 2112:        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 2113:      }*/
 2114: 
 2115: 	fprintf(ficresprob,"\n%d ",(int)age);
 2116: 	fprintf(ficresprobcov,"\n%d ",(int)age);
 2117: 	fprintf(ficresprobcor,"\n%d ",(int)age);
 2118: 
 2119: 	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
 2120: 	  fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
 2121: 	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 2122: 	  fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
 2123: 	  fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 2124: 	}
 2125: 	i=0;
 2126: 	for (k=1; k<=(nlstate);k++){
 2127:  	  for (l=1; l<=(nlstate+ndeath);l++){ 
 2128:  	    i=i++;
 2129: 	    fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
 2130: 	    fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
 2131: 	    for (j=1; j<=i;j++){
 2132: 	      fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
 2133: 	      fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
 2134: 	    }
 2135: 	  }
 2136: 	}/* end of loop for state */
 2137:       } /* end of loop for age */
 2138: 	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
 2139:       for (k1=1; k1<=(nlstate);k1++){
 2140: 	for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 2141: 	  if(l1==k1) continue;
 2142: 	  i=(k1-1)*(nlstate+ndeath)+l1;
 2143: 	  for (k2=1; k2<=(nlstate);k2++){
 2144: 	    for (l2=1; l2<=(nlstate+ndeath);l2++){ 
 2145: 	      if(l2==k2) continue;
 2146: 	      j=(k2-1)*(nlstate+ndeath)+l2;
 2147: 	      if(j<=i) continue;
 2148: 	      for (age=bage; age<=fage; age ++){ 
 2149: 		if ((int)age %5==0){
 2150: 		  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
 2151: 		  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
 2152: 		  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
 2153: 		  mu1=mu[i][(int) age]/stepm*YEARM ;
 2154: 		  mu2=mu[j][(int) age]/stepm*YEARM;
 2155: 		  /* Computing eigen value of matrix of covariance */
 2156: 		  lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
 2157: 		  lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));
 2158: 		  printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
 2159: 		  /* Eigen vectors */
 2160: 		  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 2161: 		  v21=sqrt(1.-v11*v11);
 2162: 		  v12=-v21;
 2163: 		  v22=v11;
 2164: 		  /*printf(fignu*/
 2165: 		  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
 2166: 		  /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */
 2167: 		  if(first==1){
 2168: 		    first=0;
 2169: 		    fprintf(ficgp,"\nset parametric;set nolabel");
 2170: 		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
 2171: 		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
 2172: 		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
 2173: 		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
 2174: 		    fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
 2175: 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
 2176: 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
 2177: 		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
 2178: 			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
 2179: 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
 2180: 		  }else{
 2181: 		    first=0;
 2182: 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
 2183: 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
 2184: 		    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
 2185: 			    mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
 2186: 			    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
 2187: 		  }/* if first */
 2188: 		} /* age mod 5 */
 2189: 	      } /* end loop age */
 2190: 	      fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
 2191: 	      first=1;
 2192: 	    } /*l12 */
 2193: 	  } /* k12 */
 2194: 	} /*l1 */
 2195:       }/* k1 */
 2196:     } /* loop covariates */
 2197:     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
 2198:     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
 2199:     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 2200:     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 2201:     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 2202:     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 2203:   }
 2204:   free_vector(xp,1,npar);
 2205:   fclose(ficresprob);
 2206:   fclose(ficresprobcov);
 2207:   fclose(ficresprobcor);
 2208:   fclose(ficgp);
 2209:   fclose(fichtm);
 2210: }
 2211: 
 2212: 
 2213: /******************* Printing html file ***********/
 2214: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 2215: 		  int lastpass, int stepm, int weightopt, char model[],\
 2216: 		  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
 2217: 		  int popforecast, int estepm ,\
 2218: 		  double jprev1, double mprev1,double anprev1, \
 2219: 		  double jprev2, double mprev2,double anprev2){
 2220:   int jj1, k1, i1, cpt;
 2221:   /*char optionfilehtm[FILENAMELENGTH];*/
 2222:   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
 2223:     printf("Problem with %s \n",optionfilehtm), exit(0);
 2224:   }
 2225: 
 2226:    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
 2227:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
 2228:  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
 2229:  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
 2230:  - Life expectancies by age and initial health status (estepm=%2d months): 
 2231:    <a href=\"e%s\">e%s</a> <br>\n</li>", \
 2232:   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
 2233: 
 2234:  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
 2235:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
 2236:  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
 2237:  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
 2238:  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
 2239:  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
 2240:  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
 2241:  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
 2242: 
 2243:  if(popforecast==1) fprintf(fichtm,"\n
 2244:  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
 2245:  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
 2246: 	<br>",fileres,fileres,fileres,fileres);
 2247:  else 
 2248:    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);
 2249: fprintf(fichtm," <li>Graphs</li><p>");
 2250: 
 2251:  m=cptcoveff;
 2252:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 2253: 
 2254:  jj1=0;
 2255:  for(k1=1; k1<=m;k1++){
 2256:    for(i1=1; i1<=ncodemax[k1];i1++){
 2257:      jj1++;
 2258:      if (cptcovn > 0) {
 2259:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 2260:        for (cpt=1; cpt<=cptcoveff;cpt++) 
 2261: 	 fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
 2262:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 2263:      }
 2264:      /* Pij */
 2265:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
 2266: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
 2267:      /* Quasi-incidences */
 2268:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
 2269: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
 2270:        /* Stable prevalence in each health state */
 2271:        for(cpt=1; cpt<nlstate;cpt++){
 2272: 	 fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
 2273: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
 2274:        }
 2275:     for(cpt=1; cpt<=nlstate;cpt++) {
 2276:        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
 2277: interval) in state (%d): v%s%d%d.png <br>
 2278: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
 2279:      }
 2280:      for(cpt=1; cpt<=nlstate;cpt++) {
 2281:         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
 2282: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
 2283:      }
 2284:      fprintf(fichtm,"\n<br>- Total life expectancy by age and
 2285: health expectancies in states (1) and (2): e%s%d.png<br>
 2286: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
 2287:    }
 2288:  }
 2289: fclose(fichtm);
 2290: }
 2291: 
 2292: /******************* Gnuplot file **************/
 2293: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 2294: 
 2295:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
 2296:   int ng;
 2297:   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
 2298:     printf("Problem with file %s",optionfilegnuplot);
 2299:   }
 2300: 
 2301: #ifdef windows
 2302:     fprintf(ficgp,"cd \"%s\" \n",pathc);
 2303: #endif
 2304: m=pow(2,cptcoveff);
 2305:   
 2306:  /* 1eme*/
 2307:   for (cpt=1; cpt<= nlstate ; cpt ++) {
 2308:    for (k1=1; k1<= m ; k1 ++) {
 2309: 
 2310: #ifdef windows
 2311:      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 2312:      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 2313: #endif
 2314: #ifdef unix
 2315: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 2316: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
 2317: #endif
 2318: 
 2319: for (i=1; i<= nlstate ; i ++) {
 2320:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2321:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2322: }
 2323:     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
 2324:     for (i=1; i<= nlstate ; i ++) {
 2325:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2326:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2327: } 
 2328:   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
 2329:      for (i=1; i<= nlstate ; i ++) {
 2330:   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 2331:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2332: }  
 2333:      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
 2334: #ifdef unix
 2335: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
 2336: #endif
 2337:    }
 2338:   }
 2339:   /*2 eme*/
 2340: 
 2341:   for (k1=1; k1<= m ; k1 ++) { 
 2342:     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
 2343:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
 2344:     
 2345:     for (i=1; i<= nlstate+1 ; i ++) {
 2346:       k=2*i;
 2347:       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
 2348:       for (j=1; j<= nlstate+1 ; j ++) {
 2349:   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2350:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2351: }   
 2352:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
 2353:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
 2354:     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
 2355:       for (j=1; j<= nlstate+1 ; j ++) {
 2356: 	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2357: 	else fprintf(ficgp," \%%*lf (\%%*lf)");
 2358: }   
 2359:       fprintf(ficgp,"\" t\"\" w l 0,");
 2360:      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
 2361:       for (j=1; j<= nlstate+1 ; j ++) {
 2362:   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 2363:   else fprintf(ficgp," \%%*lf (\%%*lf)");
 2364: }   
 2365:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
 2366:       else fprintf(ficgp,"\" t\"\" w l 0,");
 2367:     }
 2368:   }
 2369:  
 2370:   /*3eme*/
 2371: 
 2372:   for (k1=1; k1<= m ; k1 ++) { 
 2373:     for (cpt=1; cpt<= nlstate ; cpt ++) {
 2374:       k=2+nlstate*(2*cpt-2);
 2375:       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 2376:       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
 2377:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 2378:  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 2379: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 2380: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
 2381:  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
 2382: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
 2383: 
 2384: */
 2385:       for (i=1; i< nlstate ; i ++) {
 2386: 	fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
 2387: 
 2388:       } 
 2389:     }
 2390:   }
 2391:  
 2392:   /* CV preval stat */
 2393:     for (k1=1; k1<= m ; k1 ++) { 
 2394:     for (cpt=1; cpt<nlstate ; cpt ++) {
 2395:       k=3;
 2396:       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
 2397:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
 2398: 
 2399:       for (i=1; i< nlstate ; i ++)
 2400: 	fprintf(ficgp,"+$%d",k+i+1);
 2401:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
 2402:       
 2403:       l=3+(nlstate+ndeath)*cpt;
 2404:       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
 2405:       for (i=1; i< nlstate ; i ++) {
 2406: 	l=3+(nlstate+ndeath)*cpt;
 2407: 	fprintf(ficgp,"+$%d",l+i+1);
 2408:       }
 2409:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
 2410:     } 
 2411:   }  
 2412:   
 2413:   /* proba elementaires */
 2414:    for(i=1,jk=1; i <=nlstate; i++){
 2415:     for(k=1; k <=(nlstate+ndeath); k++){
 2416:       if (k != i) {
 2417: 	for(j=1; j <=ncovmodel; j++){
 2418: 	
 2419: 	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
 2420: 	  jk++; 
 2421: 	  fprintf(ficgp,"\n");
 2422: 	}
 2423:       }
 2424:     }
 2425:    }
 2426: 
 2427:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
 2428:      for(jk=1; jk <=m; jk++) {
 2429:        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
 2430:        if (ng==2)
 2431: 	 fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
 2432:        else
 2433: 	 fprintf(ficgp,"\nset title \"Probability\"\n");
 2434:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
 2435:        i=1;
 2436:        for(k2=1; k2<=nlstate; k2++) {
 2437: 	 k3=i;
 2438: 	 for(k=1; k<=(nlstate+ndeath); k++) {
 2439: 	   if (k != k2){
 2440: 	     if(ng==2)
 2441: 	       fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 2442: 	     else
 2443: 	       fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
 2444: 	     ij=1;
 2445: 	     for(j=3; j <=ncovmodel; j++) {
 2446: 	       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 2447: 		 fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 2448: 		 ij++;
 2449: 	       }
 2450: 	       else
 2451: 		 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 2452: 	     }
 2453: 	     fprintf(ficgp,")/(1");
 2454: 	     
 2455: 	     for(k1=1; k1 <=nlstate; k1++){   
 2456: 	       fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 2457: 	       ij=1;
 2458: 	       for(j=3; j <=ncovmodel; j++){
 2459: 		 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 2460: 		   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 2461: 		   ij++;
 2462: 		 }
 2463: 		 else
 2464: 		   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 2465: 	       }
 2466: 	       fprintf(ficgp,")");
 2467: 	     }
 2468: 	     fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 2469: 	     if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 2470: 	     i=i+ncovmodel;
 2471: 	   }
 2472: 	 }
 2473:        }
 2474:      }
 2475:    }
 2476:    fclose(ficgp); 
 2477: }  /* end gnuplot */
 2478: 
 2479: 
 2480: /*************** Moving average **************/
 2481: void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
 2482: 
 2483:   int i, cpt, cptcod;
 2484:     for (agedeb=ageminpar; agedeb<=fage; agedeb++)
 2485:       for (i=1; i<=nlstate;i++)
 2486: 	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
 2487: 	  mobaverage[(int)agedeb][i][cptcod]=0.;
 2488:     
 2489:     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
 2490:       for (i=1; i<=nlstate;i++){
 2491: 	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2492: 	  for (cpt=0;cpt<=4;cpt++){
 2493: 	    mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
 2494: 	  }
 2495: 	  mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
 2496: 	}
 2497:       }
 2498:     }
 2499:     
 2500: }
 2501: 
 2502: 
 2503: /************** Forecasting ******************/
 2504: 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){
 2505:   
 2506:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 2507:   int *popage;
 2508:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 2509:   double *popeffectif,*popcount;
 2510:   double ***p3mat;
 2511:   char fileresf[FILENAMELENGTH];
 2512: 
 2513:  agelim=AGESUP;
 2514: calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
 2515: 
 2516:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 2517:  
 2518:  
 2519:   strcpy(fileresf,"f"); 
 2520:   strcat(fileresf,fileres);
 2521:   if((ficresf=fopen(fileresf,"w"))==NULL) {
 2522:     printf("Problem with forecast resultfile: %s\n", fileresf);
 2523:   }
 2524:   printf("Computing forecasting: result on file '%s' \n", fileresf);
 2525: 
 2526:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 2527: 
 2528:   if (mobilav==1) {
 2529:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2530:     movingaverage(agedeb, fage, ageminpar, mobaverage);
 2531:   }
 2532: 
 2533:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 2534:   if (stepm<=12) stepsize=1;
 2535:   
 2536:   agelim=AGESUP;
 2537:   
 2538:   hstepm=1;
 2539:   hstepm=hstepm/stepm; 
 2540:   yp1=modf(dateintmean,&yp);
 2541:   anprojmean=yp;
 2542:   yp2=modf((yp1*12),&yp);
 2543:   mprojmean=yp;
 2544:   yp1=modf((yp2*30.5),&yp);
 2545:   jprojmean=yp;
 2546:   if(jprojmean==0) jprojmean=1;
 2547:   if(mprojmean==0) jprojmean=1;
 2548:   
 2549:   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
 2550:   
 2551:   for(cptcov=1;cptcov<=i2;cptcov++){
 2552:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2553:       k=k+1;
 2554:       fprintf(ficresf,"\n#******");
 2555:       for(j=1;j<=cptcoveff;j++) {
 2556: 	fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 2557:       }
 2558:       fprintf(ficresf,"******\n");
 2559:       fprintf(ficresf,"# StartingAge FinalAge");
 2560:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
 2561:       
 2562:       
 2563:       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
 2564: 	fprintf(ficresf,"\n");
 2565: 	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
 2566: 
 2567:      	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2568: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2569: 	  nhstepm = nhstepm/hstepm; 
 2570: 	  
 2571: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2572: 	  oldm=oldms;savm=savms;
 2573: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2574: 	
 2575: 	  for (h=0; h<=nhstepm; h++){
 2576: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2577: 	      fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
 2578: 	    } 
 2579: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2580: 	      kk1=0.;kk2=0;
 2581: 	      for(i=1; i<=nlstate;i++) {	      
 2582: 		if (mobilav==1) 
 2583: 		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 2584: 		else {
 2585: 		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 2586: 		}
 2587: 		
 2588: 	      }
 2589: 	      if (h==(int)(calagedate+12*cpt)){
 2590: 		fprintf(ficresf," %.3f", kk1);
 2591: 	     		
 2592: 	      }
 2593: 	    }
 2594: 	  }
 2595: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2596: 	}
 2597:       }
 2598:     }
 2599:   }
 2600:        
 2601:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2602: 
 2603:   fclose(ficresf);
 2604: }
 2605: /************** Forecasting ******************/
 2606: 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){
 2607:   
 2608:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
 2609:   int *popage;
 2610:   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 2611:   double *popeffectif,*popcount;
 2612:   double ***p3mat,***tabpop,***tabpopprev;
 2613:   char filerespop[FILENAMELENGTH];
 2614: 
 2615:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2616:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2617:   agelim=AGESUP;
 2618:   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
 2619:   
 2620:   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 2621:   
 2622:   
 2623:   strcpy(filerespop,"pop"); 
 2624:   strcat(filerespop,fileres);
 2625:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
 2626:     printf("Problem with forecast resultfile: %s\n", filerespop);
 2627:   }
 2628:   printf("Computing forecasting: result on file '%s' \n", filerespop);
 2629: 
 2630:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
 2631: 
 2632:   if (mobilav==1) {
 2633:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2634:     movingaverage(agedeb, fage, ageminpar, mobaverage);
 2635:   }
 2636: 
 2637:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 2638:   if (stepm<=12) stepsize=1;
 2639:   
 2640:   agelim=AGESUP;
 2641:   
 2642:   hstepm=1;
 2643:   hstepm=hstepm/stepm; 
 2644:   
 2645:   if (popforecast==1) {
 2646:     if((ficpop=fopen(popfile,"r"))==NULL) {
 2647:       printf("Problem with population file : %s\n",popfile);exit(0);
 2648:     } 
 2649:     popage=ivector(0,AGESUP);
 2650:     popeffectif=vector(0,AGESUP);
 2651:     popcount=vector(0,AGESUP);
 2652:     
 2653:     i=1;   
 2654:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
 2655:    
 2656:     imx=i;
 2657:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
 2658:   }
 2659: 
 2660:   for(cptcov=1;cptcov<=i2;cptcov++){
 2661:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
 2662:       k=k+1;
 2663:       fprintf(ficrespop,"\n#******");
 2664:       for(j=1;j<=cptcoveff;j++) {
 2665: 	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 2666:       }
 2667:       fprintf(ficrespop,"******\n");
 2668:       fprintf(ficrespop,"# Age");
 2669:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
 2670:       if (popforecast==1)  fprintf(ficrespop," [Population]");
 2671:       
 2672:       for (cpt=0; cpt<=0;cpt++) { 
 2673: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 2674: 	
 2675:      	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2676: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2677: 	  nhstepm = nhstepm/hstepm; 
 2678: 	  
 2679: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2680: 	  oldm=oldms;savm=savms;
 2681: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2682: 	
 2683: 	  for (h=0; h<=nhstepm; h++){
 2684: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2685: 	      fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 2686: 	    } 
 2687: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2688: 	      kk1=0.;kk2=0;
 2689: 	      for(i=1; i<=nlstate;i++) {	      
 2690: 		if (mobilav==1) 
 2691: 		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
 2692: 		else {
 2693: 		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 2694: 		}
 2695: 	      }
 2696: 	      if (h==(int)(calagedate+12*cpt)){
 2697: 		tabpop[(int)(agedeb)][j][cptcod]=kk1;
 2698: 		  /*fprintf(ficrespop," %.3f", kk1);
 2699: 		    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
 2700: 	      }
 2701: 	    }
 2702: 	    for(i=1; i<=nlstate;i++){
 2703: 	      kk1=0.;
 2704: 		for(j=1; j<=nlstate;j++){
 2705: 		  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
 2706: 		}
 2707: 		  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
 2708: 	    }
 2709: 
 2710: 	    if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
 2711: 	      fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
 2712: 	  }
 2713: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2714: 	}
 2715:       }
 2716:  
 2717:   /******/
 2718: 
 2719:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
 2720: 	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 2721: 	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ 
 2722: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
 2723: 	  nhstepm = nhstepm/hstepm; 
 2724: 	  
 2725: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2726: 	  oldm=oldms;savm=savms;
 2727: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 2728: 	  for (h=0; h<=nhstepm; h++){
 2729: 	    if (h==(int) (calagedate+YEARM*cpt)) {
 2730: 	      fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
 2731: 	    } 
 2732: 	    for(j=1; j<=nlstate+ndeath;j++) {
 2733: 	      kk1=0.;kk2=0;
 2734: 	      for(i=1; i<=nlstate;i++) {	      
 2735: 		kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	
 2736: 	      }
 2737: 	      if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	
 2738: 	    }
 2739: 	  }
 2740: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 2741: 	}
 2742:       }
 2743:    } 
 2744:   }
 2745:  
 2746:   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2747: 
 2748:   if (popforecast==1) {
 2749:     free_ivector(popage,0,AGESUP);
 2750:     free_vector(popeffectif,0,AGESUP);
 2751:     free_vector(popcount,0,AGESUP);
 2752:   }
 2753:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2754:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 2755:   fclose(ficrespop);
 2756: }
 2757: 
 2758: /***********************************************/
 2759: /**************** Main Program *****************/
 2760: /***********************************************/
 2761: 
 2762: int main(int argc, char *argv[])
 2763: {
 2764: 
 2765:   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
 2766:   double agedeb, agefin,hf;
 2767:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
 2768: 
 2769:   double fret;
 2770:   double **xi,tmp,delta;
 2771: 
 2772:   double dum; /* Dummy variable */
 2773:   double ***p3mat;
 2774:   int *indx;
 2775:   char line[MAXLINE], linepar[MAXLINE];
 2776:   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
 2777:   int firstobs=1, lastobs=10;
 2778:   int sdeb, sfin; /* Status at beginning and end */
 2779:   int c,  h , cpt,l;
 2780:   int ju,jl, mi;
 2781:   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
 2782:   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
 2783:   int mobilav=0,popforecast=0;
 2784:   int hstepm, nhstepm;
 2785:   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
 2786: 
 2787:   double bage, fage, age, agelim, agebase;
 2788:   double ftolpl=FTOL;
 2789:   double **prlim;
 2790:   double *severity;
 2791:   double ***param; /* Matrix of parameters */
 2792:   double  *p;
 2793:   double **matcov; /* Matrix of covariance */
 2794:   double ***delti3; /* Scale */
 2795:   double *delti; /* Scale */
 2796:   double ***eij, ***vareij;
 2797:   double **varpl; /* Variances of prevalence limits by age */
 2798:   double *epj, vepp;
 2799:   double kk1, kk2;
 2800:   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
 2801:   
 2802: 
 2803:   char *alph[]={"a","a","b","c","d","e"}, str[4];
 2804: 
 2805: 
 2806:   char z[1]="c", occ;
 2807: #include <sys/time.h>
 2808: #include <time.h>
 2809:   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
 2810:  
 2811:   /* long total_usecs;
 2812:   struct timeval start_time, end_time;
 2813:   
 2814:   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
 2815:   getcwd(pathcd, size);
 2816: 
 2817:   printf("\n%s",version);
 2818:   if(argc <=1){
 2819:     printf("\nEnter the parameter file name: ");
 2820:     scanf("%s",pathtot);
 2821:   }
 2822:   else{
 2823:     strcpy(pathtot,argv[1]);
 2824:   }
 2825:   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
 2826:   /*cygwin_split_path(pathtot,path,optionfile);
 2827:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
 2828:   /* cutv(path,optionfile,pathtot,'\\');*/
 2829: 
 2830:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
 2831:    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
 2832:   chdir(path);
 2833:   replace(pathc,path);
 2834: 
 2835: /*-------- arguments in the command line --------*/
 2836: 
 2837:   strcpy(fileres,"r");
 2838:   strcat(fileres, optionfilefiname);
 2839:   strcat(fileres,".txt");    /* Other files have txt extension */
 2840: 
 2841:   /*---------arguments file --------*/
 2842: 
 2843:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
 2844:     printf("Problem with optionfile %s\n",optionfile);
 2845:     goto end;
 2846:   }
 2847: 
 2848:   strcpy(filereso,"o");
 2849:   strcat(filereso,fileres);
 2850:   if((ficparo=fopen(filereso,"w"))==NULL) {
 2851:     printf("Problem with Output resultfile: %s\n", filereso);goto end;
 2852:   }
 2853: 
 2854:   /* Reads comments: lines beginning with '#' */
 2855:   while((c=getc(ficpar))=='#' && c!= EOF){
 2856:     ungetc(c,ficpar);
 2857:     fgets(line, MAXLINE, ficpar);
 2858:     puts(line);
 2859:     fputs(line,ficparo);
 2860:   }
 2861:   ungetc(c,ficpar);
 2862: 
 2863:   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);
 2864:   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);
 2865:   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);
 2866: while((c=getc(ficpar))=='#' && c!= EOF){
 2867:     ungetc(c,ficpar);
 2868:     fgets(line, MAXLINE, ficpar);
 2869:     puts(line);
 2870:     fputs(line,ficparo);
 2871:   }
 2872:   ungetc(c,ficpar);
 2873:   
 2874:    
 2875:   covar=matrix(0,NCOVMAX,1,n); 
 2876:   cptcovn=0; 
 2877:   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
 2878: 
 2879:   ncovmodel=2+cptcovn;
 2880:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
 2881:   
 2882:   /* Read guess parameters */
 2883:   /* Reads comments: lines beginning with '#' */
 2884:   while((c=getc(ficpar))=='#' && c!= EOF){
 2885:     ungetc(c,ficpar);
 2886:     fgets(line, MAXLINE, ficpar);
 2887:     puts(line);
 2888:     fputs(line,ficparo);
 2889:   }
 2890:   ungetc(c,ficpar);
 2891:   
 2892:   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 2893:     for(i=1; i <=nlstate; i++)
 2894:     for(j=1; j <=nlstate+ndeath-1; j++){
 2895:       fscanf(ficpar,"%1d%1d",&i1,&j1);
 2896:       fprintf(ficparo,"%1d%1d",i1,j1);
 2897:       printf("%1d%1d",i,j);
 2898:       for(k=1; k<=ncovmodel;k++){
 2899: 	fscanf(ficpar," %lf",&param[i][j][k]);
 2900: 	printf(" %lf",param[i][j][k]);
 2901: 	fprintf(ficparo," %lf",param[i][j][k]);
 2902:       }
 2903:       fscanf(ficpar,"\n");
 2904:       printf("\n");
 2905:       fprintf(ficparo,"\n");
 2906:     }
 2907:   
 2908:     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
 2909: 
 2910:   p=param[1][1];
 2911:   
 2912:   /* Reads comments: lines beginning with '#' */
 2913:   while((c=getc(ficpar))=='#' && c!= EOF){
 2914:     ungetc(c,ficpar);
 2915:     fgets(line, MAXLINE, ficpar);
 2916:     puts(line);
 2917:     fputs(line,ficparo);
 2918:   }
 2919:   ungetc(c,ficpar);
 2920: 
 2921:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
 2922:   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
 2923:   for(i=1; i <=nlstate; i++){
 2924:     for(j=1; j <=nlstate+ndeath-1; j++){
 2925:       fscanf(ficpar,"%1d%1d",&i1,&j1);
 2926:       printf("%1d%1d",i,j);
 2927:       fprintf(ficparo,"%1d%1d",i1,j1);
 2928:       for(k=1; k<=ncovmodel;k++){
 2929: 	fscanf(ficpar,"%le",&delti3[i][j][k]);
 2930: 	printf(" %le",delti3[i][j][k]);
 2931: 	fprintf(ficparo," %le",delti3[i][j][k]);
 2932:       }
 2933:       fscanf(ficpar,"\n");
 2934:       printf("\n");
 2935:       fprintf(ficparo,"\n");
 2936:     }
 2937:   }
 2938:   delti=delti3[1][1];
 2939:   
 2940:   /* Reads comments: lines beginning with '#' */
 2941:   while((c=getc(ficpar))=='#' && c!= EOF){
 2942:     ungetc(c,ficpar);
 2943:     fgets(line, MAXLINE, ficpar);
 2944:     puts(line);
 2945:     fputs(line,ficparo);
 2946:   }
 2947:   ungetc(c,ficpar);
 2948:   
 2949:   matcov=matrix(1,npar,1,npar);
 2950:   for(i=1; i <=npar; i++){
 2951:     fscanf(ficpar,"%s",&str);
 2952:     printf("%s",str);
 2953:     fprintf(ficparo,"%s",str);
 2954:     for(j=1; j <=i; j++){
 2955:       fscanf(ficpar," %le",&matcov[i][j]);
 2956:       printf(" %.5le",matcov[i][j]);
 2957:       fprintf(ficparo," %.5le",matcov[i][j]);
 2958:     }
 2959:     fscanf(ficpar,"\n");
 2960:     printf("\n");
 2961:     fprintf(ficparo,"\n");
 2962:   }
 2963:   for(i=1; i <=npar; i++)
 2964:     for(j=i+1;j<=npar;j++)
 2965:       matcov[i][j]=matcov[j][i];
 2966:    
 2967:   printf("\n");
 2968: 
 2969: 
 2970:     /*-------- Rewriting paramater file ----------*/
 2971:      strcpy(rfileres,"r");    /* "Rparameterfile */
 2972:      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
 2973:      strcat(rfileres,".");    /* */
 2974:      strcat(rfileres,optionfilext);    /* Other files have txt extension */
 2975:     if((ficres =fopen(rfileres,"w"))==NULL) {
 2976:       printf("Problem writing new parameter file: %s\n", fileres);goto end;
 2977:     }
 2978:     fprintf(ficres,"#%s\n",version);
 2979:     
 2980:     /*-------- data file ----------*/
 2981:     if((fic=fopen(datafile,"r"))==NULL)    {
 2982:       printf("Problem with datafile: %s\n", datafile);goto end;
 2983:     }
 2984: 
 2985:     n= lastobs;
 2986:     severity = vector(1,maxwav);
 2987:     outcome=imatrix(1,maxwav+1,1,n);
 2988:     num=ivector(1,n);
 2989:     moisnais=vector(1,n);
 2990:     annais=vector(1,n);
 2991:     moisdc=vector(1,n);
 2992:     andc=vector(1,n);
 2993:     agedc=vector(1,n);
 2994:     cod=ivector(1,n);
 2995:     weight=vector(1,n);
 2996:     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
 2997:     mint=matrix(1,maxwav,1,n);
 2998:     anint=matrix(1,maxwav,1,n);
 2999:     s=imatrix(1,maxwav+1,1,n);
 3000:     adl=imatrix(1,maxwav+1,1,n);    
 3001:     tab=ivector(1,NCOVMAX);
 3002:     ncodemax=ivector(1,8);
 3003: 
 3004:     i=1;
 3005:     while (fgets(line, MAXLINE, fic) != NULL)    {
 3006:       if ((i >= firstobs) && (i <=lastobs)) {
 3007: 	
 3008: 	for (j=maxwav;j>=1;j--){
 3009: 	  cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
 3010: 	  strcpy(line,stra);
 3011: 	  cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 3012: 	  cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 3013: 	}
 3014: 	
 3015: 	cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
 3016: 	cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
 3017: 
 3018: 	cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
 3019: 	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
 3020: 
 3021: 	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
 3022: 	for (j=ncovcol;j>=1;j--){
 3023: 	  cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 3024: 	} 
 3025: 	num[i]=atol(stra);
 3026: 	
 3027: 	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
 3028: 	  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;}*/
 3029: 
 3030: 	i=i+1;
 3031:       }
 3032:     } 
 3033:     /* printf("ii=%d", ij);
 3034:        scanf("%d",i);*/
 3035:   imx=i-1; /* Number of individuals */
 3036: 
 3037:   /* for (i=1; i<=imx; i++){
 3038:     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
 3039:     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
 3040:     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
 3041:     }*/
 3042:    /*  for (i=1; i<=imx; i++){
 3043:      if (s[4][i]==9)  s[4][i]=-1; 
 3044:      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]));}*/
 3045:   
 3046:  
 3047:   /* Calculation of the number of parameter from char model*/
 3048:   Tvar=ivector(1,15); 
 3049:   Tprod=ivector(1,15); 
 3050:   Tvaraff=ivector(1,15); 
 3051:   Tvard=imatrix(1,15,1,2);
 3052:   Tage=ivector(1,15);      
 3053:    
 3054:   if (strlen(model) >1){
 3055:     j=0, j1=0, k1=1, k2=1;
 3056:     j=nbocc(model,'+');
 3057:     j1=nbocc(model,'*');
 3058:     cptcovn=j+1;
 3059:     cptcovprod=j1;
 3060:     
 3061:     strcpy(modelsav,model); 
 3062:     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
 3063:       printf("Error. Non available option model=%s ",model);
 3064:       goto end;
 3065:     }
 3066:     
 3067:     for(i=(j+1); i>=1;i--){
 3068:       cutv(stra,strb,modelsav,'+');
 3069:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); 
 3070:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
 3071:       /*scanf("%d",i);*/
 3072:       if (strchr(strb,'*')) {
 3073: 	cutv(strd,strc,strb,'*');
 3074: 	if (strcmp(strc,"age")==0) {
 3075: 	  cptcovprod--;
 3076: 	  cutv(strb,stre,strd,'V');
 3077: 	  Tvar[i]=atoi(stre);
 3078: 	  cptcovage++;
 3079: 	    Tage[cptcovage]=i;
 3080: 	    /*printf("stre=%s ", stre);*/
 3081: 	}
 3082: 	else if (strcmp(strd,"age")==0) {
 3083: 	  cptcovprod--;
 3084: 	  cutv(strb,stre,strc,'V');
 3085: 	  Tvar[i]=atoi(stre);
 3086: 	  cptcovage++;
 3087: 	  Tage[cptcovage]=i;
 3088: 	}
 3089: 	else {
 3090: 	  cutv(strb,stre,strc,'V');
 3091: 	  Tvar[i]=ncovcol+k1;
 3092: 	  cutv(strb,strc,strd,'V'); 
 3093: 	  Tprod[k1]=i;
 3094: 	  Tvard[k1][1]=atoi(strc);
 3095: 	  Tvard[k1][2]=atoi(stre);
 3096: 	  Tvar[cptcovn+k2]=Tvard[k1][1];
 3097: 	  Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
 3098: 	  for (k=1; k<=lastobs;k++) 
 3099: 	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
 3100: 	  k1++;
 3101: 	  k2=k2+2;
 3102: 	}
 3103:       }
 3104:       else {
 3105: 	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
 3106:        /*  scanf("%d",i);*/
 3107:       cutv(strd,strc,strb,'V');
 3108:       Tvar[i]=atoi(strc);
 3109:       }
 3110:       strcpy(modelsav,stra);  
 3111:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
 3112: 	scanf("%d",i);*/
 3113:     }
 3114: }
 3115:   
 3116:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
 3117:   printf("cptcovprod=%d ", cptcovprod);
 3118:   scanf("%d ",i);*/
 3119:     fclose(fic);
 3120: 
 3121:     /*  if(mle==1){*/
 3122:     if (weightopt != 1) { /* Maximisation without weights*/
 3123:       for(i=1;i<=n;i++) weight[i]=1.0;
 3124:     }
 3125:     /*-calculation of age at interview from date of interview and age at death -*/
 3126:     agev=matrix(1,maxwav,1,imx);
 3127: 
 3128:     for (i=1; i<=imx; i++) {
 3129:       for(m=2; (m<= maxwav); m++) {
 3130:        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
 3131: 	 anint[m][i]=9999;
 3132: 	 s[m][i]=-1;
 3133:        }
 3134:      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
 3135:       }
 3136:     }
 3137: 
 3138:     for (i=1; i<=imx; i++)  {
 3139:       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
 3140:       for(m=1; (m<= maxwav); m++){
 3141: 	if(s[m][i] >0){
 3142: 	  if (s[m][i] >= nlstate+1) {
 3143: 	    if(agedc[i]>0)
 3144: 	      if(moisdc[i]!=99 && andc[i]!=9999)
 3145: 		agev[m][i]=agedc[i];
 3146: 	    /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
 3147: 	   else {
 3148: 	      if (andc[i]!=9999){
 3149: 	      printf("Warning negative age at death: %d line:%d\n",num[i],i);
 3150: 	      agev[m][i]=-1;
 3151: 	      }
 3152: 	    }
 3153: 	  }
 3154: 	  else if(s[m][i] !=9){ /* Should no more exist */
 3155: 	    agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
 3156: 	    if(mint[m][i]==99 || anint[m][i]==9999)
 3157: 	      agev[m][i]=1;
 3158: 	    else if(agev[m][i] <agemin){ 
 3159: 	      agemin=agev[m][i];
 3160: 	      /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
 3161: 	    }
 3162: 	    else if(agev[m][i] >agemax){
 3163: 	      agemax=agev[m][i];
 3164: 	     /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
 3165: 	    }
 3166: 	    /*agev[m][i]=anint[m][i]-annais[i];*/
 3167: 	    /*	 agev[m][i] = age[i]+2*m;*/
 3168: 	  }
 3169: 	  else { /* =9 */
 3170: 	    agev[m][i]=1;
 3171: 	    s[m][i]=-1;
 3172: 	  }
 3173: 	}
 3174: 	else /*= 0 Unknown */
 3175: 	  agev[m][i]=1;
 3176:       }
 3177:     
 3178:     }
 3179:     for (i=1; i<=imx; i++)  {
 3180:       for(m=1; (m<= maxwav); m++){
 3181: 	if (s[m][i] > (nlstate+ndeath)) {
 3182: 	  printf("Error: Wrong value in nlstate or ndeath\n");	
 3183: 	  goto end;
 3184: 	}
 3185:       }
 3186:     }
 3187: 
 3188: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
 3189: 
 3190:     free_vector(severity,1,maxwav);
 3191:     free_imatrix(outcome,1,maxwav+1,1,n);
 3192:     free_vector(moisnais,1,n);
 3193:     free_vector(annais,1,n);
 3194:     /* free_matrix(mint,1,maxwav,1,n);
 3195:        free_matrix(anint,1,maxwav,1,n);*/
 3196:     free_vector(moisdc,1,n);
 3197:     free_vector(andc,1,n);
 3198: 
 3199:    
 3200:     wav=ivector(1,imx);
 3201:     dh=imatrix(1,lastpass-firstpass+1,1,imx);
 3202:     mw=imatrix(1,lastpass-firstpass+1,1,imx);
 3203:    
 3204:     /* Concatenates waves */
 3205:       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
 3206: 
 3207: 
 3208:       Tcode=ivector(1,100);
 3209:       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
 3210:       ncodemax[1]=1;
 3211:       if (cptcovn > 0) tricode(Tvar,nbcode,imx);
 3212:       
 3213:    codtab=imatrix(1,100,1,10);
 3214:    h=0;
 3215:    m=pow(2,cptcoveff);
 3216:  
 3217:    for(k=1;k<=cptcoveff; k++){
 3218:      for(i=1; i <=(m/pow(2,k));i++){
 3219:        for(j=1; j <= ncodemax[k]; j++){
 3220: 	 for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
 3221: 	   h++;
 3222: 	   if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
 3223: 	   /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
 3224: 	 } 
 3225:        }
 3226:      }
 3227:    } 
 3228:    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
 3229:       codtab[1][2]=1;codtab[2][2]=2; */
 3230:    /* for(i=1; i <=m ;i++){ 
 3231:       for(k=1; k <=cptcovn; k++){
 3232:       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
 3233:       }
 3234:       printf("\n");
 3235:       }
 3236:       scanf("%d",i);*/
 3237:     
 3238:    /* Calculates basic frequencies. Computes observed prevalence at single age
 3239:        and prints on file fileres'p'. */
 3240: 
 3241:     
 3242:    
 3243:     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3244:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3245:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3246:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3247:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
 3248:      
 3249:     /* For Powell, parameters are in a vector p[] starting at p[1]
 3250:        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
 3251:     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
 3252: 
 3253:     if(mle==1){
 3254:     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
 3255:     }
 3256:     
 3257:     /*--------- results files --------------*/
 3258:     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);
 3259:   
 3260: 
 3261:    jk=1;
 3262:    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 3263:    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 3264:    for(i=1,jk=1; i <=nlstate; i++){
 3265:      for(k=1; k <=(nlstate+ndeath); k++){
 3266:        if (k != i) 
 3267: 	 {
 3268: 	   printf("%d%d ",i,k);
 3269: 	   fprintf(ficres,"%1d%1d ",i,k);
 3270: 	   for(j=1; j <=ncovmodel; j++){
 3271: 	     printf("%f ",p[jk]);
 3272: 	     fprintf(ficres,"%f ",p[jk]);
 3273: 	     jk++; 
 3274: 	   }
 3275: 	   printf("\n");
 3276: 	   fprintf(ficres,"\n");
 3277: 	 }
 3278:      }
 3279:    }
 3280:  if(mle==1){
 3281:     /* Computing hessian and covariance matrix */
 3282:     ftolhess=ftol; /* Usually correct */
 3283:     hesscov(matcov, p, npar, delti, ftolhess, func);
 3284:  }
 3285:     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
 3286:     printf("# Scales (for hessian or gradient estimation)\n");
 3287:      for(i=1,jk=1; i <=nlstate; i++){
 3288:       for(j=1; j <=nlstate+ndeath; j++){
 3289: 	if (j!=i) {
 3290: 	  fprintf(ficres,"%1d%1d",i,j);
 3291: 	  printf("%1d%1d",i,j);
 3292: 	  for(k=1; k<=ncovmodel;k++){
 3293: 	    printf(" %.5e",delti[jk]);
 3294: 	    fprintf(ficres," %.5e",delti[jk]);
 3295: 	    jk++;
 3296: 	  }
 3297: 	  printf("\n");
 3298: 	  fprintf(ficres,"\n");
 3299: 	}
 3300:       }
 3301:      }
 3302:     
 3303:     k=1;
 3304:     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");
 3305:     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");
 3306:     for(i=1;i<=npar;i++){
 3307:       /*  if (k>nlstate) k=1;
 3308:       i1=(i-1)/(ncovmodel*nlstate)+1; 
 3309:       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
 3310:       printf("%s%d%d",alph[k],i1,tab[i]);*/
 3311:       fprintf(ficres,"%3d",i);
 3312:       printf("%3d",i);
 3313:       for(j=1; j<=i;j++){
 3314: 	fprintf(ficres," %.5e",matcov[i][j]);
 3315: 	printf(" %.5e",matcov[i][j]);
 3316:       }
 3317:       fprintf(ficres,"\n");
 3318:       printf("\n");
 3319:       k++;
 3320:     }
 3321:     
 3322:     while((c=getc(ficpar))=='#' && c!= EOF){
 3323:       ungetc(c,ficpar);
 3324:       fgets(line, MAXLINE, ficpar);
 3325:       puts(line);
 3326:       fputs(line,ficparo);
 3327:     }
 3328:     ungetc(c,ficpar);
 3329:     estepm=0;
 3330:     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
 3331:     if (estepm==0 || estepm < stepm) estepm=stepm;
 3332:     if (fage <= 2) {
 3333:       bage = ageminpar;
 3334:       fage = agemaxpar;
 3335:     }
 3336:     
 3337:     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
 3338:     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 3339:     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
 3340:  
 3341:     while((c=getc(ficpar))=='#' && c!= EOF){
 3342:     ungetc(c,ficpar);
 3343:     fgets(line, MAXLINE, ficpar);
 3344:     puts(line);
 3345:     fputs(line,ficparo);
 3346:   }
 3347:   ungetc(c,ficpar);
 3348:   
 3349:   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
 3350:   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3351:  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3352:      
 3353:   while((c=getc(ficpar))=='#' && c!= EOF){
 3354:     ungetc(c,ficpar);
 3355:     fgets(line, MAXLINE, ficpar);
 3356:     puts(line);
 3357:     fputs(line,ficparo);
 3358:   }
 3359:   ungetc(c,ficpar);
 3360:  
 3361: 
 3362:    dateprev1=anprev1+mprev1/12.+jprev1/365.;
 3363:    dateprev2=anprev2+mprev2/12.+jprev2/365.;
 3364: 
 3365:   fscanf(ficpar,"pop_based=%d\n",&popbased);
 3366:   fprintf(ficparo,"pop_based=%d\n",popbased);   
 3367:   fprintf(ficres,"pop_based=%d\n",popbased);   
 3368:   
 3369:   while((c=getc(ficpar))=='#' && c!= EOF){
 3370:     ungetc(c,ficpar);
 3371:     fgets(line, MAXLINE, ficpar);
 3372:     puts(line);
 3373:     fputs(line,ficparo);
 3374:   }
 3375:   ungetc(c,ficpar);
 3376: 
 3377:   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);
 3378: 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);
 3379: 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);
 3380: 
 3381: 
 3382: while((c=getc(ficpar))=='#' && c!= EOF){
 3383:     ungetc(c,ficpar);
 3384:     fgets(line, MAXLINE, ficpar);
 3385:     puts(line);
 3386:     fputs(line,ficparo);
 3387:   }
 3388:   ungetc(c,ficpar);
 3389: 
 3390:   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
 3391:   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 3392:   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
 3393: 
 3394:  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
 3395: 
 3396: /*------------ gnuplot -------------*/
 3397:   strcpy(optionfilegnuplot,optionfilefiname);
 3398:   strcat(optionfilegnuplot,".gp");
 3399:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
 3400:     printf("Problem with file %s",optionfilegnuplot);
 3401:   }
 3402:   fclose(ficgp);
 3403:  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
 3404: /*--------- index.htm --------*/
 3405: 
 3406:   strcpy(optionfilehtm,optionfile);
 3407:   strcat(optionfilehtm,".htm");
 3408:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
 3409:     printf("Problem with %s \n",optionfilehtm), exit(0);
 3410:   }
 3411: 
 3412:   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
 3413: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
 3414: \n
 3415: Total number of observations=%d <br>\n
 3416: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
 3417: <hr  size=\"2\" color=\"#EC5E5E\">
 3418:  <ul><li>Parameter files<br>\n
 3419:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
 3420:  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
 3421:   fclose(fichtm);
 3422: 
 3423:  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
 3424:  
 3425: /*------------ free_vector  -------------*/
 3426:  chdir(path);
 3427:  
 3428:  free_ivector(wav,1,imx);
 3429:  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
 3430:  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
 3431:  free_ivector(num,1,n);
 3432:  free_vector(agedc,1,n);
 3433:  /*free_matrix(covar,1,NCOVMAX,1,n);*/
 3434:  fclose(ficparo);
 3435:  fclose(ficres);
 3436: 
 3437: 
 3438:   /*--------------- Prevalence limit --------------*/
 3439:   
 3440:   strcpy(filerespl,"pl");
 3441:   strcat(filerespl,fileres);
 3442:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
 3443:     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
 3444:   }
 3445:   printf("Computing prevalence limit: result on file '%s' \n", filerespl);
 3446:   fprintf(ficrespl,"#Prevalence limit\n");
 3447:   fprintf(ficrespl,"#Age ");
 3448:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
 3449:   fprintf(ficrespl,"\n");
 3450:   
 3451:   prlim=matrix(1,nlstate,1,nlstate);
 3452:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3453:   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3454:   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3455:   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
 3456:   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
 3457:   k=0;
 3458:   agebase=ageminpar;
 3459:   agelim=agemaxpar;
 3460:   ftolpl=1.e-10;
 3461:   i1=cptcoveff;
 3462:   if (cptcovn < 1){i1=1;}
 3463: 
 3464:   for(cptcov=1;cptcov<=i1;cptcov++){
 3465:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3466: 	k=k+1;
 3467: 	/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
 3468: 	fprintf(ficrespl,"\n#******");
 3469: 	for(j=1;j<=cptcoveff;j++) 
 3470: 	  fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3471: 	fprintf(ficrespl,"******\n");
 3472: 	
 3473: 	for (age=agebase; age<=agelim; age++){
 3474: 	  prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
 3475: 	  fprintf(ficrespl,"%.0f",age );
 3476: 	  for(i=1; i<=nlstate;i++)
 3477: 	  fprintf(ficrespl," %.5f", prlim[i][i]);
 3478: 	  fprintf(ficrespl,"\n");
 3479: 	}
 3480:       }
 3481:     }
 3482:   fclose(ficrespl);
 3483: 
 3484:   /*------------- h Pij x at various ages ------------*/
 3485:   
 3486:   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
 3487:   if((ficrespij=fopen(filerespij,"w"))==NULL) {
 3488:     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
 3489:   }
 3490:   printf("Computing pij: result on file '%s' \n", filerespij);
 3491:   
 3492:   stepsize=(int) (stepm+YEARM-1)/YEARM;
 3493:   /*if (stepm<=24) stepsize=2;*/
 3494: 
 3495:   agelim=AGESUP;
 3496:   hstepm=stepsize*YEARM; /* Every year of age */
 3497:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
 3498:   
 3499:   k=0;
 3500:   for(cptcov=1;cptcov<=i1;cptcov++){
 3501:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3502:       k=k+1;
 3503: 	fprintf(ficrespij,"\n#****** ");
 3504: 	for(j=1;j<=cptcoveff;j++) 
 3505: 	  fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3506: 	fprintf(ficrespij,"******\n");
 3507: 	
 3508: 	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
 3509: 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 3510: 	  nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 3511: 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3512: 	  oldm=oldms;savm=savms;
 3513: 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 3514: 	  fprintf(ficrespij,"# Age");
 3515: 	  for(i=1; i<=nlstate;i++)
 3516: 	    for(j=1; j<=nlstate+ndeath;j++)
 3517: 	      fprintf(ficrespij," %1d-%1d",i,j);
 3518: 	  fprintf(ficrespij,"\n");
 3519: 	   for (h=0; h<=nhstepm; h++){
 3520: 	    fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
 3521: 	    for(i=1; i<=nlstate;i++)
 3522: 	      for(j=1; j<=nlstate+ndeath;j++)
 3523: 		fprintf(ficrespij," %.5f", p3mat[i][j][h]);
 3524: 	    fprintf(ficrespij,"\n");
 3525: 	     }
 3526: 	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 3527: 	  fprintf(ficrespij,"\n");
 3528: 	}
 3529:     }
 3530:   }
 3531: 
 3532:   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
 3533: 
 3534:   fclose(ficrespij);
 3535: 
 3536: 
 3537:   /*---------- Forecasting ------------------*/
 3538:   if((stepm == 1) && (strcmp(model,".")==0)){
 3539:     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
 3540:     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
 3541:   } 
 3542:   else{
 3543:     erreur=108;
 3544:     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);
 3545:   }
 3546:   
 3547: 
 3548:   /*---------- Health expectancies and variances ------------*/
 3549: 
 3550:   strcpy(filerest,"t");
 3551:   strcat(filerest,fileres);
 3552:   if((ficrest=fopen(filerest,"w"))==NULL) {
 3553:     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
 3554:   }
 3555:   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
 3556: 
 3557: 
 3558:   strcpy(filerese,"e");
 3559:   strcat(filerese,fileres);
 3560:   if((ficreseij=fopen(filerese,"w"))==NULL) {
 3561:     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
 3562:   }
 3563:   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
 3564: 
 3565:  strcpy(fileresv,"v");
 3566:   strcat(fileresv,fileres);
 3567:   if((ficresvij=fopen(fileresv,"w"))==NULL) {
 3568:     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
 3569:   }
 3570:   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
 3571:   calagedate=-1;
 3572: prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
 3573: 
 3574:   k=0;
 3575:   for(cptcov=1;cptcov<=i1;cptcov++){
 3576:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3577:       k=k+1;
 3578:       fprintf(ficrest,"\n#****** ");
 3579:       for(j=1;j<=cptcoveff;j++) 
 3580: 	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3581:       fprintf(ficrest,"******\n");
 3582: 
 3583:       fprintf(ficreseij,"\n#****** ");
 3584:       for(j=1;j<=cptcoveff;j++) 
 3585: 	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3586:       fprintf(ficreseij,"******\n");
 3587: 
 3588:       fprintf(ficresvij,"\n#****** ");
 3589:       for(j=1;j<=cptcoveff;j++) 
 3590: 	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3591:       fprintf(ficresvij,"******\n");
 3592: 
 3593:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 3594:       oldm=oldms;savm=savms;
 3595:       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
 3596:  
 3597:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
 3598:       oldm=oldms;savm=savms;
 3599:        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);
 3600:     
 3601: 
 3602:  
 3603:       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
 3604:       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
 3605:       fprintf(ficrest,"\n");
 3606: 
 3607:       epj=vector(1,nlstate+1);
 3608:       for(age=bage; age <=fage ;age++){
 3609: 	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
 3610: 	if (popbased==1) {
 3611: 	  for(i=1; i<=nlstate;i++)
 3612: 	    prlim[i][i]=probs[(int)age][i][k];
 3613: 	}
 3614: 	
 3615: 	fprintf(ficrest," %4.0f",age);
 3616: 	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 3617: 	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
 3618: 	    epj[j] += prlim[i][i]*eij[i][j][(int)age];
 3619: 	    /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
 3620: 	  }
 3621: 	  epj[nlstate+1] +=epj[j];
 3622: 	}
 3623: 
 3624: 	for(i=1, vepp=0.;i <=nlstate;i++)
 3625: 	  for(j=1;j <=nlstate;j++)
 3626: 	    vepp += vareij[i][j][(int)age];
 3627: 	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
 3628: 	for(j=1;j <=nlstate;j++){
 3629: 	  fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
 3630: 	}
 3631: 	fprintf(ficrest,"\n");
 3632:       }
 3633:     }
 3634:   }
 3635: free_matrix(mint,1,maxwav,1,n);
 3636:     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
 3637:     free_vector(weight,1,n);
 3638:   fclose(ficreseij);
 3639:   fclose(ficresvij);
 3640:   fclose(ficrest);
 3641:   fclose(ficpar);
 3642:   free_vector(epj,1,nlstate+1);
 3643:   
 3644:   /*------- Variance limit prevalence------*/   
 3645: 
 3646:   strcpy(fileresvpl,"vpl");
 3647:   strcat(fileresvpl,fileres);
 3648:   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
 3649:     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
 3650:     exit(0);
 3651:   }
 3652:   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
 3653: 
 3654:   k=0;
 3655:   for(cptcov=1;cptcov<=i1;cptcov++){
 3656:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 3657:       k=k+1;
 3658:       fprintf(ficresvpl,"\n#****** ");
 3659:       for(j=1;j<=cptcoveff;j++) 
 3660: 	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 3661:       fprintf(ficresvpl,"******\n");
 3662:       
 3663:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
 3664:       oldm=oldms;savm=savms;
 3665:      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
 3666:     }
 3667:  }
 3668: 
 3669:   fclose(ficresvpl);
 3670: 
 3671:   /*---------- End : free ----------------*/
 3672:   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
 3673:   
 3674:   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 3675:   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
 3676:   
 3677:   
 3678:   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
 3679:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3680:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3681:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
 3682:  
 3683:   free_matrix(matcov,1,npar,1,npar);
 3684:   free_vector(delti,1,npar);
 3685:   free_matrix(agev,1,maxwav,1,imx);
 3686:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 3687: 
 3688:   fprintf(fichtm,"\n</body>");
 3689:   fclose(fichtm);
 3690:   fclose(ficgp);
 3691:   
 3692: 
 3693:   if(erreur >0)
 3694:     printf("End of Imach with error or warning %d\n",erreur);
 3695:   else   printf("End of Imach\n");
 3696:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
 3697:   
 3698:   /* 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);*/
 3699:   /*printf("Total time was %d uSec.\n", total_usecs);*/
 3700:   /*------ End -----------*/
 3701: 
 3702: 
 3703:  end:
 3704: #ifdef windows
 3705:   /* chdir(pathcd);*/
 3706: #endif 
 3707:  /*system("wgnuplot graph.plt");*/
 3708:  /*system("../gp37mgw/wgnuplot graph.plt");*/
 3709:  /*system("cd ../gp37mgw");*/
 3710:  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
 3711:  strcpy(plotcmd,GNUPLOTPROGRAM);
 3712:  strcat(plotcmd," ");
 3713:  strcat(plotcmd,optionfilegnuplot);
 3714:  system(plotcmd);
 3715: 
 3716: #ifdef windows
 3717:   while (z[0] != 'q') {
 3718:     /* chdir(path); */
 3719:     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
 3720:     scanf("%s",z);
 3721:     if (z[0] == 'c') system("./imach");
 3722:     else if (z[0] == 'e') system(optionfilehtm);
 3723:     else if (z[0] == 'g') system(plotcmd);
 3724:     else if (z[0] == 'q') exit(0);
 3725:   }
 3726: #endif 
 3727: }
 3728: 
 3729: 

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>