Annotation of imach096d/src/imach.c, revision 1.90

1.90    ! brouard     1: /* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $
1.83      lievre      2:   $State: Exp $
                      3:   $Log: imach.c,v $
1.90    ! brouard     4:   Revision 1.89  2003/06/24 12:30:52  brouard
        !             5:   (Module): Some bugs corrected for windows. Also, when
        !             6:   mle=-1 a template is output in file "or"mypar.txt with the design
        !             7:   of the covariance matrix to be input.
        !             8: 
1.89      brouard     9:   Revision 1.88  2003/06/23 17:54:56  brouard
                     10:   * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
                     11: 
1.88      brouard    12:   Revision 1.87  2003/06/18 12:26:01  brouard
                     13:   Version 0.96
                     14: 
1.87      brouard    15:   Revision 1.86  2003/06/17 20:04:08  brouard
                     16:   (Module): Change position of html and gnuplot routines and added
                     17:   routine fileappend.
                     18: 
1.86      brouard    19:   Revision 1.85  2003/06/17 13:12:43  brouard
                     20:   * imach.c (Repository): Check when date of death was earlier that
                     21:   current date of interview. It may happen when the death was just
                     22:   prior to the death. In this case, dh was negative and likelihood
                     23:   was wrong (infinity). We still send an "Error" but patch by
                     24:   assuming that the date of death was just one stepm after the
                     25:   interview.
                     26:   (Repository): Because some people have very long ID (first column)
                     27:   we changed int to long in num[] and we added a new lvector for
                     28:   memory allocation. But we also truncated to 8 characters (left
                     29:   truncation)
                     30:   (Repository): No more line truncation errors.
                     31: 
1.85      brouard    32:   Revision 1.84  2003/06/13 21:44:43  brouard
                     33:   * imach.c (Repository): Replace "freqsummary" at a correct
                     34:   place. It differs from routine "prevalence" which may be called
                     35:   many times. Probs is memory consuming and must be used with
                     36:   parcimony.
1.86      brouard    37:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85      brouard    38: 
1.84      brouard    39:   Revision 1.83  2003/06/10 13:39:11  lievre
                     40:   *** empty log message ***
                     41: 
1.83      lievre     42:   Revision 1.82  2003/06/05 15:57:20  brouard
                     43:   Add log in  imach.c and  fullversion number is now printed.
                     44: 
1.82      brouard    45: */
                     46: /*
1.53      brouard    47:    Interpolated Markov Chain
                     48: 
                     49:   Short summary of the programme:
                     50:   
                     51:   This program computes Healthy Life Expectancies from
                     52:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
                     53:   first survey ("cross") where individuals from different ages are
                     54:   interviewed on their health status or degree of disability (in the
                     55:   case of a health survey which is our main interest) -2- at least a
                     56:   second wave of interviews ("longitudinal") which measure each change
                     57:   (if any) in individual health status.  Health expectancies are
                     58:   computed from the time spent in each health state according to a
                     59:   model. More health states you consider, more time is necessary to reach the
                     60:   Maximum Likelihood of the parameters involved in the model.  The
                     61:   simplest model is the multinomial logistic model where pij is the
                     62:   probability to be observed in state j at the second wave
                     63:   conditional to be observed in state i at the first wave. Therefore
                     64:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
                     65:   'age' is age and 'sex' is a covariate. If you want to have a more
                     66:   complex model than "constant and age", you should modify the program
                     67:   where the markup *Covariates have to be included here again* invites
                     68:   you to do it.  More covariates you add, slower the
                     69:   convergence.
                     70: 
                     71:   The advantage of this computer programme, compared to a simple
                     72:   multinomial logistic model, is clear when the delay between waves is not
                     73:   identical for each individual. Also, if a individual missed an
                     74:   intermediate interview, the information is lost, but taken into
                     75:   account using an interpolation or extrapolation.  
                     76: 
                     77:   hPijx is the probability to be observed in state i at age x+h
                     78:   conditional to the observed state i at age x. The delay 'h' can be
                     79:   split into an exact number (nh*stepm) of unobserved intermediate
1.66      brouard    80:   states. This elementary transition (by month, quarter,
                     81:   semester or year) is modelled as a multinomial logistic.  The hPx
1.53      brouard    82:   matrix is simply the matrix product of nh*stepm elementary matrices
                     83:   and the contribution of each individual to the likelihood is simply
                     84:   hPijx.
                     85: 
                     86:   Also this programme outputs the covariance matrix of the parameters but also
1.54      brouard    87:   of the life expectancies. It also computes the stable prevalence. 
1.53      brouard    88:   
                     89:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                     90:            Institut national d'études démographiques, Paris.
                     91:   This software have been partly granted by Euro-REVES, a concerted action
                     92:   from the European Union.
                     93:   It is copyrighted identically to a GNU software product, ie programme and
                     94:   software can be distributed freely for non commercial use. Latest version
                     95:   can be accessed at http://euroreves.ined.fr/imach .
1.74      brouard    96: 
                     97:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                     98:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                     99:   
1.53      brouard   100:   **********************************************************************/
1.74      brouard   101: /*
                    102:   main
                    103:   read parameterfile
                    104:   read datafile
                    105:   concatwav
1.84      brouard   106:   freqsummary
1.74      brouard   107:   if (mle >= 1)
                    108:     mlikeli
                    109:   print results files
                    110:   if mle==1 
                    111:      computes hessian
                    112:   read end of parameter file: agemin, agemax, bage, fage, estepm
                    113:       begin-prev-date,...
                    114:   open gnuplot file
                    115:   open html file
                    116:   stable prevalence
                    117:    for age prevalim()
                    118:   h Pij x
                    119:   variance of p varprob
                    120:   forecasting if prevfcast==1 prevforecast call prevalence()
                    121:   health expectancies
                    122:   Variance-covariance of DFLE
                    123:   prevalence()
                    124:    movingaverage()
                    125:   varevsij() 
                    126:   if popbased==1 varevsij(,popbased)
                    127:   total life expectancies
                    128:   Variance of stable prevalence
                    129:  end
                    130: */
                    131: 
                    132: 
                    133: 
1.53      brouard   134:  
                    135: #include <math.h>
                    136: #include <stdio.h>
                    137: #include <stdlib.h>
                    138: #include <unistd.h>
                    139: 
1.86      brouard   140: #include <sys/time.h>
                    141: #include <time.h>
                    142: #include "timeval.h"
                    143: 
1.53      brouard   144: #define MAXLINE 256
                    145: #define GNUPLOTPROGRAM "gnuplot"
                    146: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85      brouard   147: #define FILENAMELENGTH 132
1.53      brouard   148: /*#define DEBUG*/
1.85      brouard   149: /*#define windows*/
1.53      brouard   150: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                    151: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                    152: 
                    153: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
                    154: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
                    155: 
                    156: #define NINTERVMAX 8
                    157: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
                    158: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
                    159: #define NCOVMAX 8 /* Maximum number of covariates */
                    160: #define MAXN 20000
                    161: #define YEARM 12. /* Number of months per year */
                    162: #define AGESUP 130
                    163: #define AGEBASE 40
1.85      brouard   164: #ifdef unix
                    165: #define DIRSEPARATOR '/'
                    166: #define ODIRSEPARATOR '\\'
                    167: #else
1.53      brouard   168: #define DIRSEPARATOR '\\'
                    169: #define ODIRSEPARATOR '/'
                    170: #endif
                    171: 
1.90    ! brouard   172: /* $Id: imach.c,v 1.89 2003/06/24 12:30:52 brouard Exp $ */
1.81      brouard   173: /* $State: Exp $ */
1.80      brouard   174: 
1.88      brouard   175: char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
1.90    ! brouard   176: char fullversion[]="$Revision: 1.89 $ $Date: 2003/06/24 12:30:52 $"; 
1.53      brouard   177: int erreur; /* Error number */
                    178: int nvar;
                    179: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
                    180: int npar=NPARMAX;
                    181: int nlstate=2; /* Number of live states */
                    182: int ndeath=1; /* Number of dead states */
                    183: int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
                    184: int popbased=0;
                    185: 
                    186: int *wav; /* Number of waves for this individuual 0 is possible */
                    187: int maxwav; /* Maxim number of waves */
                    188: int jmin, jmax; /* min, max spacing between 2 waves */
1.87      brouard   189: int gipmx, gsw; /* Global variables on the number of contributions 
                    190:                   to the likelihood and the sum of weights (done by funcone)*/
1.53      brouard   191: int mle, weightopt;
                    192: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                    193: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59      brouard   194: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                    195:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53      brouard   196: double jmean; /* Mean space between 2 waves */
                    197: double **oldm, **newm, **savm; /* Working pointers to matrices */
                    198: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
                    199: FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76      brouard   200: FILE *ficlog, *ficrespow;
1.85      brouard   201: int globpr; /* Global variable for printing or not */
                    202: double fretone; /* Only one call to likelihood */
                    203: long ipmx; /* Number of contributions */
                    204: double sw; /* Sum of weights */
                    205: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                    206: FILE *ficresilk;
1.53      brouard   207: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                    208: FILE *ficresprobmorprev;
                    209: FILE *fichtm; /* Html File */
                    210: FILE *ficreseij;
                    211: char filerese[FILENAMELENGTH];
                    212: FILE  *ficresvij;
                    213: char fileresv[FILENAMELENGTH];
                    214: FILE  *ficresvpl;
                    215: char fileresvpl[FILENAMELENGTH];
                    216: char title[MAXLINE];
                    217: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
                    218: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.88      brouard   219: char tmpout[FILENAMELENGTH]; 
                    220: char command[FILENAMELENGTH];
                    221: int  outcmd=0;
1.53      brouard   222: 
                    223: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.88      brouard   224: char lfileres[FILENAMELENGTH];
1.53      brouard   225: char filelog[FILENAMELENGTH]; /* Log file */
                    226: char filerest[FILENAMELENGTH];
                    227: char fileregp[FILENAMELENGTH];
                    228: char popfile[FILENAMELENGTH];
                    229: 
                    230: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
                    231: 
                    232: #define NR_END 1
                    233: #define FREE_ARG char*
                    234: #define FTOL 1.0e-10
                    235: 
                    236: #define NRANSI 
                    237: #define ITMAX 200 
                    238: 
                    239: #define TOL 2.0e-4 
                    240: 
                    241: #define CGOLD 0.3819660 
                    242: #define ZEPS 1.0e-10 
                    243: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                    244: 
                    245: #define GOLD 1.618034 
                    246: #define GLIMIT 100.0 
                    247: #define TINY 1.0e-20 
                    248: 
                    249: static double maxarg1,maxarg2;
                    250: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                    251: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                    252:   
                    253: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                    254: #define rint(a) floor(a+0.5)
                    255: 
                    256: static double sqrarg;
                    257: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                    258: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                    259: 
                    260: int imx; 
                    261: int stepm;
                    262: /* Stepm, step in month: minimum step interpolation*/
                    263: 
                    264: int estepm;
                    265: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                    266: 
                    267: int m,nb;
1.85      brouard   268: long *num;
                    269: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53      brouard   270: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55      lievre    271: double **pmmij, ***probs;
1.53      brouard   272: double dateintmean=0;
                    273: 
                    274: double *weight;
                    275: int **s; /* Status */
                    276: double *agedc, **covar, idx;
                    277: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
                    278: 
                    279: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
                    280: double ftolhess; /* Tolerance for computing hessian */
                    281: 
                    282: /**************** split *************************/
                    283: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                    284: {
1.59      brouard   285:   char *ss;                            /* pointer */
                    286:   int  l1, l2;                         /* length counters */
1.53      brouard   287: 
1.59      brouard   288:   l1 = strlen(path );                  /* length of path */
                    289:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                    290:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                    291:   if ( ss == NULL ) {                  /* no directory, so use current */
                    292:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                    293:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74      brouard   294:     /* get current working directory */
                    295:     /*    extern  char* getcwd ( char *buf , int len);*/
1.59      brouard   296:     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
                    297:       return( GLOCK_ERROR_GETCWD );
                    298:     }
                    299:     strcpy( name, path );              /* we've got it */
                    300:   } else {                             /* strip direcotry from path */
                    301:     ss++;                              /* after this, the filename */
                    302:     l2 = strlen( ss );                 /* length of filename */
                    303:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                    304:     strcpy( name, ss );                /* save file name */
                    305:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
                    306:     dirc[l1-l2] = 0;                   /* add zero */
                    307:   }
                    308:   l1 = strlen( dirc );                 /* length of directory */
1.85      brouard   309:   /*#ifdef windows
1.59      brouard   310:   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53      brouard   311: #else
1.59      brouard   312:   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53      brouard   313: #endif
1.85      brouard   314:   */
1.59      brouard   315:   ss = strrchr( name, '.' );           /* find last / */
                    316:   ss++;
                    317:   strcpy(ext,ss);                      /* save extension */
                    318:   l1= strlen( name);
                    319:   l2= strlen(ss)+1;
                    320:   strncpy( finame, name, l1-l2);
                    321:   finame[l1-l2]= 0;
                    322:   return( 0 );                         /* we're done */
1.53      brouard   323: }
                    324: 
                    325: 
                    326: /******************************************/
                    327: 
1.89      brouard   328: void replace_back_to_slash(char *s, char*t)
1.53      brouard   329: {
                    330:   int i;
1.89      brouard   331:   int lg=0;
1.53      brouard   332:   i=0;
                    333:   lg=strlen(t);
                    334:   for(i=0; i<= lg; i++) {
                    335:     (s[i] = t[i]);
                    336:     if (t[i]== '\\') s[i]='/';
                    337:   }
                    338: }
                    339: 
                    340: int nbocc(char *s, char occ)
                    341: {
                    342:   int i,j=0;
                    343:   int lg=20;
                    344:   i=0;
                    345:   lg=strlen(s);
                    346:   for(i=0; i<= lg; i++) {
                    347:   if  (s[i] == occ ) j++;
                    348:   }
                    349:   return j;
                    350: }
                    351: 
                    352: void cutv(char *u,char *v, char*t, char occ)
                    353: {
                    354:   /* cuts string t into u and v where u is ended by char occ excluding it
                    355:      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
                    356:      gives u="abcedf" and v="ghi2j" */
                    357:   int i,lg,j,p=0;
                    358:   i=0;
                    359:   for(j=0; j<=strlen(t)-1; j++) {
                    360:     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
                    361:   }
                    362: 
                    363:   lg=strlen(t);
                    364:   for(j=0; j<p; j++) {
                    365:     (u[j] = t[j]);
                    366:   }
                    367:      u[p]='\0';
                    368: 
                    369:    for(j=0; j<= lg; j++) {
                    370:     if (j>=(p+1))(v[j-p-1] = t[j]);
                    371:   }
                    372: }
                    373: 
                    374: /********************** nrerror ********************/
                    375: 
                    376: void nrerror(char error_text[])
                    377: {
                    378:   fprintf(stderr,"ERREUR ...\n");
                    379:   fprintf(stderr,"%s\n",error_text);
1.59      brouard   380:   exit(EXIT_FAILURE);
1.53      brouard   381: }
                    382: /*********************** vector *******************/
                    383: double *vector(int nl, int nh)
                    384: {
                    385:   double *v;
                    386:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                    387:   if (!v) nrerror("allocation failure in vector");
                    388:   return v-nl+NR_END;
                    389: }
                    390: 
                    391: /************************ free vector ******************/
                    392: void free_vector(double*v, int nl, int nh)
                    393: {
                    394:   free((FREE_ARG)(v+nl-NR_END));
                    395: }
                    396: 
                    397: /************************ivector *******************************/
1.85      brouard   398: int *ivector(long nl,long nh)
1.76      brouard   399: {
1.85      brouard   400:   int *v;
                    401:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                    402:   if (!v) nrerror("allocation failure in ivector");
1.76      brouard   403:   return v-nl+NR_END;
                    404: }
                    405: 
                    406: /******************free ivector **************************/
1.85      brouard   407: void free_ivector(int *v, long nl, long nh)
1.76      brouard   408: {
                    409:   free((FREE_ARG)(v+nl-NR_END));
                    410: }
                    411: 
1.85      brouard   412: /************************lvector *******************************/
                    413: long *lvector(long nl,long nh)
1.53      brouard   414: {
1.85      brouard   415:   long *v;
                    416:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53      brouard   417:   if (!v) nrerror("allocation failure in ivector");
                    418:   return v-nl+NR_END;
                    419: }
                    420: 
1.85      brouard   421: /******************free lvector **************************/
                    422: void free_lvector(long *v, long nl, long nh)
1.53      brouard   423: {
                    424:   free((FREE_ARG)(v+nl-NR_END));
                    425: }
                    426: 
                    427: /******************* imatrix *******************************/
                    428: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                    429:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                    430: { 
                    431:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                    432:   int **m; 
                    433:   
                    434:   /* allocate pointers to rows */ 
                    435:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                    436:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                    437:   m += NR_END; 
                    438:   m -= nrl; 
                    439:   
                    440:   
                    441:   /* allocate rows and set pointers to them */ 
                    442:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                    443:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                    444:   m[nrl] += NR_END; 
                    445:   m[nrl] -= ncl; 
                    446:   
                    447:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                    448:   
                    449:   /* return pointer to array of pointers to rows */ 
                    450:   return m; 
                    451: } 
                    452: 
                    453: /****************** free_imatrix *************************/
                    454: void free_imatrix(m,nrl,nrh,ncl,nch)
                    455:       int **m;
                    456:       long nch,ncl,nrh,nrl; 
                    457:      /* free an int matrix allocated by imatrix() */ 
                    458: { 
                    459:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                    460:   free((FREE_ARG) (m+nrl-NR_END)); 
                    461: } 
                    462: 
                    463: /******************* matrix *******************************/
                    464: double **matrix(long nrl, long nrh, long ncl, long nch)
                    465: {
                    466:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                    467:   double **m;
                    468: 
                    469:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    470:   if (!m) nrerror("allocation failure 1 in matrix()");
                    471:   m += NR_END;
                    472:   m -= nrl;
                    473: 
                    474:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    475:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    476:   m[nrl] += NR_END;
                    477:   m[nrl] -= ncl;
                    478: 
                    479:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    480:   return m;
1.85      brouard   481:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
1.74      brouard   482:    */
1.53      brouard   483: }
                    484: 
                    485: /*************************free matrix ************************/
                    486: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                    487: {
                    488:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    489:   free((FREE_ARG)(m+nrl-NR_END));
                    490: }
                    491: 
                    492: /******************* ma3x *******************************/
                    493: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                    494: {
                    495:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                    496:   double ***m;
                    497: 
                    498:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    499:   if (!m) nrerror("allocation failure 1 in matrix()");
                    500:   m += NR_END;
                    501:   m -= nrl;
                    502: 
                    503:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    504:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    505:   m[nrl] += NR_END;
                    506:   m[nrl] -= ncl;
                    507: 
                    508:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    509: 
                    510:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                    511:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                    512:   m[nrl][ncl] += NR_END;
                    513:   m[nrl][ncl] -= nll;
                    514:   for (j=ncl+1; j<=nch; j++) 
                    515:     m[nrl][j]=m[nrl][j-1]+nlay;
                    516:   
                    517:   for (i=nrl+1; i<=nrh; i++) {
                    518:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                    519:     for (j=ncl+1; j<=nch; j++) 
                    520:       m[i][j]=m[i][j-1]+nlay;
                    521:   }
1.74      brouard   522:   return m; 
                    523:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                    524:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                    525:   */
1.53      brouard   526: }
                    527: 
                    528: /*************************free ma3x ************************/
                    529: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                    530: {
                    531:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                    532:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    533:   free((FREE_ARG)(m+nrl-NR_END));
                    534: }
                    535: 
                    536: /***************** f1dim *************************/
                    537: extern int ncom; 
                    538: extern double *pcom,*xicom;
                    539: extern double (*nrfunc)(double []); 
                    540:  
                    541: double f1dim(double x) 
                    542: { 
                    543:   int j; 
                    544:   double f;
                    545:   double *xt; 
                    546:  
                    547:   xt=vector(1,ncom); 
                    548:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                    549:   f=(*nrfunc)(xt); 
                    550:   free_vector(xt,1,ncom); 
                    551:   return f; 
                    552: } 
                    553: 
                    554: /*****************brent *************************/
                    555: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
                    556: { 
                    557:   int iter; 
                    558:   double a,b,d,etemp;
                    559:   double fu,fv,fw,fx;
                    560:   double ftemp;
                    561:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                    562:   double e=0.0; 
                    563:  
                    564:   a=(ax < cx ? ax : cx); 
                    565:   b=(ax > cx ? ax : cx); 
                    566:   x=w=v=bx; 
                    567:   fw=fv=fx=(*f)(x); 
                    568:   for (iter=1;iter<=ITMAX;iter++) { 
                    569:     xm=0.5*(a+b); 
                    570:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                    571:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                    572:     printf(".");fflush(stdout);
                    573:     fprintf(ficlog,".");fflush(ficlog);
                    574: #ifdef DEBUG
                    575:     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);
                    576:     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
                    577:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                    578: #endif
                    579:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                    580:       *xmin=x; 
                    581:       return fx; 
                    582:     } 
                    583:     ftemp=fu;
                    584:     if (fabs(e) > tol1) { 
                    585:       r=(x-w)*(fx-fv); 
                    586:       q=(x-v)*(fx-fw); 
                    587:       p=(x-v)*q-(x-w)*r; 
                    588:       q=2.0*(q-r); 
                    589:       if (q > 0.0) p = -p; 
                    590:       q=fabs(q); 
                    591:       etemp=e; 
                    592:       e=d; 
                    593:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
                    594:        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                    595:       else { 
                    596:        d=p/q; 
                    597:        u=x+d; 
                    598:        if (u-a < tol2 || b-u < tol2) 
                    599:          d=SIGN(tol1,xm-x); 
                    600:       } 
                    601:     } else { 
                    602:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                    603:     } 
                    604:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                    605:     fu=(*f)(u); 
                    606:     if (fu <= fx) { 
                    607:       if (u >= x) a=x; else b=x; 
                    608:       SHFT(v,w,x,u) 
                    609:        SHFT(fv,fw,fx,fu) 
                    610:        } else { 
                    611:          if (u < x) a=u; else b=u; 
                    612:          if (fu <= fw || w == x) { 
                    613:            v=w; 
                    614:            w=u; 
                    615:            fv=fw; 
                    616:            fw=fu; 
                    617:          } else if (fu <= fv || v == x || v == w) { 
                    618:            v=u; 
                    619:            fv=fu; 
                    620:          } 
                    621:        } 
                    622:   } 
                    623:   nrerror("Too many iterations in brent"); 
                    624:   *xmin=x; 
                    625:   return fx; 
                    626: } 
                    627: 
                    628: /****************** mnbrak ***********************/
                    629: 
                    630: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                    631:            double (*func)(double)) 
                    632: { 
                    633:   double ulim,u,r,q, dum;
                    634:   double fu; 
                    635:  
                    636:   *fa=(*func)(*ax); 
                    637:   *fb=(*func)(*bx); 
                    638:   if (*fb > *fa) { 
                    639:     SHFT(dum,*ax,*bx,dum) 
                    640:       SHFT(dum,*fb,*fa,dum) 
                    641:       } 
                    642:   *cx=(*bx)+GOLD*(*bx-*ax); 
                    643:   *fc=(*func)(*cx); 
                    644:   while (*fb > *fc) { 
                    645:     r=(*bx-*ax)*(*fb-*fc); 
                    646:     q=(*bx-*cx)*(*fb-*fa); 
                    647:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                    648:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
                    649:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
                    650:     if ((*bx-u)*(u-*cx) > 0.0) { 
                    651:       fu=(*func)(u); 
                    652:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
                    653:       fu=(*func)(u); 
                    654:       if (fu < *fc) { 
                    655:        SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                    656:          SHFT(*fb,*fc,fu,(*func)(u)) 
                    657:          } 
                    658:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                    659:       u=ulim; 
                    660:       fu=(*func)(u); 
                    661:     } else { 
                    662:       u=(*cx)+GOLD*(*cx-*bx); 
                    663:       fu=(*func)(u); 
                    664:     } 
                    665:     SHFT(*ax,*bx,*cx,u) 
                    666:       SHFT(*fa,*fb,*fc,fu) 
                    667:       } 
                    668: } 
                    669: 
                    670: /*************** linmin ************************/
                    671: 
                    672: int ncom; 
                    673: double *pcom,*xicom;
                    674: double (*nrfunc)(double []); 
                    675:  
                    676: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                    677: { 
                    678:   double brent(double ax, double bx, double cx, 
                    679:               double (*f)(double), double tol, double *xmin); 
                    680:   double f1dim(double x); 
                    681:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                    682:              double *fc, double (*func)(double)); 
                    683:   int j; 
                    684:   double xx,xmin,bx,ax; 
                    685:   double fx,fb,fa;
                    686:  
                    687:   ncom=n; 
                    688:   pcom=vector(1,n); 
                    689:   xicom=vector(1,n); 
                    690:   nrfunc=func; 
                    691:   for (j=1;j<=n;j++) { 
                    692:     pcom[j]=p[j]; 
                    693:     xicom[j]=xi[j]; 
                    694:   } 
                    695:   ax=0.0; 
                    696:   xx=1.0; 
                    697:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
                    698:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
                    699: #ifdef DEBUG
                    700:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                    701:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                    702: #endif
                    703:   for (j=1;j<=n;j++) { 
                    704:     xi[j] *= xmin; 
                    705:     p[j] += xi[j]; 
                    706:   } 
                    707:   free_vector(xicom,1,n); 
                    708:   free_vector(pcom,1,n); 
                    709: } 
                    710: 
                    711: /*************** powell ************************/
                    712: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                    713:            double (*func)(double [])) 
                    714: { 
                    715:   void linmin(double p[], double xi[], int n, double *fret, 
                    716:              double (*func)(double [])); 
                    717:   int i,ibig,j; 
                    718:   double del,t,*pt,*ptt,*xit;
                    719:   double fp,fptt;
                    720:   double *xits;
                    721:   pt=vector(1,n); 
                    722:   ptt=vector(1,n); 
                    723:   xit=vector(1,n); 
                    724:   xits=vector(1,n); 
                    725:   *fret=(*func)(p); 
                    726:   for (j=1;j<=n;j++) pt[j]=p[j]; 
                    727:   for (*iter=1;;++(*iter)) { 
                    728:     fp=(*fret); 
                    729:     ibig=0; 
                    730:     del=0.0; 
                    731:     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
                    732:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76      brouard   733:     fprintf(ficrespow,"%d %.12f",*iter,*fret);
                    734:     for (i=1;i<=n;i++) {
1.53      brouard   735:       printf(" %d %.12f",i, p[i]);
1.76      brouard   736:       fprintf(ficlog," %d %.12lf",i, p[i]);
                    737:       fprintf(ficrespow," %.12lf", p[i]);
                    738:     }
1.53      brouard   739:     printf("\n");
                    740:     fprintf(ficlog,"\n");
1.76      brouard   741:     fprintf(ficrespow,"\n");
1.53      brouard   742:     for (i=1;i<=n;i++) { 
                    743:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                    744:       fptt=(*fret); 
                    745: #ifdef DEBUG
                    746:       printf("fret=%lf \n",*fret);
                    747:       fprintf(ficlog,"fret=%lf \n",*fret);
                    748: #endif
                    749:       printf("%d",i);fflush(stdout);
                    750:       fprintf(ficlog,"%d",i);fflush(ficlog);
                    751:       linmin(p,xit,n,fret,func); 
                    752:       if (fabs(fptt-(*fret)) > del) { 
                    753:        del=fabs(fptt-(*fret)); 
                    754:        ibig=i; 
                    755:       } 
                    756: #ifdef DEBUG
                    757:       printf("%d %.12e",i,(*fret));
                    758:       fprintf(ficlog,"%d %.12e",i,(*fret));
                    759:       for (j=1;j<=n;j++) {
                    760:        xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                    761:        printf(" x(%d)=%.12e",j,xit[j]);
                    762:        fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                    763:       }
                    764:       for(j=1;j<=n;j++) {
                    765:        printf(" p=%.12e",p[j]);
                    766:        fprintf(ficlog," p=%.12e",p[j]);
                    767:       }
                    768:       printf("\n");
                    769:       fprintf(ficlog,"\n");
                    770: #endif
                    771:     } 
                    772:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
                    773: #ifdef DEBUG
                    774:       int k[2],l;
                    775:       k[0]=1;
                    776:       k[1]=-1;
                    777:       printf("Max: %.12e",(*func)(p));
                    778:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                    779:       for (j=1;j<=n;j++) {
                    780:        printf(" %.12e",p[j]);
                    781:        fprintf(ficlog," %.12e",p[j]);
                    782:       }
                    783:       printf("\n");
                    784:       fprintf(ficlog,"\n");
                    785:       for(l=0;l<=1;l++) {
                    786:        for (j=1;j<=n;j++) {
                    787:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                    788:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                    789:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                    790:        }
                    791:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                    792:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                    793:       }
                    794: #endif
                    795: 
                    796: 
                    797:       free_vector(xit,1,n); 
                    798:       free_vector(xits,1,n); 
                    799:       free_vector(ptt,1,n); 
                    800:       free_vector(pt,1,n); 
                    801:       return; 
                    802:     } 
                    803:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
                    804:     for (j=1;j<=n;j++) { 
                    805:       ptt[j]=2.0*p[j]-pt[j]; 
                    806:       xit[j]=p[j]-pt[j]; 
                    807:       pt[j]=p[j]; 
                    808:     } 
                    809:     fptt=(*func)(ptt); 
                    810:     if (fptt < fp) { 
                    811:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                    812:       if (t < 0.0) { 
                    813:        linmin(p,xit,n,fret,func); 
                    814:        for (j=1;j<=n;j++) { 
                    815:          xi[j][ibig]=xi[j][n]; 
                    816:          xi[j][n]=xit[j]; 
                    817:        }
                    818: #ifdef DEBUG
                    819:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                    820:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                    821:        for(j=1;j<=n;j++){
                    822:          printf(" %.12e",xit[j]);
                    823:          fprintf(ficlog," %.12e",xit[j]);
                    824:        }
                    825:        printf("\n");
                    826:        fprintf(ficlog,"\n");
                    827: #endif
1.54      brouard   828:       }
1.53      brouard   829:     } 
                    830:   } 
                    831: } 
                    832: 
1.54      brouard   833: /**** Prevalence limit (stable prevalence)  ****************/
1.53      brouard   834: 
                    835: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
                    836: {
                    837:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                    838:      matrix by transitions matrix until convergence is reached */
                    839: 
                    840:   int i, ii,j,k;
                    841:   double min, max, maxmin, maxmax,sumnew=0.;
                    842:   double **matprod2();
                    843:   double **out, cov[NCOVMAX], **pmij();
                    844:   double **newm;
                    845:   double agefin, delaymax=50 ; /* Max number of years to converge */
                    846: 
                    847:   for (ii=1;ii<=nlstate+ndeath;ii++)
                    848:     for (j=1;j<=nlstate+ndeath;j++){
                    849:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    850:     }
                    851: 
                    852:    cov[1]=1.;
                    853:  
                    854:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                    855:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                    856:     newm=savm;
                    857:     /* Covariates have to be included here again */
                    858:      cov[2]=agefin;
                    859:   
                    860:       for (k=1; k<=cptcovn;k++) {
                    861:        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                    862:        /*      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]]);*/
                    863:       }
                    864:       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                    865:       for (k=1; k<=cptcovprod;k++)
                    866:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                    867: 
                    868:       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                    869:       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                    870:       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                    871:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                    872: 
                    873:     savm=oldm;
                    874:     oldm=newm;
                    875:     maxmax=0.;
                    876:     for(j=1;j<=nlstate;j++){
                    877:       min=1.;
                    878:       max=0.;
                    879:       for(i=1; i<=nlstate; i++) {
                    880:        sumnew=0;
                    881:        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                    882:        prlim[i][j]= newm[i][j]/(1-sumnew);
                    883:        max=FMAX(max,prlim[i][j]);
                    884:        min=FMIN(min,prlim[i][j]);
                    885:       }
                    886:       maxmin=max-min;
                    887:       maxmax=FMAX(maxmax,maxmin);
                    888:     }
                    889:     if(maxmax < ftolpl){
                    890:       return prlim;
                    891:     }
                    892:   }
                    893: }
                    894: 
                    895: /*************** transition probabilities ***************/ 
                    896: 
                    897: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                    898: {
                    899:   double s1, s2;
                    900:   /*double t34;*/
                    901:   int i,j,j1, nc, ii, jj;
                    902: 
                    903:     for(i=1; i<= nlstate; i++){
                    904:     for(j=1; j<i;j++){
                    905:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                    906:        /*s2 += param[i][j][nc]*cov[nc];*/
                    907:        s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                    908:        /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
                    909:       }
                    910:       ps[i][j]=s2;
                    911:       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
                    912:     }
                    913:     for(j=i+1; j<=nlstate+ndeath;j++){
                    914:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                    915:        s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                    916:        /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
                    917:       }
                    918:       ps[i][j]=s2;
                    919:     }
                    920:   }
                    921:     /*ps[3][2]=1;*/
                    922: 
                    923:   for(i=1; i<= nlstate; i++){
                    924:      s1=0;
                    925:     for(j=1; j<i; j++)
                    926:       s1+=exp(ps[i][j]);
                    927:     for(j=i+1; j<=nlstate+ndeath; j++)
                    928:       s1+=exp(ps[i][j]);
                    929:     ps[i][i]=1./(s1+1.);
                    930:     for(j=1; j<i; j++)
                    931:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                    932:     for(j=i+1; j<=nlstate+ndeath; j++)
                    933:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                    934:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                    935:   } /* end i */
                    936: 
                    937:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                    938:     for(jj=1; jj<= nlstate+ndeath; jj++){
                    939:       ps[ii][jj]=0;
                    940:       ps[ii][ii]=1;
                    941:     }
                    942:   }
                    943: 
                    944: 
                    945:   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
                    946:     for(jj=1; jj<= nlstate+ndeath; jj++){
                    947:      printf("%lf ",ps[ii][jj]);
                    948:    }
                    949:     printf("\n ");
                    950:     }
                    951:     printf("\n ");printf("%lf ",cov[2]);*/
                    952: /*
                    953:   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                    954:   goto end;*/
                    955:     return ps;
                    956: }
                    957: 
                    958: /**************** Product of 2 matrices ******************/
                    959: 
                    960: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
                    961: {
                    962:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                    963:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                    964:   /* in, b, out are matrice of pointers which should have been initialized 
                    965:      before: only the contents of out is modified. The function returns
                    966:      a pointer to pointers identical to out */
                    967:   long i, j, k;
                    968:   for(i=nrl; i<= nrh; i++)
                    969:     for(k=ncolol; k<=ncoloh; k++)
                    970:       for(j=ncl,out[i][k]=0.; j<=nch; j++)
                    971:        out[i][k] +=in[i][j]*b[j][k];
                    972: 
                    973:   return out;
                    974: }
                    975: 
                    976: 
                    977: /************* Higher Matrix Product ***************/
                    978: 
                    979: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                    980: {
1.66      brouard   981:   /* Computes the transition matrix starting at age 'age' over 
                    982:      'nhstepm*hstepm*stepm' months (i.e. until
                    983:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                    984:      nhstepm*hstepm matrices. 
1.53      brouard   985:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
1.66      brouard   986:      (typically every 2 years instead of every month which is too big 
                    987:      for the memory).
1.53      brouard   988:      Model is determined by parameters x and covariates have to be 
                    989:      included manually here. 
                    990: 
                    991:      */
                    992: 
                    993:   int i, j, d, h, k;
                    994:   double **out, cov[NCOVMAX];
                    995:   double **newm;
                    996: 
                    997:   /* Hstepm could be zero and should return the unit matrix */
                    998:   for (i=1;i<=nlstate+ndeath;i++)
                    999:     for (j=1;j<=nlstate+ndeath;j++){
                   1000:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   1001:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   1002:     }
                   1003:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   1004:   for(h=1; h <=nhstepm; h++){
                   1005:     for(d=1; d <=hstepm; d++){
                   1006:       newm=savm;
                   1007:       /* Covariates have to be included here again */
                   1008:       cov[1]=1.;
                   1009:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                   1010:       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                   1011:       for (k=1; k<=cptcovage;k++)
                   1012:        cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   1013:       for (k=1; k<=cptcovprod;k++)
                   1014:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   1015: 
                   1016: 
                   1017:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   1018:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                   1019:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   1020:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1021:       savm=oldm;
                   1022:       oldm=newm;
                   1023:     }
                   1024:     for(i=1; i<=nlstate+ndeath; i++)
                   1025:       for(j=1;j<=nlstate+ndeath;j++) {
                   1026:        po[i][j][h]=newm[i][j];
                   1027:        /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                   1028:         */
                   1029:       }
                   1030:   } /* end h */
                   1031:   return po;
                   1032: }
                   1033: 
                   1034: 
                   1035: /*************** log-likelihood *************/
                   1036: double func( double *x)
                   1037: {
                   1038:   int i, ii, j, k, mi, d, kk;
                   1039:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
                   1040:   double **out;
                   1041:   double sw; /* Sum of weights */
                   1042:   double lli; /* Individual log likelihood */
1.59      brouard  1043:   int s1, s2;
1.68      lievre   1044:   double bbh, survp;
1.53      brouard  1045:   long ipmx;
                   1046:   /*extern weight */
                   1047:   /* We are differentiating ll according to initial status */
                   1048:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1049:   /*for(i=1;i<imx;i++) 
                   1050:     printf(" %d\n",s[4][i]);
                   1051:   */
                   1052:   cov[1]=1.;
                   1053: 
                   1054:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61      brouard  1055: 
                   1056:   if(mle==1){
                   1057:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1058:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1059:       for(mi=1; mi<= wav[i]-1; mi++){
                   1060:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1061:          for (j=1;j<=nlstate+ndeath;j++){
                   1062:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1063:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1064:          }
                   1065:        for(d=0; d<dh[mi][i]; d++){
                   1066:          newm=savm;
                   1067:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1068:          for (kk=1; kk<=cptcovage;kk++) {
                   1069:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1070:          }
                   1071:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1072:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1073:          savm=oldm;
                   1074:          oldm=newm;
                   1075:        } /* end mult */
1.53      brouard  1076:       
1.61      brouard  1077:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1078:        /* But now since version 0.9 we anticipate for bias and large stepm.
                   1079:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1080:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1081:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1082:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1083:         * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                   1084:         * probability in order to take into account the bias as a fraction of the way
                   1085:         * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                   1086:         * -stepm/2 to stepm/2 .
                   1087:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1088:         * For stepm > 1 the results are less biased than in previous versions. 
                   1089:         */
                   1090:        s1=s[mw[mi][i]][i];
                   1091:        s2=s[mw[mi+1][i]][i];
1.64      lievre   1092:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1093:        /* bias is positive if real duration
                   1094:         * is higher than the multiple of stepm and negative otherwise.
                   1095:         */
                   1096:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71      brouard  1097:        if( s2 > nlstate){ 
                   1098:          /* i.e. if s2 is a death state and if the date of death is known then the contribution
                   1099:             to the likelihood is the probability to die between last step unit time and current 
                   1100:             step unit time, which is also the differences between probability to die before dh 
                   1101:             and probability to die before dh-stepm . 
                   1102:             In version up to 0.92 likelihood was computed
                   1103:        as if date of death was unknown. Death was treated as any other
                   1104:        health state: the date of the interview describes the actual state
                   1105:        and not the date of a change in health state. The former idea was
                   1106:        to consider that at each interview the state was recorded
                   1107:        (healthy, disable or death) and IMaCh was corrected; but when we
                   1108:        introduced the exact date of death then we should have modified
                   1109:        the contribution of an exact death to the likelihood. This new
                   1110:        contribution is smaller and very dependent of the step unit
                   1111:        stepm. It is no more the probability to die between last interview
                   1112:        and month of death but the probability to survive from last
                   1113:        interview up to one month before death multiplied by the
                   1114:        probability to die within a month. Thanks to Chris
                   1115:        Jackson for correcting this bug.  Former versions increased
                   1116:        mortality artificially. The bad side is that we add another loop
                   1117:        which slows down the processing. The difference can be up to 10%
                   1118:        lower mortality.
                   1119:          */
                   1120:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1121:        }else{
                   1122:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1123:          /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                   1124:        } 
1.64      lievre   1125:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   1126:        /*if(lli ==000.0)*/
                   1127:        /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.71      brouard  1128:        ipmx +=1;
1.64      lievre   1129:        sw += weight[i];
                   1130:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1131:       } /* end of wave */
                   1132:     } /* end of individual */
                   1133:   }  else if(mle==2){
                   1134:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1135:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1136:       for(mi=1; mi<= wav[i]-1; mi++){
                   1137:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1138:          for (j=1;j<=nlstate+ndeath;j++){
                   1139:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1140:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1141:          }
                   1142:        for(d=0; d<=dh[mi][i]; d++){
                   1143:          newm=savm;
                   1144:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1145:          for (kk=1; kk<=cptcovage;kk++) {
                   1146:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1147:          }
                   1148:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1149:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1150:          savm=oldm;
                   1151:          oldm=newm;
                   1152:        } /* end mult */
                   1153:       
                   1154:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1155:        /* But now since version 0.9 we anticipate for bias and large stepm.
                   1156:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1157:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1158:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1159:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1160:         * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                   1161:         * probability in order to take into account the bias as a fraction of the way
                   1162:         * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                   1163:         * -stepm/2 to stepm/2 .
                   1164:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1165:         * For stepm > 1 the results are less biased than in previous versions. 
                   1166:         */
                   1167:        s1=s[mw[mi][i]][i];
                   1168:        s2=s[mw[mi+1][i]][i];
                   1169:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1170:        /* bias is positive if real duration
                   1171:         * is higher than the multiple of stepm and negative otherwise.
                   1172:         */
1.63      lievre   1173:        lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64      lievre   1174:        /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                   1175:        /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
                   1176:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   1177:        /*if(lli ==000.0)*/
                   1178:        /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                   1179:        ipmx +=1;
                   1180:        sw += weight[i];
                   1181:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1182:       } /* end of wave */
                   1183:     } /* end of individual */
                   1184:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   1185:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1186:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1187:       for(mi=1; mi<= wav[i]-1; mi++){
                   1188:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1189:          for (j=1;j<=nlstate+ndeath;j++){
                   1190:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1191:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1192:          }
                   1193:        for(d=0; d<dh[mi][i]; d++){
                   1194:          newm=savm;
                   1195:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1196:          for (kk=1; kk<=cptcovage;kk++) {
                   1197:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1198:          }
                   1199:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1200:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1201:          savm=oldm;
                   1202:          oldm=newm;
                   1203:        } /* end mult */
                   1204:       
                   1205:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1206:        /* But now since version 0.9 we anticipate for bias and large stepm.
                   1207:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1208:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1209:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1210:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1211:         * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                   1212:         * probability in order to take into account the bias as a fraction of the way
                   1213:         * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                   1214:         * -stepm/2 to stepm/2 .
                   1215:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1216:         * For stepm > 1 the results are less biased than in previous versions. 
                   1217:         */
                   1218:        s1=s[mw[mi][i]][i];
                   1219:        s2=s[mw[mi+1][i]][i];
                   1220:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1221:        /* bias is positive if real duration
                   1222:         * is higher than the multiple of stepm and negative otherwise.
                   1223:         */
                   1224:        /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
                   1225:        lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61      brouard  1226:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   1227:        /*if(lli ==000.0)*/
                   1228:        /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                   1229:        ipmx +=1;
                   1230:        sw += weight[i];
                   1231:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1232:       } /* end of wave */
                   1233:     } /* end of individual */
1.84      brouard  1234:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
1.61      brouard  1235:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1236:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1237:       for(mi=1; mi<= wav[i]-1; mi++){
                   1238:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1239:          for (j=1;j<=nlstate+ndeath;j++){
                   1240:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1241:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1242:          }
                   1243:        for(d=0; d<dh[mi][i]; d++){
                   1244:          newm=savm;
                   1245:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1246:          for (kk=1; kk<=cptcovage;kk++) {
                   1247:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1248:          }
                   1249:        
                   1250:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1251:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1252:          savm=oldm;
                   1253:          oldm=newm;
                   1254:        } /* end mult */
                   1255:       
1.84      brouard  1256:        s1=s[mw[mi][i]][i];
                   1257:        s2=s[mw[mi+1][i]][i];
                   1258:        if( s2 > nlstate){ 
                   1259:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1260:        }else{
                   1261:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1262:        }
                   1263:        ipmx +=1;
                   1264:        sw += weight[i];
                   1265:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85      brouard  1266: /*     printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.84      brouard  1267:       } /* end of wave */
                   1268:     } /* end of individual */
                   1269:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   1270:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1271:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1272:       for(mi=1; mi<= wav[i]-1; mi++){
                   1273:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1274:          for (j=1;j<=nlstate+ndeath;j++){
                   1275:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1276:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1277:          }
                   1278:        for(d=0; d<dh[mi][i]; d++){
                   1279:          newm=savm;
                   1280:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1281:          for (kk=1; kk<=cptcovage;kk++) {
                   1282:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1283:          }
                   1284:        
                   1285:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1286:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1287:          savm=oldm;
                   1288:          oldm=newm;
                   1289:        } /* end mult */
                   1290:       
                   1291:        s1=s[mw[mi][i]][i];
                   1292:        s2=s[mw[mi+1][i]][i];
1.61      brouard  1293:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1294:        ipmx +=1;
                   1295:        sw += weight[i];
                   1296:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84      brouard  1297:        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1.61      brouard  1298:       } /* end of wave */
                   1299:     } /* end of individual */
                   1300:   } /* End of if */
1.53      brouard  1301:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1302:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1303:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85      brouard  1304:   return -l;
                   1305: }
                   1306: 
                   1307: /*************** log-likelihood *************/
                   1308: double funcone( double *x)
                   1309: {
1.87      brouard  1310:   /* Same as likeli but slower because of a lot of printf and if */
1.85      brouard  1311:   int i, ii, j, k, mi, d, kk;
                   1312:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
                   1313:   double **out;
                   1314:   double lli; /* Individual log likelihood */
1.87      brouard  1315:   double llt;
1.85      brouard  1316:   int s1, s2;
                   1317:   double bbh, survp;
                   1318:   /*extern weight */
                   1319:   /* We are differentiating ll according to initial status */
                   1320:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1321:   /*for(i=1;i<imx;i++) 
                   1322:     printf(" %d\n",s[4][i]);
                   1323:   */
                   1324:   cov[1]=1.;
                   1325: 
                   1326:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   1327: 
                   1328:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1329:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1330:     for(mi=1; mi<= wav[i]-1; mi++){
                   1331:       for (ii=1;ii<=nlstate+ndeath;ii++)
                   1332:        for (j=1;j<=nlstate+ndeath;j++){
                   1333:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1334:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1335:        }
                   1336:       for(d=0; d<dh[mi][i]; d++){
                   1337:        newm=savm;
                   1338:        cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1339:        for (kk=1; kk<=cptcovage;kk++) {
                   1340:          cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1341:        }
                   1342:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1343:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1344:        savm=oldm;
                   1345:        oldm=newm;
                   1346:       } /* end mult */
                   1347:       
                   1348:       s1=s[mw[mi][i]][i];
                   1349:       s2=s[mw[mi+1][i]][i];
                   1350:       bbh=(double)bh[mi][i]/(double)stepm; 
                   1351:       /* bias is positive if real duration
                   1352:        * is higher than the multiple of stepm and negative otherwise.
                   1353:        */
                   1354:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
                   1355:        lli=log(out[s1][s2] - savm[s1][s2]);
                   1356:       } else if (mle==1){
                   1357:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1358:       } else if(mle==2){
                   1359:        lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                   1360:       } else if(mle==3){  /* exponential inter-extrapolation */
                   1361:        lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                   1362:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
                   1363:        lli=log(out[s1][s2]); /* Original formula */
                   1364:       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
                   1365:        lli=log(out[s1][s2]); /* Original formula */
                   1366:       } /* End of if */
                   1367:       ipmx +=1;
                   1368:       sw += weight[i];
                   1369:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1370: /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
                   1371:       if(globpr){
1.88      brouard  1372:        fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86      brouard  1373:  %10.6f %10.6f %10.6f ", \
                   1374:                num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   1375:                2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87      brouard  1376:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   1377:          llt +=ll[k]*gipmx/gsw;
                   1378:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   1379:        }
                   1380:        fprintf(ficresilk," %10.6f\n", -llt);
1.85      brouard  1381:       }
                   1382:     } /* end of wave */
                   1383:   } /* end of individual */
                   1384:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1385:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1386:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87      brouard  1387:   if(globpr==0){ /* First time we count the contributions and weights */
                   1388:     gipmx=ipmx;
                   1389:     gsw=sw;
                   1390:   }
1.53      brouard  1391:   return -l;
                   1392: }
                   1393: 
1.88      brouard  1394: char *subdirf(char fileres[])
                   1395: {
                   1396:   
                   1397:   strcpy(tmpout,optionfilefiname);
                   1398:   strcat(tmpout,"/"); /* Add to the right */
                   1399:   strcat(tmpout,fileres);
                   1400:   return tmpout;
                   1401: }
                   1402: 
                   1403: char *subdirf2(char fileres[], char *preop)
                   1404: {
                   1405:   
                   1406:   strcpy(tmpout,optionfilefiname);
                   1407:   strcat(tmpout,"/");
                   1408:   strcat(tmpout,preop);
                   1409:   strcat(tmpout,fileres);
                   1410:   return tmpout;
                   1411: }
                   1412: char *subdirf3(char fileres[], char *preop, char *preop2)
                   1413: {
                   1414:   
                   1415:   strcpy(tmpout,optionfilefiname);
                   1416:   strcat(tmpout,"/");
                   1417:   strcat(tmpout,preop);
                   1418:   strcat(tmpout,preop2);
                   1419:   strcat(tmpout,fileres);
                   1420:   return tmpout;
                   1421: }
1.53      brouard  1422: 
1.87      brouard  1423: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85      brouard  1424: {
1.87      brouard  1425:   /* This routine should help understanding what is done with 
                   1426:      the selection of individuals/waves and
1.85      brouard  1427:      to check the exact contribution to the likelihood.
                   1428:      Plotting could be done.
                   1429:    */
                   1430:   int k;
1.87      brouard  1431: 
1.88      brouard  1432:   if(*globpri !=0){ /* Just counts and sums, no printings */
1.85      brouard  1433:     strcpy(fileresilk,"ilk"); 
                   1434:     strcat(fileresilk,fileres);
                   1435:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   1436:       printf("Problem with resultfile: %s\n", fileresilk);
                   1437:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   1438:     }
1.87      brouard  1439:     fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1.88      brouard  1440:     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85      brouard  1441:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   1442:     for(k=1; k<=nlstate; k++) 
1.87      brouard  1443:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   1444:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85      brouard  1445:   }
                   1446: 
                   1447:   *fretone=(*funcone)(p);
1.87      brouard  1448:   if(*globpri !=0){
1.85      brouard  1449:     fclose(ficresilk);
1.88      brouard  1450:     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87      brouard  1451:     fflush(fichtm); 
                   1452:   } 
1.85      brouard  1453:   return;
                   1454: }
                   1455: 
1.88      brouard  1456: 
1.53      brouard  1457: /*********** Maximum Likelihood Estimation ***************/
                   1458: 
                   1459: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   1460: {
                   1461:   int i,j, iter;
1.74      brouard  1462:   double **xi;
1.53      brouard  1463:   double fret;
1.85      brouard  1464:   double fretone; /* Only one call to likelihood */
1.76      brouard  1465:   char filerespow[FILENAMELENGTH];
1.53      brouard  1466:   xi=matrix(1,npar,1,npar);
                   1467:   for (i=1;i<=npar;i++)
                   1468:     for (j=1;j<=npar;j++)
                   1469:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   1470:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.76      brouard  1471:   strcpy(filerespow,"pow"); 
                   1472:   strcat(filerespow,fileres);
                   1473:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   1474:     printf("Problem with resultfile: %s\n", filerespow);
                   1475:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   1476:   }
                   1477:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   1478:   for (i=1;i<=nlstate;i++)
                   1479:     for(j=1;j<=nlstate+ndeath;j++)
                   1480:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   1481:   fprintf(ficrespow,"\n");
1.85      brouard  1482: 
1.53      brouard  1483:   powell(p,xi,npar,ftol,&iter,&fret,func);
                   1484: 
1.76      brouard  1485:   fclose(ficrespow);
                   1486:   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65      lievre   1487:   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53      brouard  1488:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                   1489: 
                   1490: }
                   1491: 
                   1492: /**** Computes Hessian and covariance matrix ***/
                   1493: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                   1494: {
                   1495:   double  **a,**y,*x,pd;
                   1496:   double **hess;
                   1497:   int i, j,jk;
                   1498:   int *indx;
                   1499: 
                   1500:   double hessii(double p[], double delta, int theta, double delti[]);
                   1501:   double hessij(double p[], double delti[], int i, int j);
                   1502:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   1503:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   1504: 
                   1505:   hess=matrix(1,npar,1,npar);
                   1506: 
                   1507:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   1508:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   1509:   for (i=1;i<=npar;i++){
                   1510:     printf("%d",i);fflush(stdout);
                   1511:     fprintf(ficlog,"%d",i);fflush(ficlog);
                   1512:     hess[i][i]=hessii(p,ftolhess,i,delti);
                   1513:     /*printf(" %f ",p[i]);*/
                   1514:     /*printf(" %lf ",hess[i][i]);*/
                   1515:   }
                   1516:   
                   1517:   for (i=1;i<=npar;i++) {
                   1518:     for (j=1;j<=npar;j++)  {
                   1519:       if (j>i) { 
                   1520:        printf(".%d%d",i,j);fflush(stdout);
                   1521:        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                   1522:        hess[i][j]=hessij(p,delti,i,j);
                   1523:        hess[j][i]=hess[i][j];    
                   1524:        /*printf(" %lf ",hess[i][j]);*/
                   1525:       }
                   1526:     }
                   1527:   }
                   1528:   printf("\n");
                   1529:   fprintf(ficlog,"\n");
                   1530: 
                   1531:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   1532:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   1533:   
                   1534:   a=matrix(1,npar,1,npar);
                   1535:   y=matrix(1,npar,1,npar);
                   1536:   x=vector(1,npar);
                   1537:   indx=ivector(1,npar);
                   1538:   for (i=1;i<=npar;i++)
                   1539:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   1540:   ludcmp(a,npar,indx,&pd);
                   1541: 
                   1542:   for (j=1;j<=npar;j++) {
                   1543:     for (i=1;i<=npar;i++) x[i]=0;
                   1544:     x[j]=1;
                   1545:     lubksb(a,npar,indx,x);
                   1546:     for (i=1;i<=npar;i++){ 
                   1547:       matcov[i][j]=x[i];
                   1548:     }
                   1549:   }
                   1550: 
                   1551:   printf("\n#Hessian matrix#\n");
                   1552:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   1553:   for (i=1;i<=npar;i++) { 
                   1554:     for (j=1;j<=npar;j++) { 
                   1555:       printf("%.3e ",hess[i][j]);
                   1556:       fprintf(ficlog,"%.3e ",hess[i][j]);
                   1557:     }
                   1558:     printf("\n");
                   1559:     fprintf(ficlog,"\n");
                   1560:   }
                   1561: 
                   1562:   /* Recompute Inverse */
                   1563:   for (i=1;i<=npar;i++)
                   1564:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
                   1565:   ludcmp(a,npar,indx,&pd);
                   1566: 
                   1567:   /*  printf("\n#Hessian matrix recomputed#\n");
                   1568: 
                   1569:   for (j=1;j<=npar;j++) {
                   1570:     for (i=1;i<=npar;i++) x[i]=0;
                   1571:     x[j]=1;
                   1572:     lubksb(a,npar,indx,x);
                   1573:     for (i=1;i<=npar;i++){ 
                   1574:       y[i][j]=x[i];
                   1575:       printf("%.3e ",y[i][j]);
                   1576:       fprintf(ficlog,"%.3e ",y[i][j]);
                   1577:     }
                   1578:     printf("\n");
                   1579:     fprintf(ficlog,"\n");
                   1580:   }
                   1581:   */
                   1582: 
                   1583:   free_matrix(a,1,npar,1,npar);
                   1584:   free_matrix(y,1,npar,1,npar);
                   1585:   free_vector(x,1,npar);
                   1586:   free_ivector(indx,1,npar);
                   1587:   free_matrix(hess,1,npar,1,npar);
                   1588: 
                   1589: 
                   1590: }
                   1591: 
                   1592: /*************** hessian matrix ****************/
                   1593: double hessii( double x[], double delta, int theta, double delti[])
                   1594: {
                   1595:   int i;
                   1596:   int l=1, lmax=20;
                   1597:   double k1,k2;
                   1598:   double p2[NPARMAX+1];
                   1599:   double res;
                   1600:   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   1601:   double fx;
                   1602:   int k=0,kmax=10;
                   1603:   double l1;
                   1604: 
                   1605:   fx=func(x);
                   1606:   for (i=1;i<=npar;i++) p2[i]=x[i];
                   1607:   for(l=0 ; l <=lmax; l++){
                   1608:     l1=pow(10,l);
                   1609:     delts=delt;
                   1610:     for(k=1 ; k <kmax; k=k+1){
                   1611:       delt = delta*(l1*k);
                   1612:       p2[theta]=x[theta] +delt;
                   1613:       k1=func(p2)-fx;
                   1614:       p2[theta]=x[theta]-delt;
                   1615:       k2=func(p2)-fx;
                   1616:       /*res= (k1-2.0*fx+k2)/delt/delt; */
                   1617:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   1618:       
                   1619: #ifdef DEBUG
                   1620:       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);
                   1621:       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                   1622: #endif
                   1623:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   1624:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   1625:        k=kmax;
                   1626:       }
                   1627:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                   1628:        k=kmax; l=lmax*10.;
                   1629:       }
                   1630:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   1631:        delts=delt;
                   1632:       }
                   1633:     }
                   1634:   }
                   1635:   delti[theta]=delts;
                   1636:   return res; 
                   1637:   
                   1638: }
                   1639: 
                   1640: double hessij( double x[], double delti[], int thetai,int thetaj)
                   1641: {
                   1642:   int i;
                   1643:   int l=1, l1, lmax=20;
                   1644:   double k1,k2,k3,k4,res,fx;
                   1645:   double p2[NPARMAX+1];
                   1646:   int k;
                   1647: 
                   1648:   fx=func(x);
                   1649:   for (k=1; k<=2; k++) {
                   1650:     for (i=1;i<=npar;i++) p2[i]=x[i];
                   1651:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   1652:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   1653:     k1=func(p2)-fx;
                   1654:   
                   1655:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   1656:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   1657:     k2=func(p2)-fx;
                   1658:   
                   1659:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   1660:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   1661:     k3=func(p2)-fx;
                   1662:   
                   1663:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   1664:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   1665:     k4=func(p2)-fx;
                   1666:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   1667: #ifdef DEBUG
                   1668:     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);
                   1669:     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
                   1670: #endif
                   1671:   }
                   1672:   return res;
                   1673: }
                   1674: 
                   1675: /************** Inverse of matrix **************/
                   1676: void ludcmp(double **a, int n, int *indx, double *d) 
                   1677: { 
                   1678:   int i,imax,j,k; 
                   1679:   double big,dum,sum,temp; 
                   1680:   double *vv; 
                   1681:  
                   1682:   vv=vector(1,n); 
                   1683:   *d=1.0; 
                   1684:   for (i=1;i<=n;i++) { 
                   1685:     big=0.0; 
                   1686:     for (j=1;j<=n;j++) 
                   1687:       if ((temp=fabs(a[i][j])) > big) big=temp; 
                   1688:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   1689:     vv[i]=1.0/big; 
                   1690:   } 
                   1691:   for (j=1;j<=n;j++) { 
                   1692:     for (i=1;i<j;i++) { 
                   1693:       sum=a[i][j]; 
                   1694:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   1695:       a[i][j]=sum; 
                   1696:     } 
                   1697:     big=0.0; 
                   1698:     for (i=j;i<=n;i++) { 
                   1699:       sum=a[i][j]; 
                   1700:       for (k=1;k<j;k++) 
                   1701:        sum -= a[i][k]*a[k][j]; 
                   1702:       a[i][j]=sum; 
                   1703:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   1704:        big=dum; 
                   1705:        imax=i; 
                   1706:       } 
                   1707:     } 
                   1708:     if (j != imax) { 
                   1709:       for (k=1;k<=n;k++) { 
                   1710:        dum=a[imax][k]; 
                   1711:        a[imax][k]=a[j][k]; 
                   1712:        a[j][k]=dum; 
                   1713:       } 
                   1714:       *d = -(*d); 
                   1715:       vv[imax]=vv[j]; 
                   1716:     } 
                   1717:     indx[j]=imax; 
                   1718:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   1719:     if (j != n) { 
                   1720:       dum=1.0/(a[j][j]); 
                   1721:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   1722:     } 
                   1723:   } 
                   1724:   free_vector(vv,1,n);  /* Doesn't work */
                   1725: ;
                   1726: } 
                   1727: 
                   1728: void lubksb(double **a, int n, int *indx, double b[]) 
                   1729: { 
                   1730:   int i,ii=0,ip,j; 
                   1731:   double sum; 
                   1732:  
                   1733:   for (i=1;i<=n;i++) { 
                   1734:     ip=indx[i]; 
                   1735:     sum=b[ip]; 
                   1736:     b[ip]=b[i]; 
                   1737:     if (ii) 
                   1738:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   1739:     else if (sum) ii=i; 
                   1740:     b[i]=sum; 
                   1741:   } 
                   1742:   for (i=n;i>=1;i--) { 
                   1743:     sum=b[i]; 
                   1744:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   1745:     b[i]=sum/a[i][i]; 
                   1746:   } 
                   1747: } 
                   1748: 
                   1749: /************ Frequencies ********************/
1.84      brouard  1750: void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
1.53      brouard  1751: {  /* Some frequencies */
                   1752:   
                   1753:   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
                   1754:   int first;
                   1755:   double ***freq; /* Frequencies */
1.73      lievre   1756:   double *pp, **prop;
                   1757:   double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53      brouard  1758:   FILE *ficresp;
                   1759:   char fileresp[FILENAMELENGTH];
                   1760:   
                   1761:   pp=vector(1,nlstate);
1.74      brouard  1762:   prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53      brouard  1763:   strcpy(fileresp,"p");
                   1764:   strcat(fileresp,fileres);
                   1765:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   1766:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   1767:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   1768:     exit(0);
                   1769:   }
1.74      brouard  1770:   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53      brouard  1771:   j1=0;
                   1772:   
                   1773:   j=cptcoveff;
                   1774:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   1775: 
                   1776:   first=1;
                   1777: 
                   1778:   for(k1=1; k1<=j;k1++){
                   1779:     for(i1=1; i1<=ncodemax[k1];i1++){
                   1780:       j1++;
                   1781:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   1782:        scanf("%d", i);*/
                   1783:       for (i=-1; i<=nlstate+ndeath; i++)  
                   1784:        for (jk=-1; jk<=nlstate+ndeath; jk++)  
1.74      brouard  1785:          for(m=iagemin; m <= iagemax+3; m++)
1.53      brouard  1786:            freq[i][jk][m]=0;
1.73      lievre   1787: 
                   1788:     for (i=1; i<=nlstate; i++)  
1.74      brouard  1789:       for(m=iagemin; m <= iagemax+3; m++)
1.73      lievre   1790:        prop[i][m]=0;
1.53      brouard  1791:       
                   1792:       dateintsum=0;
                   1793:       k2cpt=0;
                   1794:       for (i=1; i<=imx; i++) {
                   1795:        bool=1;
                   1796:        if  (cptcovn>0) {
                   1797:          for (z1=1; z1<=cptcoveff; z1++) 
                   1798:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   1799:              bool=0;
                   1800:        }
1.58      lievre   1801:        if (bool==1){
1.53      brouard  1802:          for(m=firstpass; m<=lastpass; m++){
                   1803:            k2=anint[m][i]+(mint[m][i]/12.);
1.84      brouard  1804:            /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74      brouard  1805:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   1806:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73      lievre   1807:              if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53      brouard  1808:              if (m<lastpass) {
                   1809:                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74      brouard  1810:                freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53      brouard  1811:              }
                   1812:              
1.74      brouard  1813:              if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53      brouard  1814:                dateintsum=dateintsum+k2;
                   1815:                k2cpt++;
                   1816:              }
1.84      brouard  1817:              /*}*/
1.53      brouard  1818:          }
                   1819:        }
                   1820:       }
                   1821:        
1.84      brouard  1822:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53      brouard  1823: 
                   1824:       if  (cptcovn>0) {
                   1825:        fprintf(ficresp, "\n#********** Variable "); 
                   1826:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   1827:        fprintf(ficresp, "**********\n#");
                   1828:       }
                   1829:       for(i=1; i<=nlstate;i++) 
                   1830:        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                   1831:       fprintf(ficresp, "\n");
                   1832:       
1.74      brouard  1833:       for(i=iagemin; i <= iagemax+3; i++){
                   1834:        if(i==iagemax+3){
1.53      brouard  1835:          fprintf(ficlog,"Total");
                   1836:        }else{
                   1837:          if(first==1){
                   1838:            first=0;
                   1839:            printf("See log file for details...\n");
                   1840:          }
                   1841:          fprintf(ficlog,"Age %d", i);
                   1842:        }
                   1843:        for(jk=1; jk <=nlstate ; jk++){
                   1844:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                   1845:            pp[jk] += freq[jk][m][i]; 
                   1846:        }
                   1847:        for(jk=1; jk <=nlstate ; jk++){
                   1848:          for(m=-1, pos=0; m <=0 ; m++)
                   1849:            pos += freq[jk][m][i];
                   1850:          if(pp[jk]>=1.e-10){
                   1851:            if(first==1){
                   1852:            printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   1853:            }
                   1854:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   1855:          }else{
                   1856:            if(first==1)
                   1857:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   1858:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   1859:          }
                   1860:        }
                   1861: 
                   1862:        for(jk=1; jk <=nlstate ; jk++){
                   1863:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                   1864:            pp[jk] += freq[jk][m][i];
1.73      lievre   1865:        }       
                   1866:        for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                   1867:          pos += pp[jk];
                   1868:          posprop += prop[jk][i];
1.53      brouard  1869:        }
                   1870:        for(jk=1; jk <=nlstate ; jk++){
                   1871:          if(pos>=1.e-5){
                   1872:            if(first==1)
                   1873:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   1874:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   1875:          }else{
                   1876:            if(first==1)
                   1877:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   1878:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   1879:          }
1.74      brouard  1880:          if( i <= iagemax){
1.53      brouard  1881:            if(pos>=1.e-5){
1.73      lievre   1882:              fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84      brouard  1883:              /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53      brouard  1884:              /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                   1885:            }
                   1886:            else
1.73      lievre   1887:              fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53      brouard  1888:          }
                   1889:        }
                   1890:        
1.69      brouard  1891:        for(jk=-1; jk <=nlstate+ndeath; jk++)
                   1892:          for(m=-1; m <=nlstate+ndeath; m++)
1.53      brouard  1893:            if(freq[jk][m][i] !=0 ) {
                   1894:            if(first==1)
                   1895:              printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                   1896:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                   1897:            }
1.74      brouard  1898:        if(i <= iagemax)
1.53      brouard  1899:          fprintf(ficresp,"\n");
                   1900:        if(first==1)
                   1901:          printf("Others in log...\n");
                   1902:        fprintf(ficlog,"\n");
                   1903:       }
                   1904:     }
                   1905:   }
                   1906:   dateintmean=dateintsum/k2cpt; 
                   1907:  
                   1908:   fclose(ficresp);
1.74      brouard  1909:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53      brouard  1910:   free_vector(pp,1,nlstate);
1.74      brouard  1911:   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53      brouard  1912:   /* End of Freq */
                   1913: }
                   1914: 
                   1915: /************ Prevalence ********************/
1.84      brouard  1916: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1.69      brouard  1917: {  
                   1918:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   1919:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   1920:      We still use firstpass and lastpass as another selection.
                   1921:   */
1.53      brouard  1922:  
                   1923:   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
                   1924:   double ***freq; /* Frequencies */
1.73      lievre   1925:   double *pp, **prop;
                   1926:   double pos,posprop; 
1.69      brouard  1927:   double  y2; /* in fractional years */
1.74      brouard  1928:   int iagemin, iagemax;
1.53      brouard  1929: 
1.74      brouard  1930:   iagemin= (int) agemin;
                   1931:   iagemax= (int) agemax;
                   1932:   /*pp=vector(1,nlstate);*/
                   1933:   prop=matrix(1,nlstate,iagemin,iagemax+3); 
                   1934:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53      brouard  1935:   j1=0;
                   1936:   
                   1937:   j=cptcoveff;
                   1938:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   1939:   
                   1940:   for(k1=1; k1<=j;k1++){
                   1941:     for(i1=1; i1<=ncodemax[k1];i1++){
                   1942:       j1++;
                   1943:       
1.73      lievre   1944:       for (i=1; i<=nlstate; i++)  
1.74      brouard  1945:        for(m=iagemin; m <= iagemax+3; m++)
                   1946:          prop[i][m]=0.0;
1.53      brouard  1947:      
1.69      brouard  1948:       for (i=1; i<=imx; i++) { /* Each individual */
1.53      brouard  1949:        bool=1;
                   1950:        if  (cptcovn>0) {
                   1951:          for (z1=1; z1<=cptcoveff; z1++) 
                   1952:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   1953:              bool=0;
                   1954:        } 
                   1955:        if (bool==1) { 
1.69      brouard  1956:          for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                   1957:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   1958:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74      brouard  1959:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   1960:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   1961:              if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                   1962:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   1963:                /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   1964:                prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   1965:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   1966:              } 
1.53      brouard  1967:            }
1.69      brouard  1968:          } /* end selection of waves */
1.53      brouard  1969:        }
                   1970:       }
1.74      brouard  1971:       for(i=iagemin; i <= iagemax+3; i++){  
1.53      brouard  1972:        
1.74      brouard  1973:        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   1974:          posprop += prop[jk][i]; 
                   1975:        } 
                   1976: 
                   1977:        for(jk=1; jk <=nlstate ; jk++){     
                   1978:          if( i <=  iagemax){ 
                   1979:            if(posprop>=1.e-5){ 
                   1980:              probs[i][jk][j1]= prop[jk][i]/posprop;
                   1981:            } 
                   1982:          } 
                   1983:        }/* end jk */ 
                   1984:       }/* end i */ 
1.53      brouard  1985:     } /* end i1 */
                   1986:   } /* end k1 */
                   1987:   
1.74      brouard  1988:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   1989:   /*free_vector(pp,1,nlstate);*/
                   1990:   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   1991: }  /* End of prevalence */
1.53      brouard  1992: 
                   1993: /************* Waves Concatenation ***************/
                   1994: 
1.59      brouard  1995: void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
1.53      brouard  1996: {
                   1997:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   1998:      Death is a valid wave (if date is known).
                   1999:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
1.59      brouard  2000:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53      brouard  2001:      and mw[mi+1][i]. dh depends on stepm.
                   2002:      */
                   2003: 
                   2004:   int i, mi, m;
                   2005:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   2006:      double sum=0., jmean=0.;*/
                   2007:   int first;
                   2008:   int j, k=0,jk, ju, jl;
                   2009:   double sum=0.;
                   2010:   first=0;
                   2011:   jmin=1e+5;
                   2012:   jmax=-1;
                   2013:   jmean=0.;
                   2014:   for(i=1; i<=imx; i++){
                   2015:     mi=0;
                   2016:     m=firstpass;
                   2017:     while(s[m][i] <= nlstate){
1.69      brouard  2018:       if(s[m][i]>=1)
1.53      brouard  2019:        mw[++mi][i]=m;
                   2020:       if(m >=lastpass)
                   2021:        break;
                   2022:       else
                   2023:        m++;
                   2024:     }/* end while */
                   2025:     if (s[m][i] > nlstate){
                   2026:       mi++;    /* Death is another wave */
                   2027:       /* if(mi==0)  never been interviewed correctly before death */
                   2028:         /* Only death is a correct wave */
                   2029:       mw[mi][i]=m;
                   2030:     }
                   2031: 
                   2032:     wav[i]=mi;
                   2033:     if(mi==0){
                   2034:       if(first==0){
1.85      brouard  2035:        printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53      brouard  2036:        first=1;
                   2037:       }
                   2038:       if(first==1){
1.85      brouard  2039:        fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53      brouard  2040:       }
                   2041:     } /* end mi==0 */
1.77      brouard  2042:   } /* End individuals */
1.53      brouard  2043: 
                   2044:   for(i=1; i<=imx; i++){
                   2045:     for(mi=1; mi<wav[i];mi++){
                   2046:       if (stepm <=0)
                   2047:        dh[mi][i]=1;
                   2048:       else{
1.77      brouard  2049:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53      brouard  2050:          if (agedc[i] < 2*AGESUP) {
1.85      brouard  2051:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   2052:            if(j==0) j=1;  /* Survives at least one month after exam */
                   2053:            else if(j<0){
                   2054:              printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   2055:              j=1; /* Careful Patch */
1.86      brouard  2056:              printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
1.85      brouard  2057:              printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   2058:              fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
                   2059:            }
                   2060:            k=k+1;
                   2061:            if (j >= jmax) jmax=j;
                   2062:            if (j <= jmin) jmin=j;
                   2063:            sum=sum+j;
                   2064:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   2065:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53      brouard  2066:          }
                   2067:        }
                   2068:        else{
                   2069:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68      lievre   2070:          /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53      brouard  2071:          k=k+1;
                   2072:          if (j >= jmax) jmax=j;
                   2073:          else if (j <= jmin)jmin=j;
                   2074:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73      lievre   2075:          /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1.85      brouard  2076:          if(j<0){
                   2077:            printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   2078:            fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   2079:          }
1.53      brouard  2080:          sum=sum+j;
                   2081:        }
                   2082:        jk= j/stepm;
                   2083:        jl= j -jk*stepm;
                   2084:        ju= j -(jk+1)*stepm;
1.85      brouard  2085:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64      lievre   2086:          if(jl==0){
                   2087:            dh[mi][i]=jk;
                   2088:            bh[mi][i]=0;
                   2089:          }else{ /* We want a negative bias in order to only have interpolation ie
                   2090:                  * at the price of an extra matrix product in likelihood */
                   2091:            dh[mi][i]=jk+1;
                   2092:            bh[mi][i]=ju;
                   2093:          }
                   2094:        }else{
                   2095:          if(jl <= -ju){
                   2096:            dh[mi][i]=jk;
                   2097:            bh[mi][i]=jl;       /* bias is positive if real duration
                   2098:                                 * is higher than the multiple of stepm and negative otherwise.
                   2099:                                 */
                   2100:          }
                   2101:          else{
                   2102:            dh[mi][i]=jk+1;
                   2103:            bh[mi][i]=ju;
                   2104:          }
                   2105:          if(dh[mi][i]==0){
                   2106:            dh[mi][i]=1; /* At least one step */
                   2107:            bh[mi][i]=ju; /* At least one step */
1.71      brouard  2108:            /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
1.64      lievre   2109:          }
1.85      brouard  2110:        } /* end if mle */
                   2111:       }
1.64      lievre   2112:     } /* end wave */
1.53      brouard  2113:   }
                   2114:   jmean=sum/k;
                   2115:   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   2116:   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   2117:  }
                   2118: 
                   2119: /*********** Tricode ****************************/
                   2120: void tricode(int *Tvar, int **nbcode, int imx)
                   2121: {
1.58      lievre   2122:   
                   2123:   int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53      brouard  2124:   int cptcode=0;
                   2125:   cptcoveff=0; 
                   2126:  
1.58      lievre   2127:   for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53      brouard  2128:   for (k=1; k<=7; k++) ncodemax[k]=0;
                   2129: 
                   2130:   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58      lievre   2131:     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                   2132:                               modality*/ 
                   2133:       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   2134:       Ndum[ij]++; /*store the modality */
1.53      brouard  2135:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58      lievre   2136:       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                   2137:                                       Tvar[j]. If V=sex and male is 0 and 
                   2138:                                       female is 1, then  cptcode=1.*/
1.53      brouard  2139:     }
                   2140: 
                   2141:     for (i=0; i<=cptcode; i++) {
1.58      lievre   2142:       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1.53      brouard  2143:     }
1.58      lievre   2144: 
1.53      brouard  2145:     ij=1; 
                   2146:     for (i=1; i<=ncodemax[j]; i++) {
1.58      lievre   2147:       for (k=0; k<= maxncov; k++) {
1.53      brouard  2148:        if (Ndum[k] != 0) {
                   2149:          nbcode[Tvar[j]][ij]=k; 
1.58      lievre   2150:          /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.53      brouard  2151:          
                   2152:          ij++;
                   2153:        }
                   2154:        if (ij > ncodemax[j]) break; 
                   2155:       }  
                   2156:     } 
                   2157:   }  
                   2158: 
1.58      lievre   2159:  for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53      brouard  2160: 
1.58      lievre   2161:  for (i=1; i<=ncovmodel-2; i++) { 
                   2162:    /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53      brouard  2163:    ij=Tvar[i];
1.58      lievre   2164:    Ndum[ij]++;
1.53      brouard  2165:  }
                   2166: 
                   2167:  ij=1;
1.58      lievre   2168:  for (i=1; i<= maxncov; i++) {
1.53      brouard  2169:    if((Ndum[i]!=0) && (i<=ncovcol)){
1.58      lievre   2170:      Tvaraff[ij]=i; /*For printing */
1.53      brouard  2171:      ij++;
                   2172:    }
                   2173:  }
                   2174:  
1.58      lievre   2175:  cptcoveff=ij-1; /*Number of simple covariates*/
1.53      brouard  2176: }
                   2177: 
                   2178: /*********** Health Expectancies ****************/
                   2179: 
                   2180: 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 )
                   2181: 
                   2182: {
                   2183:   /* Health expectancies */
                   2184:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                   2185:   double age, agelim, hf;
                   2186:   double ***p3mat,***varhe;
                   2187:   double **dnewm,**doldm;
                   2188:   double *xp;
                   2189:   double **gp, **gm;
                   2190:   double ***gradg, ***trgradg;
                   2191:   int theta;
                   2192: 
1.74      brouard  2193:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53      brouard  2194:   xp=vector(1,npar);
1.74      brouard  2195:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   2196:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53      brouard  2197:   
                   2198:   fprintf(ficreseij,"# Health expectancies\n");
                   2199:   fprintf(ficreseij,"# Age");
                   2200:   for(i=1; i<=nlstate;i++)
                   2201:     for(j=1; j<=nlstate;j++)
                   2202:       fprintf(ficreseij," %1d-%1d (SE)",i,j);
                   2203:   fprintf(ficreseij,"\n");
                   2204: 
                   2205:   if(estepm < stepm){
                   2206:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2207:   }
                   2208:   else  hstepm=estepm;   
                   2209:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   2210:    * This is mainly to measure the difference between two models: for example
                   2211:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   2212:    * we are calculating an estimate of the Life Expectancy assuming a linear 
1.66      brouard  2213:    * progression in between and thus overestimating or underestimating according
1.53      brouard  2214:    * to the curvature of the survival function. If, for the same date, we 
                   2215:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   2216:    * to compare the new estimate of Life expectancy with the same linear 
                   2217:    * hypothesis. A more precise result, taking into account a more precise
                   2218:    * curvature will be obtained if estepm is as small as stepm. */
                   2219: 
                   2220:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2221:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2222:      nhstepm is the number of hstepm from age to agelim 
                   2223:      nstepm is the number of stepm from age to agelin. 
                   2224:      Look at hpijx to understand the reason of that which relies in memory size
                   2225:      and note for a fixed period like estepm months */
                   2226:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2227:      survival function given by stepm (the optimization length). Unfortunately it
                   2228:      means that if the survival funtion is printed only each two years of age and if
                   2229:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2230:      results. So we changed our mind and took the option of the best precision.
                   2231:   */
                   2232:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2233: 
                   2234:   agelim=AGESUP;
                   2235:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2236:     /* nhstepm age range expressed in number of stepm */
                   2237:     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
                   2238:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2239:     /* if (stepm >= YEARM) hstepm=1;*/
                   2240:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2241:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74      brouard  2242:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   2243:     gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   2244:     gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53      brouard  2245: 
                   2246:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   2247:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   2248:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
                   2249:  
                   2250: 
                   2251:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2252: 
                   2253:     /* Computing Variances of health expectancies */
                   2254: 
                   2255:      for(theta=1; theta <=npar; theta++){
                   2256:       for(i=1; i<=npar; i++){ 
                   2257:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2258:       }
                   2259:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2260:   
                   2261:       cptj=0;
                   2262:       for(j=1; j<= nlstate; j++){
                   2263:        for(i=1; i<=nlstate; i++){
                   2264:          cptj=cptj+1;
                   2265:          for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                   2266:            gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   2267:          }
                   2268:        }
                   2269:       }
                   2270:      
                   2271:      
                   2272:       for(i=1; i<=npar; i++) 
                   2273:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2274:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2275:       
                   2276:       cptj=0;
                   2277:       for(j=1; j<= nlstate; j++){
                   2278:        for(i=1;i<=nlstate;i++){
                   2279:          cptj=cptj+1;
                   2280:          for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77      brouard  2281: 
1.53      brouard  2282:            gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   2283:          }
                   2284:        }
                   2285:       }
1.74      brouard  2286:       for(j=1; j<= nlstate*nlstate; j++)
1.53      brouard  2287:        for(h=0; h<=nhstepm-1; h++){
                   2288:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   2289:        }
                   2290:      } 
                   2291:    
                   2292: /* End theta */
                   2293: 
1.74      brouard  2294:      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53      brouard  2295: 
                   2296:      for(h=0; h<=nhstepm-1; h++)
1.74      brouard  2297:       for(j=1; j<=nlstate*nlstate;j++)
1.53      brouard  2298:        for(theta=1; theta <=npar; theta++)
                   2299:          trgradg[h][j][theta]=gradg[h][theta][j];
                   2300:      
                   2301: 
1.74      brouard  2302:      for(i=1;i<=nlstate*nlstate;i++)
                   2303:       for(j=1;j<=nlstate*nlstate;j++)
1.53      brouard  2304:        varhe[i][j][(int)age] =0.;
                   2305: 
                   2306:      printf("%d|",(int)age);fflush(stdout);
                   2307:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   2308:      for(h=0;h<=nhstepm-1;h++){
                   2309:       for(k=0;k<=nhstepm-1;k++){
1.74      brouard  2310:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   2311:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   2312:        for(i=1;i<=nlstate*nlstate;i++)
                   2313:          for(j=1;j<=nlstate*nlstate;j++)
1.53      brouard  2314:            varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                   2315:       }
                   2316:     }
                   2317:     /* Computing expectancies */
                   2318:     for(i=1; i<=nlstate;i++)
                   2319:       for(j=1; j<=nlstate;j++)
                   2320:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   2321:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   2322:          
                   2323: /* 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]);*/
                   2324: 
                   2325:        }
                   2326: 
                   2327:     fprintf(ficreseij,"%3.0f",age );
                   2328:     cptj=0;
                   2329:     for(i=1; i<=nlstate;i++)
                   2330:       for(j=1; j<=nlstate;j++){
                   2331:        cptj++;
                   2332:        fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                   2333:       }
                   2334:     fprintf(ficreseij,"\n");
                   2335:    
1.74      brouard  2336:     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   2337:     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   2338:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   2339:     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53      brouard  2340:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2341:   }
                   2342:   printf("\n");
                   2343:   fprintf(ficlog,"\n");
                   2344: 
                   2345:   free_vector(xp,1,npar);
1.74      brouard  2346:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   2347:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   2348:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53      brouard  2349: }
                   2350: 
                   2351: /************ Variance ******************/
                   2352: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
                   2353: {
                   2354:   /* Variance of health expectancies */
                   2355:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   2356:   /* double **newm;*/
                   2357:   double **dnewm,**doldm;
                   2358:   double **dnewmp,**doldmp;
                   2359:   int i, j, nhstepm, hstepm, h, nstepm ;
                   2360:   int k, cptcode;
                   2361:   double *xp;
                   2362:   double **gp, **gm;  /* for var eij */
                   2363:   double ***gradg, ***trgradg; /*for var eij */
                   2364:   double **gradgp, **trgradgp; /* for var p point j */
                   2365:   double *gpp, *gmp; /* for var p point j */
                   2366:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   2367:   double ***p3mat;
                   2368:   double age,agelim, hf;
                   2369:   double ***mobaverage;
                   2370:   int theta;
                   2371:   char digit[4];
1.55      lievre   2372:   char digitp[25];
1.53      brouard  2373: 
                   2374:   char fileresprobmorprev[FILENAMELENGTH];
                   2375: 
1.55      lievre   2376:   if(popbased==1){
1.58      lievre   2377:     if(mobilav!=0)
1.55      lievre   2378:       strcpy(digitp,"-populbased-mobilav-");
                   2379:     else strcpy(digitp,"-populbased-nomobil-");
                   2380:   }
                   2381:   else 
1.53      brouard  2382:     strcpy(digitp,"-stablbased-");
1.56      lievre   2383: 
1.54      brouard  2384:   if (mobilav!=0) {
1.53      brouard  2385:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  2386:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   2387:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   2388:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   2389:     }
1.53      brouard  2390:   }
                   2391: 
                   2392:   strcpy(fileresprobmorprev,"prmorprev"); 
                   2393:   sprintf(digit,"%-d",ij);
                   2394:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   2395:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   2396:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   2397:   strcat(fileresprobmorprev,fileres);
                   2398:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   2399:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   2400:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   2401:   }
                   2402:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   2403:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66      brouard  2404:   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.53      brouard  2405:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   2406:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   2407:     fprintf(ficresprobmorprev," p.%-d SE",j);
                   2408:     for(i=1; i<=nlstate;i++)
                   2409:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   2410:   }  
                   2411:   fprintf(ficresprobmorprev,"\n");
1.88      brouard  2412:   fprintf(ficgp,"\n# Routine varevsij");
1.87      brouard  2413:   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
                   2414:   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   2415: /*   } */
1.53      brouard  2416:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2417: 
                   2418:   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");
                   2419:   fprintf(ficresvij,"# Age");
                   2420:   for(i=1; i<=nlstate;i++)
                   2421:     for(j=1; j<=nlstate;j++)
                   2422:       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                   2423:   fprintf(ficresvij,"\n");
                   2424: 
                   2425:   xp=vector(1,npar);
                   2426:   dnewm=matrix(1,nlstate,1,npar);
                   2427:   doldm=matrix(1,nlstate,1,nlstate);
                   2428:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   2429:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2430: 
                   2431:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   2432:   gpp=vector(nlstate+1,nlstate+ndeath);
                   2433:   gmp=vector(nlstate+1,nlstate+ndeath);
                   2434:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   2435:   
                   2436:   if(estepm < stepm){
                   2437:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2438:   }
                   2439:   else  hstepm=estepm;   
                   2440:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2441:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2442:      nhstepm is the number of hstepm from age to agelim 
                   2443:      nstepm is the number of stepm from age to agelin. 
                   2444:      Look at hpijx to understand the reason of that which relies in memory size
                   2445:      and note for a fixed period like k years */
                   2446:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2447:      survival function given by stepm (the optimization length). Unfortunately it
1.66      brouard  2448:      means that if the survival funtion is printed every two years of age and if
1.53      brouard  2449:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2450:      results. So we changed our mind and took the option of the best precision.
                   2451:   */
                   2452:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2453:   agelim = AGESUP;
                   2454:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2455:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   2456:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2457:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2458:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   2459:     gp=matrix(0,nhstepm,1,nlstate);
                   2460:     gm=matrix(0,nhstepm,1,nlstate);
                   2461: 
                   2462: 
                   2463:     for(theta=1; theta <=npar; theta++){
1.66      brouard  2464:       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53      brouard  2465:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2466:       }
                   2467:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2468:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2469: 
                   2470:       if (popbased==1) {
1.54      brouard  2471:        if(mobilav ==0){
1.53      brouard  2472:          for(i=1; i<=nlstate;i++)
                   2473:            prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2474:        }else{ /* mobilav */ 
1.53      brouard  2475:          for(i=1; i<=nlstate;i++)
                   2476:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   2477:        }
                   2478:       }
                   2479:   
                   2480:       for(j=1; j<= nlstate; j++){
                   2481:        for(h=0; h<=nhstepm; h++){
                   2482:          for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   2483:            gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   2484:        }
                   2485:       }
1.66      brouard  2486:       /* This for computing probability of death (h=1 means
                   2487:          computed over hstepm matrices product = hstepm*stepm months) 
                   2488:          as a weighted average of prlim.
                   2489:       */
1.69      brouard  2490:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68      lievre   2491:        for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53      brouard  2492:          gpp[j] += prlim[i][i]*p3mat[i][j][1];
                   2493:       }    
1.66      brouard  2494:       /* end probability of death */
1.53      brouard  2495: 
1.66      brouard  2496:       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53      brouard  2497:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2498:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2499:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2500:  
                   2501:       if (popbased==1) {
1.54      brouard  2502:        if(mobilav ==0){
1.53      brouard  2503:          for(i=1; i<=nlstate;i++)
                   2504:            prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2505:        }else{ /* mobilav */ 
1.53      brouard  2506:          for(i=1; i<=nlstate;i++)
                   2507:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   2508:        }
                   2509:       }
                   2510: 
                   2511:       for(j=1; j<= nlstate; j++){
                   2512:        for(h=0; h<=nhstepm; h++){
                   2513:          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   2514:            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   2515:        }
                   2516:       }
1.66      brouard  2517:       /* This for computing probability of death (h=1 means
                   2518:          computed over hstepm matrices product = hstepm*stepm months) 
                   2519:          as a weighted average of prlim.
                   2520:       */
1.69      brouard  2521:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68      lievre   2522:        for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   2523:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53      brouard  2524:       }    
1.66      brouard  2525:       /* end probability of death */
1.53      brouard  2526: 
                   2527:       for(j=1; j<= nlstate; j++) /* vareij */
                   2528:        for(h=0; h<=nhstepm; h++){
                   2529:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   2530:        }
1.68      lievre   2531: 
1.53      brouard  2532:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                   2533:        gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   2534:       }
                   2535: 
                   2536:     } /* End theta */
                   2537: 
                   2538:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   2539: 
                   2540:     for(h=0; h<=nhstepm; h++) /* veij */
                   2541:       for(j=1; j<=nlstate;j++)
                   2542:        for(theta=1; theta <=npar; theta++)
                   2543:          trgradg[h][j][theta]=gradg[h][theta][j];
                   2544: 
                   2545:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69      brouard  2546:       for(theta=1; theta <=npar; theta++)
1.53      brouard  2547:        trgradgp[j][theta]=gradgp[theta][j];
1.69      brouard  2548:   
1.53      brouard  2549: 
                   2550:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2551:     for(i=1;i<=nlstate;i++)
                   2552:       for(j=1;j<=nlstate;j++)
                   2553:        vareij[i][j][(int)age] =0.;
                   2554: 
                   2555:     for(h=0;h<=nhstepm;h++){
                   2556:       for(k=0;k<=nhstepm;k++){
                   2557:        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   2558:        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   2559:        for(i=1;i<=nlstate;i++)
                   2560:          for(j=1;j<=nlstate;j++)
                   2561:            vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   2562:       }
                   2563:     }
1.70      brouard  2564:   
1.53      brouard  2565:     /* pptj */
                   2566:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   2567:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70      brouard  2568:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   2569:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53      brouard  2570:        varppt[j][i]=doldmp[j][i];
                   2571:     /* end ppptj */
1.66      brouard  2572:     /*  x centered again */
1.53      brouard  2573:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   2574:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   2575:  
                   2576:     if (popbased==1) {
1.54      brouard  2577:       if(mobilav ==0){
1.53      brouard  2578:        for(i=1; i<=nlstate;i++)
                   2579:          prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2580:       }else{ /* mobilav */ 
1.53      brouard  2581:        for(i=1; i<=nlstate;i++)
                   2582:          prlim[i][i]=mobaverage[(int)age][i][ij];
                   2583:       }
                   2584:     }
1.70      brouard  2585:              
1.66      brouard  2586:     /* This for computing probability of death (h=1 means
                   2587:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   2588:        as a weighted average of prlim.
                   2589:     */
1.68      lievre   2590:     for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   2591:       for(i=1,gmp[j]=0.;i<= nlstate; i++) 
1.53      brouard  2592:        gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   2593:     }    
1.66      brouard  2594:     /* end probability of death */
1.53      brouard  2595: 
                   2596:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   2597:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   2598:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   2599:       for(i=1; i<=nlstate;i++){
                   2600:        fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   2601:       }
                   2602:     } 
                   2603:     fprintf(ficresprobmorprev,"\n");
                   2604: 
                   2605:     fprintf(ficresvij,"%.0f ",age );
                   2606:     for(i=1; i<=nlstate;i++)
                   2607:       for(j=1; j<=nlstate;j++){
                   2608:        fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   2609:       }
                   2610:     fprintf(ficresvij,"\n");
                   2611:     free_matrix(gp,0,nhstepm,1,nlstate);
                   2612:     free_matrix(gm,0,nhstepm,1,nlstate);
                   2613:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   2614:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   2615:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2616:   } /* End age */
                   2617:   free_vector(gpp,nlstate+1,nlstate+ndeath);
                   2618:   free_vector(gmp,nlstate+1,nlstate+ndeath);
                   2619:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   2620:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   2621:   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
                   2622:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                   2623:   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67      brouard  2624: /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   2625: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   2626: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88      brouard  2627:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
                   2628:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
                   2629:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
                   2630:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   2631:   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53      brouard  2632:   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
                   2633: */
1.88      brouard  2634: /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89      brouard  2635:   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53      brouard  2636: 
                   2637:   free_vector(xp,1,npar);
                   2638:   free_matrix(doldm,1,nlstate,1,nlstate);
                   2639:   free_matrix(dnewm,1,nlstate,1,npar);
                   2640:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2641:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   2642:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55      lievre   2643:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  2644:   fclose(ficresprobmorprev);
1.88      brouard  2645:   fflush(ficgp);
                   2646:   fflush(fichtm); 
1.84      brouard  2647: }  /* end varevsij */
1.53      brouard  2648: 
                   2649: /************ Variance of prevlim ******************/
                   2650: 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)
                   2651: {
                   2652:   /* Variance of prevalence limit */
1.59      brouard  2653:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53      brouard  2654:   double **newm;
                   2655:   double **dnewm,**doldm;
                   2656:   int i, j, nhstepm, hstepm;
                   2657:   int k, cptcode;
                   2658:   double *xp;
                   2659:   double *gp, *gm;
                   2660:   double **gradg, **trgradg;
                   2661:   double age,agelim;
                   2662:   int theta;
                   2663:    
1.54      brouard  2664:   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53      brouard  2665:   fprintf(ficresvpl,"# Age");
                   2666:   for(i=1; i<=nlstate;i++)
                   2667:       fprintf(ficresvpl," %1d-%1d",i,i);
                   2668:   fprintf(ficresvpl,"\n");
                   2669: 
                   2670:   xp=vector(1,npar);
                   2671:   dnewm=matrix(1,nlstate,1,npar);
                   2672:   doldm=matrix(1,nlstate,1,nlstate);
                   2673:   
                   2674:   hstepm=1*YEARM; /* Every year of age */
                   2675:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   2676:   agelim = AGESUP;
                   2677:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2678:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   2679:     if (stepm >= YEARM) hstepm=1;
                   2680:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   2681:     gradg=matrix(1,npar,1,nlstate);
                   2682:     gp=vector(1,nlstate);
                   2683:     gm=vector(1,nlstate);
                   2684: 
                   2685:     for(theta=1; theta <=npar; theta++){
                   2686:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   2687:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2688:       }
                   2689:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2690:       for(i=1;i<=nlstate;i++)
                   2691:        gp[i] = prlim[i][i];
                   2692:     
                   2693:       for(i=1; i<=npar; i++) /* Computes gradient */
                   2694:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2695:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2696:       for(i=1;i<=nlstate;i++)
                   2697:        gm[i] = prlim[i][i];
                   2698: 
                   2699:       for(i=1;i<=nlstate;i++)
                   2700:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                   2701:     } /* End theta */
                   2702: 
                   2703:     trgradg =matrix(1,nlstate,1,npar);
                   2704: 
                   2705:     for(j=1; j<=nlstate;j++)
                   2706:       for(theta=1; theta <=npar; theta++)
                   2707:        trgradg[j][theta]=gradg[theta][j];
                   2708: 
                   2709:     for(i=1;i<=nlstate;i++)
                   2710:       varpl[i][(int)age] =0.;
                   2711:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   2712:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   2713:     for(i=1;i<=nlstate;i++)
                   2714:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   2715: 
                   2716:     fprintf(ficresvpl,"%.0f ",age );
                   2717:     for(i=1; i<=nlstate;i++)
                   2718:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   2719:     fprintf(ficresvpl,"\n");
                   2720:     free_vector(gp,1,nlstate);
                   2721:     free_vector(gm,1,nlstate);
                   2722:     free_matrix(gradg,1,npar,1,nlstate);
                   2723:     free_matrix(trgradg,1,nlstate,1,npar);
                   2724:   } /* End age */
                   2725: 
                   2726:   free_vector(xp,1,npar);
                   2727:   free_matrix(doldm,1,nlstate,1,npar);
                   2728:   free_matrix(dnewm,1,nlstate,1,nlstate);
                   2729: 
                   2730: }
                   2731: 
                   2732: /************ Variance of one-step probabilities  ******************/
                   2733: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
                   2734: {
                   2735:   int i, j=0,  i1, k1, l1, t, tj;
                   2736:   int k2, l2, j1,  z1;
                   2737:   int k=0,l, cptcode;
                   2738:   int first=1, first1;
                   2739:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   2740:   double **dnewm,**doldm;
                   2741:   double *xp;
                   2742:   double *gp, *gm;
                   2743:   double **gradg, **trgradg;
                   2744:   double **mu;
                   2745:   double age,agelim, cov[NCOVMAX];
                   2746:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   2747:   int theta;
                   2748:   char fileresprob[FILENAMELENGTH];
                   2749:   char fileresprobcov[FILENAMELENGTH];
                   2750:   char fileresprobcor[FILENAMELENGTH];
                   2751: 
                   2752:   double ***varpij;
                   2753: 
                   2754:   strcpy(fileresprob,"prob"); 
                   2755:   strcat(fileresprob,fileres);
                   2756:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   2757:     printf("Problem with resultfile: %s\n", fileresprob);
                   2758:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   2759:   }
                   2760:   strcpy(fileresprobcov,"probcov"); 
                   2761:   strcat(fileresprobcov,fileres);
                   2762:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   2763:     printf("Problem with resultfile: %s\n", fileresprobcov);
                   2764:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   2765:   }
                   2766:   strcpy(fileresprobcor,"probcor"); 
                   2767:   strcat(fileresprobcor,fileres);
                   2768:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   2769:     printf("Problem with resultfile: %s\n", fileresprobcor);
                   2770:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   2771:   }
                   2772:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   2773:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   2774:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   2775:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   2776:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   2777:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   2778:   
                   2779:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   2780:   fprintf(ficresprob,"# Age");
                   2781:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   2782:   fprintf(ficresprobcov,"# Age");
                   2783:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   2784:   fprintf(ficresprobcov,"# Age");
                   2785: 
                   2786: 
                   2787:   for(i=1; i<=nlstate;i++)
                   2788:     for(j=1; j<=(nlstate+ndeath);j++){
                   2789:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   2790:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   2791:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   2792:     }  
1.69      brouard  2793:  /* fprintf(ficresprob,"\n");
1.53      brouard  2794:   fprintf(ficresprobcov,"\n");
                   2795:   fprintf(ficresprobcor,"\n");
1.69      brouard  2796:  */
                   2797:  xp=vector(1,npar);
1.53      brouard  2798:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   2799:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   2800:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   2801:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   2802:   first=1;
1.88      brouard  2803:   fprintf(ficgp,"\n# Routine varprob");
                   2804:   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   2805:   fprintf(fichtm,"\n");
                   2806: 
                   2807:   fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
                   2808:   fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                   2809:   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");
1.53      brouard  2810: 
                   2811:   cov[1]=1;
                   2812:   tj=cptcoveff;
                   2813:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   2814:   j1=0;
                   2815:   for(t=1; t<=tj;t++){
                   2816:     for(i1=1; i1<=ncodemax[t];i1++){ 
                   2817:       j1++;
                   2818:       if  (cptcovn>0) {
                   2819:        fprintf(ficresprob, "\n#********** Variable "); 
                   2820:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2821:        fprintf(ficresprob, "**********\n#\n");
1.53      brouard  2822:        fprintf(ficresprobcov, "\n#********** Variable "); 
                   2823:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2824:        fprintf(ficresprobcov, "**********\n#\n");
1.53      brouard  2825:        
                   2826:        fprintf(ficgp, "\n#********** Variable "); 
1.69      brouard  2827:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2828:        fprintf(ficgp, "**********\n#\n");
1.53      brouard  2829:        
                   2830:        
                   2831:        fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                   2832:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2833:        fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   2834:        
                   2835:        fprintf(ficresprobcor, "\n#********** Variable ");    
                   2836:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2837:        fprintf(ficresprobcor, "**********\n#");    
1.53      brouard  2838:       }
                   2839:       
                   2840:       for (age=bage; age<=fage; age ++){ 
                   2841:        cov[2]=age;
                   2842:        for (k=1; k<=cptcovn;k++) {
                   2843:          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                   2844:        }
                   2845:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   2846:        for (k=1; k<=cptcovprod;k++)
                   2847:          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   2848:        
                   2849:        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   2850:        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   2851:        gp=vector(1,(nlstate)*(nlstate+ndeath));
                   2852:        gm=vector(1,(nlstate)*(nlstate+ndeath));
                   2853:     
                   2854:        for(theta=1; theta <=npar; theta++){
                   2855:          for(i=1; i<=npar; i++)
1.74      brouard  2856:            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53      brouard  2857:          
                   2858:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   2859:          
                   2860:          k=0;
                   2861:          for(i=1; i<= (nlstate); i++){
                   2862:            for(j=1; j<=(nlstate+ndeath);j++){
                   2863:              k=k+1;
                   2864:              gp[k]=pmmij[i][j];
                   2865:            }
                   2866:          }
                   2867:          
                   2868:          for(i=1; i<=npar; i++)
1.74      brouard  2869:            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53      brouard  2870:     
                   2871:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   2872:          k=0;
                   2873:          for(i=1; i<=(nlstate); i++){
                   2874:            for(j=1; j<=(nlstate+ndeath);j++){
                   2875:              k=k+1;
                   2876:              gm[k]=pmmij[i][j];
                   2877:            }
                   2878:          }
                   2879:      
                   2880:          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
1.74      brouard  2881:            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
1.53      brouard  2882:        }
                   2883: 
                   2884:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   2885:          for(theta=1; theta <=npar; theta++)
                   2886:            trgradg[j][theta]=gradg[theta][j];
                   2887:        
                   2888:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   2889:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59      brouard  2890:        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   2891:        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   2892:        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   2893:        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   2894: 
1.53      brouard  2895:        pmij(pmmij,cov,ncovmodel,x,nlstate);
                   2896:        
                   2897:        k=0;
                   2898:        for(i=1; i<=(nlstate); i++){
                   2899:          for(j=1; j<=(nlstate+ndeath);j++){
                   2900:            k=k+1;
                   2901:            mu[k][(int) age]=pmmij[i][j];
                   2902:          }
                   2903:        }
                   2904:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   2905:          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   2906:            varpij[i][j][(int)age] = doldm[i][j];
                   2907: 
                   2908:        /*printf("\n%d ",(int)age);
1.59      brouard  2909:          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   2910:          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   2911:          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   2912:          }*/
1.53      brouard  2913: 
                   2914:        fprintf(ficresprob,"\n%d ",(int)age);
                   2915:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   2916:        fprintf(ficresprobcor,"\n%d ",(int)age);
                   2917: 
                   2918:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   2919:          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   2920:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   2921:          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   2922:          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   2923:        }
                   2924:        i=0;
                   2925:        for (k=1; k<=(nlstate);k++){
                   2926:          for (l=1; l<=(nlstate+ndeath);l++){ 
                   2927:            i=i++;
                   2928:            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   2929:            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   2930:            for (j=1; j<=i;j++){
                   2931:              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   2932:              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   2933:            }
                   2934:          }
                   2935:        }/* end of loop for state */
                   2936:       } /* end of loop for age */
                   2937: 
                   2938:       /* Confidence intervalle of pij  */
                   2939:       /*
1.59      brouard  2940:        fprintf(ficgp,"\nset noparametric;unset label");
                   2941:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   2942:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   2943:        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                   2944:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   2945:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   2946:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53      brouard  2947:       */
                   2948: 
                   2949:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                   2950:       first1=1;
                   2951:       for (k2=1; k2<=(nlstate);k2++){
                   2952:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   2953:          if(l2==k2) continue;
                   2954:          j=(k2-1)*(nlstate+ndeath)+l2;
                   2955:          for (k1=1; k1<=(nlstate);k1++){
                   2956:            for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   2957:              if(l1==k1) continue;
                   2958:              i=(k1-1)*(nlstate+ndeath)+l1;
                   2959:              if(i<=j) continue;
                   2960:              for (age=bage; age<=fage; age ++){ 
                   2961:                if ((int)age %5==0){
                   2962:                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   2963:                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   2964:                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   2965:                  mu1=mu[i][(int) age]/stepm*YEARM ;
                   2966:                  mu2=mu[j][(int) age]/stepm*YEARM;
                   2967:                  c12=cv12/sqrt(v1*v2);
                   2968:                  /* Computing eigen value of matrix of covariance */
                   2969:                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   2970:                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   2971:                  /* Eigen vectors */
                   2972:                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   2973:                  /*v21=sqrt(1.-v11*v11); *//* error */
                   2974:                  v21=(lc1-v1)/cv12*v11;
                   2975:                  v12=-v21;
                   2976:                  v22=v11;
                   2977:                  tnalp=v21/v11;
                   2978:                  if(first1==1){
                   2979:                    first1=0;
                   2980:                    printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                   2981:                  }
                   2982:                  fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                   2983:                  /*printf(fignu*/
                   2984:                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   2985:                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   2986:                  if(first==1){
                   2987:                    first=0;
                   2988:                    fprintf(ficgp,"\nset parametric;unset label");
                   2989:                    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                   2990:                    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.88      brouard  2991:                    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                   2992:  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                   2993: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                   2994:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                   2995:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   2996:                    fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53      brouard  2997:                    fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88      brouard  2998:                    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53      brouard  2999:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3000:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3001:                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                   3002:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3003:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3004:                  }else{
                   3005:                    first=0;
                   3006:                    fprintf(fichtm," %d (%.3f),",(int) age, c12);
                   3007:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3008:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3009:                    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                   3010:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3011:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3012:                  }/* if first */
                   3013:                } /* age mod 5 */
                   3014:              } /* end loop age */
1.88      brouard  3015:              fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53      brouard  3016:              first=1;
                   3017:            } /*l12 */
                   3018:          } /* k12 */
                   3019:        } /*l1 */
                   3020:       }/* k1 */
                   3021:     } /* loop covariates */
                   3022:   }
1.59      brouard  3023:   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   3024:   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53      brouard  3025:   free_vector(xp,1,npar);
                   3026:   fclose(ficresprob);
                   3027:   fclose(ficresprobcov);
                   3028:   fclose(ficresprobcor);
1.88      brouard  3029:   /*  fclose(ficgp);*/
1.53      brouard  3030: }
                   3031: 
                   3032: 
                   3033: /******************* Printing html file ***********/
                   3034: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                   3035:                  int lastpass, int stepm, int weightopt, char model[],\
                   3036:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   3037:                  int popforecast, int estepm ,\
                   3038:                  double jprev1, double mprev1,double anprev1, \
                   3039:                  double jprev2, double mprev2,double anprev2){
                   3040:   int jj1, k1, i1, cpt;
                   3041:   /*char optionfilehtm[FILENAMELENGTH];*/
1.87      brouard  3042: /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
                   3043: /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
                   3044: /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
                   3045: /*   } */
1.53      brouard  3046: 
1.85      brouard  3047:    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.88      brouard  3048:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
                   3049:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
                   3050:  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
1.85      brouard  3051:  - Life expectancies by age and initial health status (estepm=%2d months): \
1.88      brouard  3052:    <a href=\"%s\">%s</a> <br>\n</li>", \
                   3053:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
                   3054:           stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
                   3055:           subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
                   3056:           estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53      brouard  3057: 
                   3058: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                   3059: 
                   3060:  m=cptcoveff;
                   3061:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3062: 
                   3063:  jj1=0;
                   3064:  for(k1=1; k1<=m;k1++){
                   3065:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3066:      jj1++;
                   3067:      if (cptcovn > 0) {
                   3068:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3069:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3070:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3071:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3072:      }
                   3073:      /* Pij */
1.88      brouard  3074:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
                   3075: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
1.53      brouard  3076:      /* Quasi-incidences */
1.85      brouard  3077:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88      brouard  3078:  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
                   3079: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
1.53      brouard  3080:        /* Stable prevalence in each health state */
                   3081:        for(cpt=1; cpt<nlstate;cpt++){
1.85      brouard  3082:         fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88      brouard  3083: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53      brouard  3084:        }
                   3085:      for(cpt=1; cpt<=nlstate;cpt++) {
1.88      brouard  3086:         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89      brouard  3087: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53      brouard  3088:      }
1.85      brouard  3089:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.88      brouard  3090: health expectancies in states (1) and (2): %s%d.png<br>\
                   3091: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53      brouard  3092:    } /* end i1 */
                   3093:  }/* End k1 */
                   3094:  fprintf(fichtm,"</ul>");
                   3095: 
                   3096: 
1.85      brouard  3097:  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
                   3098:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
1.88      brouard  3099:  - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
                   3100:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
                   3101:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
                   3102:  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
                   3103:  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
                   3104:  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
                   3105:         rfileres,rfileres,\
                   3106:         subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
                   3107:         subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
                   3108:         subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
                   3109:         estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
                   3110:         subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
                   3111:         subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53      brouard  3112: 
1.76      brouard  3113: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   3114: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   3115: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   3116: /*     <br>",fileres,fileres,fileres,fileres); */
                   3117: /*  else  */
                   3118: /*    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); */
1.53      brouard  3119: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
                   3120: 
                   3121:  m=cptcoveff;
                   3122:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3123: 
                   3124:  jj1=0;
                   3125:  for(k1=1; k1<=m;k1++){
                   3126:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3127:      jj1++;
                   3128:      if (cptcovn > 0) {
                   3129:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3130:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3131:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3132:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3133:      }
                   3134:      for(cpt=1; cpt<=nlstate;cpt++) {
1.85      brouard  3135:        fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
1.88      brouard  3136: interval) in state (%d): %s%d%d.png <br>\
1.90    ! brouard  3137: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
1.53      brouard  3138:      }
                   3139:    } /* end i1 */
                   3140:  }/* End k1 */
                   3141:  fprintf(fichtm,"</ul>");
1.87      brouard  3142:  fflush(fichtm);
1.53      brouard  3143: }
                   3144: 
                   3145: /******************* Gnuplot file **************/
1.89      brouard  3146: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53      brouard  3147: 
1.88      brouard  3148:   char dirfileres[132],optfileres[132];
1.53      brouard  3149:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
                   3150:   int ng;
1.88      brouard  3151: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   3152: /*     printf("Problem with file %s",optionfilegnuplot); */
                   3153: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   3154: /*   } */
1.53      brouard  3155: 
1.54      brouard  3156:   /*#ifdef windows */
1.89      brouard  3157:   fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54      brouard  3158:     /*#endif */
1.88      brouard  3159:   m=pow(2,cptcoveff);
                   3160: 
                   3161:   strcpy(dirfileres,optionfilefiname);
                   3162:   strcpy(optfileres,"vpl");
1.53      brouard  3163:  /* 1eme*/
                   3164:   for (cpt=1; cpt<= nlstate ; cpt ++) {
                   3165:    for (k1=1; k1<= m ; k1 ++) {
1.88      brouard  3166:      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
                   3167:      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
                   3168:      fprintf(ficgp,"set xlabel \"Age\" \n\
                   3169: set ylabel \"Probability\" \n\
                   3170: set ter png small\n\
                   3171: set size 0.65,0.65\n\
                   3172: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53      brouard  3173: 
                   3174:      for (i=1; i<= nlstate ; i ++) {
                   3175:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3176:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3177:      }
1.88      brouard  3178:      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53      brouard  3179:      for (i=1; i<= nlstate ; i ++) {
                   3180:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3181:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3182:      } 
1.88      brouard  3183:      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
1.53      brouard  3184:      for (i=1; i<= nlstate ; i ++) {
                   3185:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3186:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3187:      }  
1.88      brouard  3188:      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53      brouard  3189:    }
                   3190:   }
                   3191:   /*2 eme*/
                   3192:   
                   3193:   for (k1=1; k1<= m ; k1 ++) { 
1.88      brouard  3194:     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53      brouard  3195:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
                   3196:     
                   3197:     for (i=1; i<= nlstate+1 ; i ++) {
                   3198:       k=2*i;
1.88      brouard  3199:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3200:       for (j=1; j<= nlstate+1 ; j ++) {
                   3201:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3202:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3203:       }   
                   3204:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                   3205:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88      brouard  3206:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3207:       for (j=1; j<= nlstate+1 ; j ++) {
                   3208:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3209:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3210:       }   
                   3211:       fprintf(ficgp,"\" t\"\" w l 0,");
1.88      brouard  3212:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3213:       for (j=1; j<= nlstate+1 ; j ++) {
                   3214:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3215:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3216:       }   
                   3217:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                   3218:       else fprintf(ficgp,"\" t\"\" w l 0,");
                   3219:     }
                   3220:   }
                   3221:   
                   3222:   /*3eme*/
                   3223:   
                   3224:   for (k1=1; k1<= m ; k1 ++) { 
                   3225:     for (cpt=1; cpt<= nlstate ; cpt ++) {
                   3226:       k=2+nlstate*(2*cpt-2);
1.88      brouard  3227:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
                   3228:       fprintf(ficgp,"set ter png small\n\
                   3229: set size 0.65,0.65\n\
                   3230: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53      brouard  3231:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   3232:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   3233:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   3234:        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   3235:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   3236:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   3237:        
                   3238:       */
                   3239:       for (i=1; i< nlstate ; i ++) {
1.88      brouard  3240:        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
1.53      brouard  3241:        
                   3242:       } 
                   3243:     }
                   3244:   }
                   3245:   
1.76      brouard  3246:   /* CV preval stable (period) */
1.53      brouard  3247:   for (k1=1; k1<= m ; k1 ++) { 
1.76      brouard  3248:     for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53      brouard  3249:       k=3;
1.88      brouard  3250:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
                   3251:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
                   3252: set ter png small\nset size 0.65,0.65\n\
1.89      brouard  3253: unset log y\n\
1.88      brouard  3254: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53      brouard  3255:       
1.83      lievre   3256:       for (i=1; i< nlstate ; i ++)
1.53      brouard  3257:        fprintf(ficgp,"+$%d",k+i+1);
                   3258:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
                   3259:       
                   3260:       l=3+(nlstate+ndeath)*cpt;
1.88      brouard  3261:       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53      brouard  3262:       for (i=1; i< nlstate ; i ++) {
                   3263:        l=3+(nlstate+ndeath)*cpt;
                   3264:        fprintf(ficgp,"+$%d",l+i+1);
                   3265:       }
                   3266:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
                   3267:     } 
                   3268:   }  
                   3269:   
                   3270:   /* proba elementaires */
                   3271:   for(i=1,jk=1; i <=nlstate; i++){
                   3272:     for(k=1; k <=(nlstate+ndeath); k++){
                   3273:       if (k != i) {
                   3274:        for(j=1; j <=ncovmodel; j++){
                   3275:          fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                   3276:          jk++; 
                   3277:          fprintf(ficgp,"\n");
                   3278:        }
                   3279:       }
                   3280:     }
                   3281:    }
                   3282: 
                   3283:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
                   3284:      for(jk=1; jk <=m; jk++) {
1.88      brouard  3285:        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
1.53      brouard  3286:        if (ng==2)
                   3287:         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   3288:        else
                   3289:         fprintf(ficgp,"\nset title \"Probability\"\n");
                   3290:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                   3291:        i=1;
                   3292:        for(k2=1; k2<=nlstate; k2++) {
                   3293:         k3=i;
                   3294:         for(k=1; k<=(nlstate+ndeath); k++) {
                   3295:           if (k != k2){
                   3296:             if(ng==2)
                   3297:               fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   3298:             else
                   3299:               fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   3300:             ij=1;
                   3301:             for(j=3; j <=ncovmodel; j++) {
                   3302:               if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                   3303:                 fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                   3304:                 ij++;
                   3305:               }
                   3306:               else
                   3307:                 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   3308:             }
                   3309:             fprintf(ficgp,")/(1");
                   3310:             
                   3311:             for(k1=1; k1 <=nlstate; k1++){   
                   3312:               fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   3313:               ij=1;
                   3314:               for(j=3; j <=ncovmodel; j++){
                   3315:                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                   3316:                   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                   3317:                   ij++;
                   3318:                 }
                   3319:                 else
                   3320:                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   3321:               }
                   3322:               fprintf(ficgp,")");
                   3323:             }
                   3324:             fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   3325:             if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   3326:             i=i+ncovmodel;
                   3327:           }
                   3328:         } /* end k */
                   3329:        } /* end k2 */
                   3330:      } /* end jk */
                   3331:    } /* end ng */
1.88      brouard  3332:    fflush(ficgp); 
1.53      brouard  3333: }  /* end gnuplot */
                   3334: 
                   3335: 
                   3336: /*************** Moving average **************/
1.54      brouard  3337: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53      brouard  3338: 
                   3339:   int i, cpt, cptcod;
1.58      lievre   3340:   int modcovmax =1;
1.54      brouard  3341:   int mobilavrange, mob;
1.53      brouard  3342:   double age;
1.58      lievre   3343: 
                   3344:   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                   3345:                           a covariate has 2 modalities */
                   3346:   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
                   3347: 
1.54      brouard  3348:   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   3349:     if(mobilav==1) mobilavrange=5; /* default */
                   3350:     else mobilavrange=mobilav;
                   3351:     for (age=bage; age<=fage; age++)
                   3352:       for (i=1; i<=nlstate;i++)
1.58      lievre   3353:        for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54      brouard  3354:          mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   3355:     /* We keep the original values on the extreme ages bage, fage and for 
                   3356:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   3357:        we use a 5 terms etc. until the borders are no more concerned. 
                   3358:     */ 
                   3359:     for (mob=3;mob <=mobilavrange;mob=mob+2){
                   3360:       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                   3361:        for (i=1; i<=nlstate;i++){
1.58      lievre   3362:          for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54      brouard  3363:            mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   3364:              for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   3365:                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   3366:                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   3367:              }
                   3368:            mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                   3369:          }
1.53      brouard  3370:        }
1.54      brouard  3371:       }/* end age */
                   3372:     }/* end mob */
                   3373:   }else return -1;
                   3374:   return 0;
                   3375: }/* End movingaverage */
1.53      brouard  3376: 
                   3377: 
                   3378: /************** Forecasting ******************/
1.70      brouard  3379: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69      brouard  3380:   /* proj1, year, month, day of starting projection 
                   3381:      agemin, agemax range of age
                   3382:      dateprev1 dateprev2 range of dates during which prevalence is computed
1.70      brouard  3383:      anproj2 year of en of projection (same day and month as proj1).
1.69      brouard  3384:   */
1.73      lievre   3385:   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53      brouard  3386:   int *popage;
1.70      brouard  3387:   double agec; /* generic age */
                   3388:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53      brouard  3389:   double *popeffectif,*popcount;
                   3390:   double ***p3mat;
1.55      lievre   3391:   double ***mobaverage;
1.53      brouard  3392:   char fileresf[FILENAMELENGTH];
                   3393: 
1.69      brouard  3394:   agelim=AGESUP;
1.84      brouard  3395:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53      brouard  3396:  
                   3397:   strcpy(fileresf,"f"); 
                   3398:   strcat(fileresf,fileres);
                   3399:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   3400:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   3401:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   3402:   }
                   3403:   printf("Computing forecasting: result on file '%s' \n", fileresf);
                   3404:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                   3405: 
                   3406:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   3407: 
1.54      brouard  3408:   if (mobilav!=0) {
1.53      brouard  3409:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  3410:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   3411:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3412:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3413:     }
1.53      brouard  3414:   }
                   3415: 
                   3416:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   3417:   if (stepm<=12) stepsize=1;
1.74      brouard  3418:   if(estepm < stepm){
                   3419:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3420:   }
                   3421:   else  hstepm=estepm;   
                   3422: 
1.53      brouard  3423:   hstepm=hstepm/stepm; 
1.69      brouard  3424:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                   3425:                                fractional in yp1 */
1.53      brouard  3426:   anprojmean=yp;
                   3427:   yp2=modf((yp1*12),&yp);
                   3428:   mprojmean=yp;
                   3429:   yp1=modf((yp2*30.5),&yp);
                   3430:   jprojmean=yp;
                   3431:   if(jprojmean==0) jprojmean=1;
                   3432:   if(mprojmean==0) jprojmean=1;
1.73      lievre   3433: 
                   3434:   i1=cptcoveff;
                   3435:   if (cptcovn < 1){i1=1;}
1.53      brouard  3436:   
1.70      brouard  3437:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
1.53      brouard  3438:   
1.70      brouard  3439:   fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73      lievre   3440: 
1.75      brouard  3441: /*           if (h==(int)(YEARM*yearp)){ */
1.73      lievre   3442:   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53      brouard  3443:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   3444:       k=k+1;
                   3445:       fprintf(ficresf,"\n#******");
                   3446:       for(j=1;j<=cptcoveff;j++) {
1.70      brouard  3447:        fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.53      brouard  3448:       }
                   3449:       fprintf(ficresf,"******\n");
1.70      brouard  3450:       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
                   3451:       for(j=1; j<=nlstate+ndeath;j++){ 
                   3452:        for(i=1; i<=nlstate;i++)              
                   3453:           fprintf(ficresf," p%d%d",i,j);
                   3454:        fprintf(ficresf," p.%d",j);
                   3455:       }
1.74      brouard  3456:       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
1.53      brouard  3457:        fprintf(ficresf,"\n");
1.70      brouard  3458:        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
1.53      brouard  3459: 
1.71      brouard  3460:        for (agec=fage; agec>=(ageminpar-1); agec--){ 
1.70      brouard  3461:          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
1.53      brouard  3462:          nhstepm = nhstepm/hstepm; 
                   3463:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3464:          oldm=oldms;savm=savms;
1.70      brouard  3465:          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
1.53      brouard  3466:        
                   3467:          for (h=0; h<=nhstepm; h++){
1.75      brouard  3468:            if (h*hstepm/YEARM*stepm ==yearp) {
1.69      brouard  3469:               fprintf(ficresf,"\n");
                   3470:               for(j=1;j<=cptcoveff;j++) 
                   3471:                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70      brouard  3472:              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53      brouard  3473:            } 
                   3474:            for(j=1; j<=nlstate+ndeath;j++) {
1.70      brouard  3475:              ppij=0.;
1.71      brouard  3476:              for(i=1; i<=nlstate;i++) {
1.53      brouard  3477:                if (mobilav==1) 
1.71      brouard  3478:                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53      brouard  3479:                else {
1.71      brouard  3480:                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53      brouard  3481:                }
1.75      brouard  3482:                if (h*hstepm/YEARM*stepm== yearp) {
1.70      brouard  3483:                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75      brouard  3484:                }
                   3485:              } /* end i */
                   3486:              if (h*hstepm/YEARM*stepm==yearp) {
1.70      brouard  3487:                fprintf(ficresf," %.3f", ppij);
1.53      brouard  3488:              }
1.75      brouard  3489:            }/* end j */
                   3490:          } /* end h */
1.53      brouard  3491:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75      brouard  3492:        } /* end agec */
                   3493:       } /* end yearp */
                   3494:     } /* end cptcod */
                   3495:   } /* end  cptcov */
1.53      brouard  3496:        
1.54      brouard  3497:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  3498: 
                   3499:   fclose(ficresf);
                   3500: }
1.70      brouard  3501: 
                   3502: /************** Forecasting *****not tested NB*************/
1.53      brouard  3503: 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){
                   3504:   
                   3505:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
                   3506:   int *popage;
1.69      brouard  3507:   double calagedatem, agelim, kk1, kk2;
1.53      brouard  3508:   double *popeffectif,*popcount;
                   3509:   double ***p3mat,***tabpop,***tabpopprev;
1.55      lievre   3510:   double ***mobaverage;
1.53      brouard  3511:   char filerespop[FILENAMELENGTH];
                   3512: 
                   3513:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3514:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3515:   agelim=AGESUP;
1.69      brouard  3516:   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53      brouard  3517:   
1.84      brouard  3518:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53      brouard  3519:   
                   3520:   
                   3521:   strcpy(filerespop,"pop"); 
                   3522:   strcat(filerespop,fileres);
                   3523:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
                   3524:     printf("Problem with forecast resultfile: %s\n", filerespop);
                   3525:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
                   3526:   }
                   3527:   printf("Computing forecasting: result on file '%s' \n", filerespop);
                   3528:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
                   3529: 
                   3530:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   3531: 
1.54      brouard  3532:   if (mobilav!=0) {
1.53      brouard  3533:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  3534:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   3535:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3536:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3537:     }
1.53      brouard  3538:   }
                   3539: 
                   3540:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   3541:   if (stepm<=12) stepsize=1;
                   3542:   
                   3543:   agelim=AGESUP;
                   3544:   
                   3545:   hstepm=1;
                   3546:   hstepm=hstepm/stepm; 
                   3547:   
                   3548:   if (popforecast==1) {
                   3549:     if((ficpop=fopen(popfile,"r"))==NULL) {
                   3550:       printf("Problem with population file : %s\n",popfile);exit(0);
                   3551:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
                   3552:     } 
                   3553:     popage=ivector(0,AGESUP);
                   3554:     popeffectif=vector(0,AGESUP);
                   3555:     popcount=vector(0,AGESUP);
                   3556:     
                   3557:     i=1;   
                   3558:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
                   3559:    
                   3560:     imx=i;
                   3561:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
                   3562:   }
                   3563: 
1.69      brouard  3564:   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53      brouard  3565:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   3566:       k=k+1;
                   3567:       fprintf(ficrespop,"\n#******");
                   3568:       for(j=1;j<=cptcoveff;j++) {
                   3569:        fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   3570:       }
                   3571:       fprintf(ficrespop,"******\n");
                   3572:       fprintf(ficrespop,"# Age");
                   3573:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
                   3574:       if (popforecast==1)  fprintf(ficrespop," [Population]");
                   3575:       
                   3576:       for (cpt=0; cpt<=0;cpt++) { 
                   3577:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   3578:        
1.69      brouard  3579:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
1.53      brouard  3580:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   3581:          nhstepm = nhstepm/hstepm; 
                   3582:          
                   3583:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3584:          oldm=oldms;savm=savms;
                   3585:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   3586:        
                   3587:          for (h=0; h<=nhstepm; h++){
1.69      brouard  3588:            if (h==(int) (calagedatem+YEARM*cpt)) {
1.53      brouard  3589:              fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   3590:            } 
                   3591:            for(j=1; j<=nlstate+ndeath;j++) {
                   3592:              kk1=0.;kk2=0;
                   3593:              for(i=1; i<=nlstate;i++) {              
                   3594:                if (mobilav==1) 
                   3595:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   3596:                else {
                   3597:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   3598:                }
                   3599:              }
1.69      brouard  3600:              if (h==(int)(calagedatem+12*cpt)){
1.53      brouard  3601:                tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   3602:                  /*fprintf(ficrespop," %.3f", kk1);
                   3603:                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                   3604:              }
                   3605:            }
                   3606:            for(i=1; i<=nlstate;i++){
                   3607:              kk1=0.;
                   3608:                for(j=1; j<=nlstate;j++){
                   3609:                  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   3610:                }
1.69      brouard  3611:                  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53      brouard  3612:            }
                   3613: 
1.69      brouard  3614:            if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
1.53      brouard  3615:              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
                   3616:          }
                   3617:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3618:        }
                   3619:       }
                   3620:  
                   3621:   /******/
                   3622: 
                   3623:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
                   3624:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
1.69      brouard  3625:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
1.53      brouard  3626:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   3627:          nhstepm = nhstepm/hstepm; 
                   3628:          
                   3629:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3630:          oldm=oldms;savm=savms;
                   3631:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   3632:          for (h=0; h<=nhstepm; h++){
1.69      brouard  3633:            if (h==(int) (calagedatem+YEARM*cpt)) {
1.53      brouard  3634:              fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   3635:            } 
                   3636:            for(j=1; j<=nlstate+ndeath;j++) {
                   3637:              kk1=0.;kk2=0;
                   3638:              for(i=1; i<=nlstate;i++) {              
                   3639:                kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                   3640:              }
1.69      brouard  3641:              if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
1.53      brouard  3642:            }
                   3643:          }
                   3644:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3645:        }
                   3646:       }
                   3647:    } 
                   3648:   }
                   3649:  
1.54      brouard  3650:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  3651: 
                   3652:   if (popforecast==1) {
                   3653:     free_ivector(popage,0,AGESUP);
                   3654:     free_vector(popeffectif,0,AGESUP);
                   3655:     free_vector(popcount,0,AGESUP);
                   3656:   }
                   3657:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3658:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3659:   fclose(ficrespop);
1.84      brouard  3660: } /* End of popforecast */
1.53      brouard  3661: 
1.87      brouard  3662: int fileappend(FILE *fichier, char *optionfich)
1.86      brouard  3663: {
1.87      brouard  3664:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   3665:     printf("Problem with file: %s\n", optionfich);
                   3666:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   3667:     return (0);
1.86      brouard  3668:   }
1.87      brouard  3669:   fflush(fichier);
                   3670:   return (1);
1.86      brouard  3671: }
1.88      brouard  3672: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   3673: {
                   3674: 
                   3675:   char ca[32], cb[32], cc[32];
                   3676:   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
                   3677:   int numlinepar;
                   3678: 
                   3679:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   3680:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   3681:   for(i=1; i <=nlstate; i++){
                   3682:     jj=0;
                   3683:     for(j=1; j <=nlstate+ndeath; j++){
                   3684:       if(j==i) continue;
                   3685:       jj++;
                   3686:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   3687:       printf("%1d%1d",i,j);
                   3688:       fprintf(ficparo,"%1d%1d",i,j);
                   3689:       for(k=1; k<=ncovmodel;k++){
                   3690:        /*        printf(" %lf",param[i][j][k]); */
                   3691:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   3692:        printf(" 0.");
                   3693:        fprintf(ficparo," 0.");
                   3694:       }
                   3695:       printf("\n");
                   3696:       fprintf(ficparo,"\n");
                   3697:     }
                   3698:   }
                   3699:   printf("# Scales (for hessian or gradient estimation)\n");
                   3700:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   3701:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   3702:   for(i=1; i <=nlstate; i++){
                   3703:     jj=0;
                   3704:     for(j=1; j <=nlstate+ndeath; j++){
                   3705:       if(j==i) continue;
                   3706:       jj++;
                   3707:       fprintf(ficparo,"%1d%1d",i,j);
                   3708:       printf("%1d%1d",i,j);
                   3709:       fflush(stdout);
                   3710:       for(k=1; k<=ncovmodel;k++){
                   3711:        /*      printf(" %le",delti3[i][j][k]); */
                   3712:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   3713:        printf(" 0.");
                   3714:        fprintf(ficparo," 0.");
                   3715:       }
                   3716:       numlinepar++;
                   3717:       printf("\n");
                   3718:       fprintf(ficparo,"\n");
                   3719:     }
                   3720:   }
                   3721:   printf("# Covariance matrix\n");
                   3722: /* # 121 Var(a12)\n\ */
                   3723: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   3724: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   3725: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   3726: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   3727: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   3728: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   3729: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   3730:   fflush(stdout);
                   3731:   fprintf(ficparo,"# Covariance matrix\n");
                   3732:   /* # 121 Var(a12)\n\ */
                   3733:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   3734:   /* #   ...\n\ */
                   3735:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   3736:   
                   3737:   for(itimes=1;itimes<=2;itimes++){
                   3738:     jj=0;
                   3739:     for(i=1; i <=nlstate; i++){
                   3740:       for(j=1; j <=nlstate+ndeath; j++){
                   3741:        if(j==i) continue;
                   3742:        for(k=1; k<=ncovmodel;k++){
                   3743:          jj++;
                   3744:          ca[0]= k+'a'-1;ca[1]='\0';
                   3745:          if(itimes==1){
                   3746:            printf("#%1d%1d%d",i,j,k);
                   3747:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   3748:          }else{
                   3749:            printf("%1d%1d%d",i,j,k);
                   3750:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   3751:            /*  printf(" %.5le",matcov[i][j]); */
                   3752:          }
                   3753:          ll=0;
                   3754:          for(li=1;li <=nlstate; li++){
                   3755:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   3756:              if(lj==li) continue;
                   3757:              for(lk=1;lk<=ncovmodel;lk++){
                   3758:                ll++;
                   3759:                if(ll<=jj){
                   3760:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   3761:                  if(ll<jj){
                   3762:                    if(itimes==1){
                   3763:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   3764:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   3765:                    }else{
                   3766:                      printf(" 0.");
                   3767:                      fprintf(ficparo," 0.");
                   3768:                    }
                   3769:                  }else{
                   3770:                    if(itimes==1){
                   3771:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   3772:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   3773:                    }else{
                   3774:                      printf(" 0.");
                   3775:                      fprintf(ficparo," 0.");
                   3776:                    }
                   3777:                  }
                   3778:                }
                   3779:              } /* end lk */
                   3780:            } /* end lj */
                   3781:          } /* end li */
                   3782:          printf("\n");
                   3783:          fprintf(ficparo,"\n");
                   3784:          numlinepar++;
                   3785:        } /* end k*/
                   3786:       } /*end j */
                   3787:     } /* end i */
                   3788:   }
                   3789: 
                   3790: } /* end of prwizard */
                   3791: 
1.53      brouard  3792: /***********************************************/
                   3793: /**************** Main Program *****************/
                   3794: /***********************************************/
                   3795: 
                   3796: int main(int argc, char *argv[])
                   3797: {
1.61      brouard  3798:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74      brouard  3799:   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.88      brouard  3800:   int jj, imk;
1.85      brouard  3801:   int numlinepar=0; /* Current linenumber of parameter file */
1.87      brouard  3802:   /*  FILE *fichtm; *//* Html File */
                   3803:   /* FILE *ficgp;*/ /*Gnuplot File */
1.53      brouard  3804:   double agedeb, agefin,hf;
                   3805:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
                   3806: 
                   3807:   double fret;
                   3808:   double **xi,tmp,delta;
                   3809: 
                   3810:   double dum; /* Dummy variable */
                   3811:   double ***p3mat;
                   3812:   double ***mobaverage;
                   3813:   int *indx;
                   3814:   char line[MAXLINE], linepar[MAXLINE];
1.88      brouard  3815:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
                   3816:   char pathr[MAXLINE]; 
1.53      brouard  3817:   int firstobs=1, lastobs=10;
                   3818:   int sdeb, sfin; /* Status at beginning and end */
                   3819:   int c,  h , cpt,l;
                   3820:   int ju,jl, mi;
                   3821:   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59      brouard  3822:   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
1.69      brouard  3823:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53      brouard  3824:   int mobilav=0,popforecast=0;
                   3825:   int hstepm, nhstepm;
1.74      brouard  3826:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   3827:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53      brouard  3828: 
                   3829:   double bage, fage, age, agelim, agebase;
                   3830:   double ftolpl=FTOL;
                   3831:   double **prlim;
                   3832:   double *severity;
                   3833:   double ***param; /* Matrix of parameters */
                   3834:   double  *p;
                   3835:   double **matcov; /* Matrix of covariance */
                   3836:   double ***delti3; /* Scale */
                   3837:   double *delti; /* Scale */
                   3838:   double ***eij, ***vareij;
                   3839:   double **varpl; /* Variances of prevalence limits by age */
                   3840:   double *epj, vepp;
                   3841:   double kk1, kk2;
1.74      brouard  3842:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53      brouard  3843: 
                   3844:   char *alph[]={"a","a","b","c","d","e"}, str[4];
                   3845: 
                   3846: 
                   3847:   char z[1]="c", occ;
1.86      brouard  3848: 
1.53      brouard  3849:   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88      brouard  3850:   char strstart[80], *strt, strtend[80];
1.85      brouard  3851:   char *stratrunc;
                   3852:   int lstra;
                   3853: 
                   3854:   long total_usecs;
                   3855:   struct timeval start_time, end_time, curr_time;
                   3856:   struct timezone tzp;
                   3857:   extern int gettimeofday();
                   3858:   struct tm tmg, tm, *gmtime(), *localtime();
                   3859:   long time_value;
                   3860:   extern long time();
1.53      brouard  3861:  
1.85      brouard  3862:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
                   3863:   (void) gettimeofday(&start_time,&tzp);
                   3864:   tm = *localtime(&start_time.tv_sec);
                   3865:   tmg = *gmtime(&start_time.tv_sec);
1.88      brouard  3866:   strcpy(strstart,asctime(&tm));
1.86      brouard  3867: 
1.88      brouard  3868: /*  printf("Localtime (at start)=%s",strstart); */
1.85      brouard  3869: /*  tp.tv_sec = tp.tv_sec +86400; */
                   3870: /*  tm = *localtime(&start_time.tv_sec); */
                   3871: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   3872: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   3873: /*   tmg.tm_hour=tmg.tm_hour + 1; */
                   3874: /*   tp.tv_sec = mktime(&tmg); */
                   3875: /*   strt=asctime(&tmg); */
1.88      brouard  3876: /*   printf("Time(after) =%s",strstart);  */
1.85      brouard  3877: /*  (void) time (&time_value);
                   3878: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   3879: *  tm = *localtime(&time_value);
1.88      brouard  3880: *  strstart=asctime(&tm);
                   3881: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
1.85      brouard  3882: */
                   3883: 
1.53      brouard  3884:   getcwd(pathcd, size);
                   3885: 
1.81      brouard  3886:   printf("\n%s\n%s",version,fullversion);
1.53      brouard  3887:   if(argc <=1){
                   3888:     printf("\nEnter the parameter file name: ");
                   3889:     scanf("%s",pathtot);
                   3890:   }
                   3891:   else{
                   3892:     strcpy(pathtot,argv[1]);
                   3893:   }
1.88      brouard  3894:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53      brouard  3895:   /*cygwin_split_path(pathtot,path,optionfile);
                   3896:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   3897:   /* cutv(path,optionfile,pathtot,'\\');*/
                   3898: 
                   3899:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85      brouard  3900:   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53      brouard  3901:   chdir(path);
1.88      brouard  3902:   strcpy(command,"mkdir ");
                   3903:   strcat(command,optionfilefiname);
                   3904:   if((outcmd=system(command)) != 0){
                   3905:     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
                   3906:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   3907:     /* fclose(ficlog); */
                   3908: /*     exit(1); */
                   3909:   }
                   3910: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   3911: /*     perror("mkdir"); */
                   3912: /*   } */
1.53      brouard  3913: 
1.59      brouard  3914:   /*-------- arguments in the command line --------*/
1.53      brouard  3915: 
                   3916:   /* Log file */
                   3917:   strcat(filelog, optionfilefiname);
                   3918:   strcat(filelog,".log");    /* */
                   3919:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   3920:     printf("Problem with logfile %s\n",filelog);
                   3921:     goto end;
                   3922:   }
                   3923:   fprintf(ficlog,"Log filename:%s\n",filelog);
1.85      brouard  3924:   fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53      brouard  3925:   fprintf(ficlog,"\nEnter the parameter file name: ");
1.88      brouard  3926:   fprintf(ficlog,"pathtot=%s\n\
                   3927:  path=%s \n\
                   3928:  optionfile=%s\n\
                   3929:  optionfilext=%s\n\
                   3930:  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86      brouard  3931: 
1.88      brouard  3932:   printf("Localtime (at start):%s",strstart);
                   3933:   fprintf(ficlog,"Localtime (at start): %s",strstart);
1.53      brouard  3934:   fflush(ficlog);
                   3935: 
                   3936:   /* */
                   3937:   strcpy(fileres,"r");
                   3938:   strcat(fileres, optionfilefiname);
                   3939:   strcat(fileres,".txt");    /* Other files have txt extension */
                   3940: 
                   3941:   /*---------arguments file --------*/
                   3942: 
                   3943:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
                   3944:     printf("Problem with optionfile %s\n",optionfile);
                   3945:     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85      brouard  3946:     fflush(ficlog);
1.53      brouard  3947:     goto end;
                   3948:   }
                   3949: 
1.88      brouard  3950: 
                   3951: 
1.53      brouard  3952:   strcpy(filereso,"o");
                   3953:   strcat(filereso,fileres);
1.88      brouard  3954:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53      brouard  3955:     printf("Problem with Output resultfile: %s\n", filereso);
                   3956:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85      brouard  3957:     fflush(ficlog);
1.53      brouard  3958:     goto end;
                   3959:   }
                   3960: 
                   3961:   /* Reads comments: lines beginning with '#' */
1.85      brouard  3962:   numlinepar=0;
1.53      brouard  3963:   while((c=getc(ficpar))=='#' && c!= EOF){
                   3964:     ungetc(c,ficpar);
                   3965:     fgets(line, MAXLINE, ficpar);
1.85      brouard  3966:     numlinepar++;
1.53      brouard  3967:     puts(line);
                   3968:     fputs(line,ficparo);
1.85      brouard  3969:     fputs(line,ficlog);
1.53      brouard  3970:   }
                   3971:   ungetc(c,ficpar);
                   3972: 
                   3973:   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
1.85      brouard  3974:   numlinepar++;
1.53      brouard  3975:   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);
                   3976:   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);
1.85      brouard  3977:   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
                   3978:   fflush(ficlog);
1.59      brouard  3979:   while((c=getc(ficpar))=='#' && c!= EOF){
1.53      brouard  3980:     ungetc(c,ficpar);
                   3981:     fgets(line, MAXLINE, ficpar);
1.85      brouard  3982:     numlinepar++;
1.53      brouard  3983:     puts(line);
                   3984:     fputs(line,ficparo);
1.85      brouard  3985:     fputs(line,ficlog);
1.53      brouard  3986:   }
                   3987:   ungetc(c,ficpar);
1.85      brouard  3988: 
1.53      brouard  3989:    
                   3990:   covar=matrix(0,NCOVMAX,1,n); 
1.58      lievre   3991:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53      brouard  3992:   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
                   3993: 
1.58      lievre   3994:   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53      brouard  3995:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88      brouard  3996:  
                   3997:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
                   3998:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   3999:     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   4000:     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   4001:     fclose (ficparo);
                   4002:     fclose (ficlog);
                   4003:     exit(0);
                   4004:   }
1.53      brouard  4005:   /* Read guess parameters */
                   4006:   /* Reads comments: lines beginning with '#' */
                   4007:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4008:     ungetc(c,ficpar);
                   4009:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4010:     numlinepar++;
1.53      brouard  4011:     puts(line);
                   4012:     fputs(line,ficparo);
1.85      brouard  4013:     fputs(line,ficlog);
1.53      brouard  4014:   }
                   4015:   ungetc(c,ficpar);
1.85      brouard  4016: 
1.53      brouard  4017:   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85      brouard  4018:   for(i=1; i <=nlstate; i++){
                   4019:     j=0;
                   4020:     for(jj=1; jj <=nlstate+ndeath; jj++){
                   4021:       if(jj==i) continue;
                   4022:       j++;
1.53      brouard  4023:       fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85      brouard  4024:       if ((i1 != i) && (j1 != j)){
                   4025:        printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   4026:        exit(1);
                   4027:       }
1.53      brouard  4028:       fprintf(ficparo,"%1d%1d",i1,j1);
                   4029:       if(mle==1)
                   4030:        printf("%1d%1d",i,j);
                   4031:       fprintf(ficlog,"%1d%1d",i,j);
                   4032:       for(k=1; k<=ncovmodel;k++){
                   4033:        fscanf(ficpar," %lf",&param[i][j][k]);
                   4034:        if(mle==1){
                   4035:          printf(" %lf",param[i][j][k]);
                   4036:          fprintf(ficlog," %lf",param[i][j][k]);
                   4037:        }
                   4038:        else
                   4039:          fprintf(ficlog," %lf",param[i][j][k]);
                   4040:        fprintf(ficparo," %lf",param[i][j][k]);
                   4041:       }
                   4042:       fscanf(ficpar,"\n");
1.85      brouard  4043:       numlinepar++;
1.53      brouard  4044:       if(mle==1)
                   4045:        printf("\n");
                   4046:       fprintf(ficlog,"\n");
                   4047:       fprintf(ficparo,"\n");
                   4048:     }
1.85      brouard  4049:   }  
                   4050:   fflush(ficlog);
                   4051: 
1.59      brouard  4052:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53      brouard  4053: 
                   4054:   p=param[1][1];
                   4055:   
                   4056:   /* Reads comments: lines beginning with '#' */
                   4057:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4058:     ungetc(c,ficpar);
                   4059:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4060:     numlinepar++;
1.53      brouard  4061:     puts(line);
                   4062:     fputs(line,ficparo);
1.85      brouard  4063:     fputs(line,ficlog);
1.53      brouard  4064:   }
                   4065:   ungetc(c,ficpar);
                   4066: 
                   4067:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74      brouard  4068:   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53      brouard  4069:   for(i=1; i <=nlstate; i++){
                   4070:     for(j=1; j <=nlstate+ndeath-1; j++){
                   4071:       fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85      brouard  4072:       if ((i1-i)*(j1-j)!=0){
                   4073:        printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   4074:        exit(1);
                   4075:       }
1.53      brouard  4076:       printf("%1d%1d",i,j);
                   4077:       fprintf(ficparo,"%1d%1d",i1,j1);
1.85      brouard  4078:       fprintf(ficlog,"%1d%1d",i1,j1);
1.53      brouard  4079:       for(k=1; k<=ncovmodel;k++){
                   4080:        fscanf(ficpar,"%le",&delti3[i][j][k]);
                   4081:        printf(" %le",delti3[i][j][k]);
                   4082:        fprintf(ficparo," %le",delti3[i][j][k]);
1.85      brouard  4083:        fprintf(ficlog," %le",delti3[i][j][k]);
1.53      brouard  4084:       }
                   4085:       fscanf(ficpar,"\n");
1.85      brouard  4086:       numlinepar++;
1.53      brouard  4087:       printf("\n");
                   4088:       fprintf(ficparo,"\n");
1.85      brouard  4089:       fprintf(ficlog,"\n");
1.53      brouard  4090:     }
                   4091:   }
1.85      brouard  4092:   fflush(ficlog);
                   4093: 
1.53      brouard  4094:   delti=delti3[1][1];
1.74      brouard  4095: 
                   4096: 
                   4097:   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53      brouard  4098:   
                   4099:   /* Reads comments: lines beginning with '#' */
                   4100:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4101:     ungetc(c,ficpar);
                   4102:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4103:     numlinepar++;
1.53      brouard  4104:     puts(line);
                   4105:     fputs(line,ficparo);
1.85      brouard  4106:     fputs(line,ficlog);
1.53      brouard  4107:   }
                   4108:   ungetc(c,ficpar);
                   4109:   
                   4110:   matcov=matrix(1,npar,1,npar);
                   4111:   for(i=1; i <=npar; i++){
                   4112:     fscanf(ficpar,"%s",&str);
                   4113:     if(mle==1)
                   4114:       printf("%s",str);
                   4115:     fprintf(ficlog,"%s",str);
                   4116:     fprintf(ficparo,"%s",str);
                   4117:     for(j=1; j <=i; j++){
                   4118:       fscanf(ficpar," %le",&matcov[i][j]);
                   4119:       if(mle==1){
                   4120:        printf(" %.5le",matcov[i][j]);
                   4121:       }
1.85      brouard  4122:       fprintf(ficlog," %.5le",matcov[i][j]);
1.53      brouard  4123:       fprintf(ficparo," %.5le",matcov[i][j]);
                   4124:     }
                   4125:     fscanf(ficpar,"\n");
1.85      brouard  4126:     numlinepar++;
1.53      brouard  4127:     if(mle==1)
                   4128:       printf("\n");
                   4129:     fprintf(ficlog,"\n");
                   4130:     fprintf(ficparo,"\n");
                   4131:   }
                   4132:   for(i=1; i <=npar; i++)
                   4133:     for(j=i+1;j<=npar;j++)
                   4134:       matcov[i][j]=matcov[j][i];
                   4135:    
                   4136:   if(mle==1)
                   4137:     printf("\n");
                   4138:   fprintf(ficlog,"\n");
                   4139: 
1.85      brouard  4140:   fflush(ficlog);
1.53      brouard  4141: 
1.59      brouard  4142:   /*-------- Rewriting paramater file ----------*/
                   4143:   strcpy(rfileres,"r");    /* "Rparameterfile */
                   4144:   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
                   4145:   strcat(rfileres,".");    /* */
                   4146:   strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   4147:   if((ficres =fopen(rfileres,"w"))==NULL) {
                   4148:     printf("Problem writing new parameter file: %s\n", fileres);goto end;
                   4149:     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
                   4150:   }
                   4151:   fprintf(ficres,"#%s\n",version);
1.53      brouard  4152:     
1.59      brouard  4153:   /*-------- data file ----------*/
                   4154:   if((fic=fopen(datafile,"r"))==NULL)    {
                   4155:     printf("Problem with datafile: %s\n", datafile);goto end;
                   4156:     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
                   4157:   }
                   4158: 
                   4159:   n= lastobs;
                   4160:   severity = vector(1,maxwav);
                   4161:   outcome=imatrix(1,maxwav+1,1,n);
1.85      brouard  4162:   num=lvector(1,n);
1.59      brouard  4163:   moisnais=vector(1,n);
                   4164:   annais=vector(1,n);
                   4165:   moisdc=vector(1,n);
                   4166:   andc=vector(1,n);
                   4167:   agedc=vector(1,n);
                   4168:   cod=ivector(1,n);
                   4169:   weight=vector(1,n);
                   4170:   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
                   4171:   mint=matrix(1,maxwav,1,n);
                   4172:   anint=matrix(1,maxwav,1,n);
                   4173:   s=imatrix(1,maxwav+1,1,n);
                   4174:   tab=ivector(1,NCOVMAX);
                   4175:   ncodemax=ivector(1,8);
                   4176: 
                   4177:   i=1;
                   4178:   while (fgets(line, MAXLINE, fic) != NULL)    {
                   4179:     if ((i >= firstobs) && (i <=lastobs)) {
1.53      brouard  4180:        
1.59      brouard  4181:       for (j=maxwav;j>=1;j--){
                   4182:        cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
                   4183:        strcpy(line,stra);
                   4184:        cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4185:        cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4186:       }
1.53      brouard  4187:        
1.59      brouard  4188:       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4189:       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53      brouard  4190: 
1.59      brouard  4191:       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4192:       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53      brouard  4193: 
1.59      brouard  4194:       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4195:       for (j=ncovcol;j>=1;j--){
                   4196:        cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4197:       } 
1.85      brouard  4198:       lstra=strlen(stra);
                   4199:       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   4200:        stratrunc = &(stra[lstra-9]);
                   4201:        num[i]=atol(stratrunc);
                   4202:       }
                   4203:       else
                   4204:        num[i]=atol(stra);
1.53      brouard  4205:        
1.59      brouard  4206:       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85      brouard  4207:        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
1.53      brouard  4208: 
1.59      brouard  4209:       i=i+1;
                   4210:     }
                   4211:   }
                   4212:   /* printf("ii=%d", ij);
                   4213:      scanf("%d",i);*/
1.53      brouard  4214:   imx=i-1; /* Number of individuals */
                   4215: 
                   4216:   /* for (i=1; i<=imx; i++){
                   4217:     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
                   4218:     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
                   4219:     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
                   4220:     }*/
                   4221:    /*  for (i=1; i<=imx; i++){
                   4222:      if (s[4][i]==9)  s[4][i]=-1; 
1.85      brouard  4223:      printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
1.53      brouard  4224:   
1.71      brouard  4225:  for (i=1; i<=imx; i++)
1.53      brouard  4226:  
1.71      brouard  4227:    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
                   4228:      else weight[i]=1;*/
                   4229: 
1.53      brouard  4230:   /* Calculation of the number of parameter from char model*/
                   4231:   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
                   4232:   Tprod=ivector(1,15); 
                   4233:   Tvaraff=ivector(1,15); 
                   4234:   Tvard=imatrix(1,15,1,2);
                   4235:   Tage=ivector(1,15);      
                   4236:    
1.58      lievre   4237:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53      brouard  4238:     j=0, j1=0, k1=1, k2=1;
1.58      lievre   4239:     j=nbocc(model,'+'); /* j=Number of '+' */
                   4240:     j1=nbocc(model,'*'); /* j1=Number of '*' */
                   4241:     cptcovn=j+1; 
                   4242:     cptcovprod=j1; /*Number of products */
1.53      brouard  4243:     
                   4244:     strcpy(modelsav,model); 
                   4245:     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
                   4246:       printf("Error. Non available option model=%s ",model);
                   4247:       fprintf(ficlog,"Error. Non available option model=%s ",model);
                   4248:       goto end;
                   4249:     }
                   4250:     
1.59      brouard  4251:     /* This loop fills the array Tvar from the string 'model'.*/
1.58      lievre   4252: 
1.53      brouard  4253:     for(i=(j+1); i>=1;i--){
                   4254:       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
1.59      brouard  4255:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53      brouard  4256:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   4257:       /*scanf("%d",i);*/
                   4258:       if (strchr(strb,'*')) {  /* Model includes a product */
                   4259:        cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
                   4260:        if (strcmp(strc,"age")==0) { /* Vn*age */
                   4261:          cptcovprod--;
                   4262:          cutv(strb,stre,strd,'V');
                   4263:          Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
                   4264:          cptcovage++;
                   4265:            Tage[cptcovage]=i;
                   4266:            /*printf("stre=%s ", stre);*/
                   4267:        }
                   4268:        else if (strcmp(strd,"age")==0) { /* or age*Vn */
                   4269:          cptcovprod--;
                   4270:          cutv(strb,stre,strc,'V');
                   4271:          Tvar[i]=atoi(stre);
                   4272:          cptcovage++;
                   4273:          Tage[cptcovage]=i;
                   4274:        }
                   4275:        else {  /* Age is not in the model */
                   4276:          cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
                   4277:          Tvar[i]=ncovcol+k1;
                   4278:          cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
                   4279:          Tprod[k1]=i;
                   4280:          Tvard[k1][1]=atoi(strc); /* m*/
                   4281:          Tvard[k1][2]=atoi(stre); /* n */
                   4282:          Tvar[cptcovn+k2]=Tvard[k1][1];
                   4283:          Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
                   4284:          for (k=1; k<=lastobs;k++) 
                   4285:            covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
                   4286:          k1++;
                   4287:          k2=k2+2;
                   4288:        }
                   4289:       }
                   4290:       else { /* no more sum */
                   4291:        /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   4292:        /*  scanf("%d",i);*/
                   4293:       cutv(strd,strc,strb,'V');
                   4294:       Tvar[i]=atoi(strc);
                   4295:       }
                   4296:       strcpy(modelsav,stra);  
                   4297:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                   4298:        scanf("%d",i);*/
                   4299:     } /* end of loop + */
                   4300:   } /* end model */
                   4301:   
1.58      lievre   4302:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   4303:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
                   4304: 
1.53      brouard  4305:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
                   4306:   printf("cptcovprod=%d ", cptcovprod);
                   4307:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58      lievre   4308: 
                   4309:   scanf("%d ",i);
                   4310:   fclose(fic);*/
1.53      brouard  4311: 
                   4312:     /*  if(mle==1){*/
1.59      brouard  4313:   if (weightopt != 1) { /* Maximisation without weights*/
                   4314:     for(i=1;i<=n;i++) weight[i]=1.0;
                   4315:   }
1.53      brouard  4316:     /*-calculation of age at interview from date of interview and age at death -*/
1.59      brouard  4317:   agev=matrix(1,maxwav,1,imx);
1.53      brouard  4318: 
1.59      brouard  4319:   for (i=1; i<=imx; i++) {
                   4320:     for(m=2; (m<= maxwav); m++) {
1.76      brouard  4321:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59      brouard  4322:        anint[m][i]=9999;
                   4323:        s[m][i]=-1;
                   4324:       }
1.76      brouard  4325:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85      brouard  4326:        printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
                   4327:        fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
1.76      brouard  4328:        s[m][i]=-1;
                   4329:       }
                   4330:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85      brouard  4331:        printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
                   4332:        fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
1.84      brouard  4333:        s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76      brouard  4334:       }
1.53      brouard  4335:     }
1.59      brouard  4336:   }
1.53      brouard  4337: 
1.59      brouard  4338:   for (i=1; i<=imx; i++)  {
                   4339:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71      brouard  4340:     for(m=firstpass; (m<= lastpass); m++){
1.69      brouard  4341:       if(s[m][i] >0){
1.59      brouard  4342:        if (s[m][i] >= nlstate+1) {
                   4343:          if(agedc[i]>0)
1.76      brouard  4344:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69      brouard  4345:              agev[m][i]=agedc[i];
1.59      brouard  4346:          /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
                   4347:            else {
1.76      brouard  4348:              if ((int)andc[i]!=9999){
1.85      brouard  4349:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   4350:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59      brouard  4351:                agev[m][i]=-1;
1.53      brouard  4352:              }
                   4353:            }
1.70      brouard  4354:        }
1.69      brouard  4355:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   4356:                                 years but with the precision of a
                   4357:                                 month */
1.59      brouard  4358:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76      brouard  4359:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59      brouard  4360:            agev[m][i]=1;
                   4361:          else if(agev[m][i] <agemin){ 
                   4362:            agemin=agev[m][i];
                   4363:            /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53      brouard  4364:          }
1.59      brouard  4365:          else if(agev[m][i] >agemax){
                   4366:            agemax=agev[m][i];
                   4367:            /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53      brouard  4368:          }
1.59      brouard  4369:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   4370:          /*     agev[m][i] = age[i]+2*m;*/
1.53      brouard  4371:        }
1.59      brouard  4372:        else { /* =9 */
1.53      brouard  4373:          agev[m][i]=1;
1.59      brouard  4374:          s[m][i]=-1;
                   4375:        }
1.53      brouard  4376:       }
1.59      brouard  4377:       else /*= 0 Unknown */
                   4378:        agev[m][i]=1;
                   4379:     }
1.53      brouard  4380:     
1.59      brouard  4381:   }
                   4382:   for (i=1; i<=imx; i++)  {
1.71      brouard  4383:     for(m=firstpass; (m<=lastpass); m++){
1.59      brouard  4384:       if (s[m][i] > (nlstate+ndeath)) {
                   4385:        printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
                   4386:        fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
                   4387:        goto end;
1.53      brouard  4388:       }
                   4389:     }
1.59      brouard  4390:   }
1.53      brouard  4391: 
1.71      brouard  4392:   /*for (i=1; i<=imx; i++){
                   4393:   for (m=firstpass; (m<lastpass); m++){
1.85      brouard  4394:      printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
1.71      brouard  4395: }
                   4396: 
                   4397: }*/
                   4398: 
1.59      brouard  4399:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
                   4400:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
                   4401: 
                   4402:   free_vector(severity,1,maxwav);
                   4403:   free_imatrix(outcome,1,maxwav+1,1,n);
                   4404:   free_vector(moisnais,1,n);
                   4405:   free_vector(annais,1,n);
                   4406:   /* free_matrix(mint,1,maxwav,1,n);
                   4407:      free_matrix(anint,1,maxwav,1,n);*/
                   4408:   free_vector(moisdc,1,n);
                   4409:   free_vector(andc,1,n);
1.53      brouard  4410: 
                   4411:    
1.59      brouard  4412:   wav=ivector(1,imx);
                   4413:   dh=imatrix(1,lastpass-firstpass+1,1,imx);
                   4414:   bh=imatrix(1,lastpass-firstpass+1,1,imx);
                   4415:   mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69      brouard  4416:    
1.59      brouard  4417:   /* Concatenates waves */
                   4418:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.53      brouard  4419: 
1.59      brouard  4420:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53      brouard  4421: 
1.59      brouard  4422:   Tcode=ivector(1,100);
                   4423:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   4424:   ncodemax[1]=1;
                   4425:   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53      brouard  4426:       
1.59      brouard  4427:   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                   4428:                                 the estimations*/
                   4429:   h=0;
                   4430:   m=pow(2,cptcoveff);
1.53      brouard  4431:  
1.59      brouard  4432:   for(k=1;k<=cptcoveff; k++){
                   4433:     for(i=1; i <=(m/pow(2,k));i++){
                   4434:       for(j=1; j <= ncodemax[k]; j++){
                   4435:        for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
                   4436:          h++;
                   4437:          if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
                   4438:          /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
                   4439:        } 
                   4440:       }
                   4441:     }
                   4442:   } 
                   4443:   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
                   4444:      codtab[1][2]=1;codtab[2][2]=2; */
                   4445:   /* for(i=1; i <=m ;i++){ 
                   4446:      for(k=1; k <=cptcovn; k++){
                   4447:      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
                   4448:      }
                   4449:      printf("\n");
1.53      brouard  4450:      }
1.59      brouard  4451:      scanf("%d",i);*/
1.53      brouard  4452:     
1.86      brouard  4453:   /*------------ gnuplot -------------*/
                   4454:   strcpy(optionfilegnuplot,optionfilefiname);
                   4455:   strcat(optionfilegnuplot,".gp");
                   4456:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   4457:     printf("Problem with file %s",optionfilegnuplot);
                   4458:   }
                   4459:   else{
                   4460:     fprintf(ficgp,"\n# %s\n", version); 
                   4461:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
                   4462:     fprintf(ficgp,"set missing 'NaNq'\n");
                   4463:   }
1.88      brouard  4464:   /*  fclose(ficgp);*/
1.86      brouard  4465:   /*--------- index.htm --------*/
                   4466: 
1.87      brouard  4467:   strcpy(optionfilehtm,optionfilefiname);
1.86      brouard  4468:   strcat(optionfilehtm,".htm");
                   4469:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
                   4470:     printf("Problem with %s \n",optionfilehtm), exit(0);
                   4471:   }
                   4472: 
1.87      brouard  4473:   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86      brouard  4474: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   4475: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
                   4476: \n\
                   4477: <hr  size=\"2\" color=\"#EC5E5E\">\
                   4478:  <ul><li><h4>Parameter files</h4>\n\
                   4479:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   4480:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87      brouard  4481:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86      brouard  4482:  - Date and time at start: %s</ul>\n",\
1.87      brouard  4483:          fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
1.86      brouard  4484:          model,fileres,fileres,\
1.88      brouard  4485:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87      brouard  4486:   /*fclose(fichtm);*/
                   4487:   fflush(fichtm);
1.86      brouard  4488: 
1.88      brouard  4489:   strcpy(pathr,path);
                   4490:   strcat(pathr,optionfilefiname);
                   4491:   chdir(optionfilefiname); /* Move to directory named optionfile */
                   4492:   strcpy(lfileres,fileres);
                   4493:   strcat(lfileres,"/");
                   4494:   strcat(lfileres,optionfilefiname);
                   4495:   
1.59      brouard  4496:   /* Calculates basic frequencies. Computes observed prevalence at single age
                   4497:      and prints on file fileres'p'. */
1.84      brouard  4498:   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53      brouard  4499: 
1.88      brouard  4500:   fprintf(fichtm,"\n");
                   4501:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86      brouard  4502: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   4503: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88      brouard  4504:          imx,agemin,agemax,jmin,jmax,jmean);
                   4505:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60      brouard  4506:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4507:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4508:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4509:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53      brouard  4510:     
                   4511:    
1.59      brouard  4512:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   4513:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   4514:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53      brouard  4515: 
1.86      brouard  4516:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85      brouard  4517:   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   4518:   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   4519:   for (k=1; k<=npar;k++)
                   4520:     printf(" %d %8.5f",k,p[k]);
                   4521:   printf("\n");
                   4522:   globpr=1; /* to print the contributions */
                   4523:   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   4524:   printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   4525:   for (k=1; k<=npar;k++)
                   4526:     printf(" %d %8.5f",k,p[k]);
                   4527:   printf("\n");
1.61      brouard  4528:   if(mle>=1){ /* Could be 1 or 2 */
1.53      brouard  4529:     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59      brouard  4530:   }
1.53      brouard  4531:     
1.59      brouard  4532:   /*--------- results files --------------*/
                   4533:   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);
1.53      brouard  4534:   
                   4535: 
1.59      brouard  4536:   jk=1;
                   4537:   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4538:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4539:   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4540:   for(i=1,jk=1; i <=nlstate; i++){
                   4541:     for(k=1; k <=(nlstate+ndeath); k++){
                   4542:       if (k != i) 
                   4543:        {
                   4544:          printf("%d%d ",i,k);
                   4545:          fprintf(ficlog,"%d%d ",i,k);
                   4546:          fprintf(ficres,"%1d%1d ",i,k);
                   4547:          for(j=1; j <=ncovmodel; j++){
                   4548:            printf("%f ",p[jk]);
                   4549:            fprintf(ficlog,"%f ",p[jk]);
                   4550:            fprintf(ficres,"%f ",p[jk]);
                   4551:            jk++; 
                   4552:          }
                   4553:          printf("\n");
                   4554:          fprintf(ficlog,"\n");
                   4555:          fprintf(ficres,"\n");
                   4556:        }
                   4557:     }
                   4558:   }
1.84      brouard  4559:   if(mle!=0){
1.59      brouard  4560:     /* Computing hessian and covariance matrix */
                   4561:     ftolhess=ftol; /* Usually correct */
                   4562:     hesscov(matcov, p, npar, delti, ftolhess, func);
                   4563:   }
                   4564:   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   4565:   printf("# Scales (for hessian or gradient estimation)\n");
                   4566:   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   4567:   for(i=1,jk=1; i <=nlstate; i++){
                   4568:     for(j=1; j <=nlstate+ndeath; j++){
                   4569:       if (j!=i) {
                   4570:        fprintf(ficres,"%1d%1d",i,j);
                   4571:        printf("%1d%1d",i,j);
                   4572:        fprintf(ficlog,"%1d%1d",i,j);
                   4573:        for(k=1; k<=ncovmodel;k++){
                   4574:          printf(" %.5e",delti[jk]);
                   4575:          fprintf(ficlog," %.5e",delti[jk]);
                   4576:          fprintf(ficres," %.5e",delti[jk]);
                   4577:          jk++;
                   4578:        }
                   4579:        printf("\n");
                   4580:        fprintf(ficlog,"\n");
                   4581:        fprintf(ficres,"\n");
                   4582:       }
                   4583:     }
                   4584:   }
1.53      brouard  4585:    
1.59      brouard  4586:   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");
                   4587:   if(mle==1)
                   4588:     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");
                   4589:   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
                   4590:   for(i=1,k=1;i<=npar;i++){
                   4591:     /*  if (k>nlstate) k=1;
                   4592:        i1=(i-1)/(ncovmodel*nlstate)+1; 
                   4593:        fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
                   4594:        printf("%s%d%d",alph[k],i1,tab[i]);
                   4595:     */
                   4596:     fprintf(ficres,"%3d",i);
                   4597:     if(mle==1)
                   4598:       printf("%3d",i);
                   4599:     fprintf(ficlog,"%3d",i);
                   4600:     for(j=1; j<=i;j++){
                   4601:       fprintf(ficres," %.5e",matcov[i][j]);
                   4602:       if(mle==1)
                   4603:        printf(" %.5e",matcov[i][j]);
                   4604:       fprintf(ficlog," %.5e",matcov[i][j]);
                   4605:     }
                   4606:     fprintf(ficres,"\n");
                   4607:     if(mle==1)
                   4608:       printf("\n");
                   4609:     fprintf(ficlog,"\n");
                   4610:     k++;
                   4611:   }
1.53      brouard  4612:    
1.59      brouard  4613:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4614:     ungetc(c,ficpar);
                   4615:     fgets(line, MAXLINE, ficpar);
                   4616:     puts(line);
                   4617:     fputs(line,ficparo);
                   4618:   }
                   4619:   ungetc(c,ficpar);
                   4620: 
                   4621:   estepm=0;
                   4622:   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
                   4623:   if (estepm==0 || estepm < stepm) estepm=stepm;
                   4624:   if (fage <= 2) {
                   4625:     bage = ageminpar;
                   4626:     fage = agemaxpar;
                   4627:   }
1.53      brouard  4628:    
1.59      brouard  4629:   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
                   4630:   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   4631:   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53      brouard  4632:    
1.59      brouard  4633:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4634:     ungetc(c,ficpar);
                   4635:     fgets(line, MAXLINE, ficpar);
                   4636:     puts(line);
                   4637:     fputs(line,ficparo);
                   4638:   }
                   4639:   ungetc(c,ficpar);
1.53      brouard  4640:   
1.59      brouard  4641:   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
                   4642:   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   4643:   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.69      brouard  4644:   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   4645:   fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.53      brouard  4646:    
1.59      brouard  4647:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4648:     ungetc(c,ficpar);
                   4649:     fgets(line, MAXLINE, ficpar);
                   4650:     puts(line);
                   4651:     fputs(line,ficparo);
                   4652:   }
                   4653:   ungetc(c,ficpar);
1.53      brouard  4654:  
                   4655: 
1.70      brouard  4656:   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   4657:   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53      brouard  4658: 
                   4659:   fscanf(ficpar,"pop_based=%d\n",&popbased);
                   4660:   fprintf(ficparo,"pop_based=%d\n",popbased);   
                   4661:   fprintf(ficres,"pop_based=%d\n",popbased);   
                   4662:   
                   4663:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4664:     ungetc(c,ficpar);
                   4665:     fgets(line, MAXLINE, ficpar);
                   4666:     puts(line);
                   4667:     fputs(line,ficparo);
                   4668:   }
                   4669:   ungetc(c,ficpar);
                   4670: 
1.69      brouard  4671:   fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
1.70      brouard  4672:   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.71      brouard  4673:   printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
                   4674:   fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
                   4675:   fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.69      brouard  4676:   /* day and month of proj2 are not used but only year anproj2.*/
1.53      brouard  4677: 
1.59      brouard  4678:   while((c=getc(ficpar))=='#' && c!= EOF){
1.53      brouard  4679:     ungetc(c,ficpar);
                   4680:     fgets(line, MAXLINE, ficpar);
                   4681:     puts(line);
                   4682:     fputs(line,ficparo);
                   4683:   }
                   4684:   ungetc(c,ficpar);
                   4685: 
                   4686:   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
                   4687:   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
                   4688:   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
                   4689: 
1.86      brouard  4690:   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84      brouard  4691:   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58      lievre   4692: 
1.89      brouard  4693:   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
                   4694:   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53      brouard  4695: 
1.85      brouard  4696:   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                   4697:               model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                   4698:               jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53      brouard  4699:  
1.59      brouard  4700:   /*------------ free_vector  -------------*/
1.88      brouard  4701:   /*  chdir(path); */
1.53      brouard  4702:  
1.59      brouard  4703:   free_ivector(wav,1,imx);
                   4704:   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
                   4705:   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
                   4706:   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
1.85      brouard  4707:   free_lvector(num,1,n);
1.59      brouard  4708:   free_vector(agedc,1,n);
1.65      lievre   4709:   /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59      brouard  4710:   /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   4711:   fclose(ficparo);
                   4712:   fclose(ficres);
1.53      brouard  4713: 
                   4714: 
1.54      brouard  4715:   /*--------------- Prevalence limit  (stable prevalence) --------------*/
1.53      brouard  4716:   
                   4717:   strcpy(filerespl,"pl");
                   4718:   strcat(filerespl,fileres);
                   4719:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54      brouard  4720:     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
                   4721:     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53      brouard  4722:   }
1.54      brouard  4723:   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
                   4724:   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
                   4725:   fprintf(ficrespl,"#Stable prevalence \n");
1.53      brouard  4726:   fprintf(ficrespl,"#Age ");
                   4727:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   4728:   fprintf(ficrespl,"\n");
                   4729:   
                   4730:   prlim=matrix(1,nlstate,1,nlstate);
1.59      brouard  4731: 
1.53      brouard  4732:   agebase=ageminpar;
                   4733:   agelim=agemaxpar;
                   4734:   ftolpl=1.e-10;
                   4735:   i1=cptcoveff;
                   4736:   if (cptcovn < 1){i1=1;}
                   4737: 
1.59      brouard  4738:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4739:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59      brouard  4740:       k=k+1;
                   4741:       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
                   4742:       fprintf(ficrespl,"\n#******");
                   4743:       printf("\n#******");
                   4744:       fprintf(ficlog,"\n#******");
                   4745:       for(j=1;j<=cptcoveff;j++) {
                   4746:        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4747:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4748:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4749:       }
                   4750:       fprintf(ficrespl,"******\n");
                   4751:       printf("******\n");
                   4752:       fprintf(ficlog,"******\n");
1.53      brouard  4753:        
1.59      brouard  4754:       for (age=agebase; age<=agelim; age++){
                   4755:        prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69      brouard  4756:        fprintf(ficrespl,"%.0f ",age );
                   4757:         for(j=1;j<=cptcoveff;j++)
                   4758:          fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59      brouard  4759:        for(i=1; i<=nlstate;i++)
1.53      brouard  4760:          fprintf(ficrespl," %.5f", prlim[i][i]);
1.59      brouard  4761:        fprintf(ficrespl,"\n");
1.53      brouard  4762:       }
                   4763:     }
1.59      brouard  4764:   }
1.53      brouard  4765:   fclose(ficrespl);
                   4766: 
                   4767:   /*------------- h Pij x at various ages ------------*/
                   4768:   
                   4769:   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
                   4770:   if((ficrespij=fopen(filerespij,"w"))==NULL) {
                   4771:     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
                   4772:     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
                   4773:   }
                   4774:   printf("Computing pij: result on file '%s' \n", filerespij);
                   4775:   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
                   4776:   
                   4777:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4778:   /*if (stepm<=24) stepsize=2;*/
                   4779: 
                   4780:   agelim=AGESUP;
                   4781:   hstepm=stepsize*YEARM; /* Every year of age */
                   4782:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   4783: 
                   4784:   /* hstepm=1;   aff par mois*/
                   4785: 
1.70      brouard  4786:   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59      brouard  4787:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4788:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   4789:       k=k+1;
1.59      brouard  4790:       fprintf(ficrespij,"\n#****** ");
                   4791:       for(j=1;j<=cptcoveff;j++) 
                   4792:        fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4793:       fprintf(ficrespij,"******\n");
1.53      brouard  4794:        
1.59      brouard  4795:       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                   4796:        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   4797:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   4798: 
                   4799:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   4800: 
                   4801:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4802:        oldm=oldms;savm=savms;
                   4803:        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
1.70      brouard  4804:        fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59      brouard  4805:        for(i=1; i<=nlstate;i++)
                   4806:          for(j=1; j<=nlstate+ndeath;j++)
                   4807:            fprintf(ficrespij," %1d-%1d",i,j);
                   4808:        fprintf(ficrespij,"\n");
                   4809:        for (h=0; h<=nhstepm; h++){
1.70      brouard  4810:          fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53      brouard  4811:          for(i=1; i<=nlstate;i++)
                   4812:            for(j=1; j<=nlstate+ndeath;j++)
1.59      brouard  4813:              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53      brouard  4814:          fprintf(ficrespij,"\n");
                   4815:        }
1.59      brouard  4816:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4817:        fprintf(ficrespij,"\n");
                   4818:       }
1.53      brouard  4819:     }
                   4820:   }
                   4821: 
1.74      brouard  4822:   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53      brouard  4823: 
                   4824:   fclose(ficrespij);
                   4825: 
1.84      brouard  4826:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  4827: 
                   4828:   /*---------- Forecasting ------------------*/
1.69      brouard  4829:   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
                   4830:   if(prevfcast==1){
1.74      brouard  4831:     /*    if(stepm ==1){*/
1.70      brouard  4832:       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74      brouard  4833:       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
                   4834: /*      }  */
                   4835: /*      else{ */
                   4836: /*        erreur=108; */
                   4837: /*        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); */
                   4838: /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
                   4839: /*      } */
1.69      brouard  4840:   }
1.53      brouard  4841:   
                   4842: 
                   4843:   /*---------- Health expectancies and variances ------------*/
                   4844: 
                   4845:   strcpy(filerest,"t");
                   4846:   strcat(filerest,fileres);
                   4847:   if((ficrest=fopen(filerest,"w"))==NULL) {
                   4848:     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   4849:     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   4850:   }
                   4851:   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
                   4852:   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
                   4853: 
                   4854: 
                   4855:   strcpy(filerese,"e");
                   4856:   strcat(filerese,fileres);
                   4857:   if((ficreseij=fopen(filerese,"w"))==NULL) {
                   4858:     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   4859:     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   4860:   }
                   4861:   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
                   4862:   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68      lievre   4863: 
1.53      brouard  4864:   strcpy(fileresv,"v");
                   4865:   strcat(fileresv,fileres);
                   4866:   if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   4867:     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   4868:     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   4869:   }
                   4870:   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   4871:   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58      lievre   4872: 
1.74      brouard  4873:   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84      brouard  4874:   prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74      brouard  4875:   /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
                   4876: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
                   4877:   */
1.58      lievre   4878: 
1.54      brouard  4879:   if (mobilav!=0) {
1.53      brouard  4880:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  4881:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   4882:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   4883:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   4884:     }
1.53      brouard  4885:   }
                   4886: 
1.59      brouard  4887:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4888:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   4889:       k=k+1; 
                   4890:       fprintf(ficrest,"\n#****** ");
                   4891:       for(j=1;j<=cptcoveff;j++) 
                   4892:        fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4893:       fprintf(ficrest,"******\n");
                   4894: 
                   4895:       fprintf(ficreseij,"\n#****** ");
                   4896:       for(j=1;j<=cptcoveff;j++) 
                   4897:        fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4898:       fprintf(ficreseij,"******\n");
                   4899: 
                   4900:       fprintf(ficresvij,"\n#****** ");
                   4901:       for(j=1;j<=cptcoveff;j++) 
                   4902:        fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4903:       fprintf(ficresvij,"******\n");
                   4904: 
                   4905:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   4906:       oldm=oldms;savm=savms;
                   4907:       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
                   4908:  
                   4909:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   4910:       oldm=oldms;savm=savms;
                   4911:       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
                   4912:       if(popbased==1){
                   4913:        varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59      brouard  4914:       }
1.53      brouard  4915: 
                   4916:  
                   4917:       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
                   4918:       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   4919:       fprintf(ficrest,"\n");
                   4920: 
                   4921:       epj=vector(1,nlstate+1);
                   4922:       for(age=bage; age <=fage ;age++){
                   4923:        prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
                   4924:        if (popbased==1) {
1.54      brouard  4925:          if(mobilav ==0){
1.53      brouard  4926:            for(i=1; i<=nlstate;i++)
                   4927:              prlim[i][i]=probs[(int)age][i][k];
1.54      brouard  4928:          }else{ /* mobilav */ 
1.53      brouard  4929:            for(i=1; i<=nlstate;i++)
                   4930:              prlim[i][i]=mobaverage[(int)age][i][k];
                   4931:          }
                   4932:        }
                   4933:        
                   4934:        fprintf(ficrest," %4.0f",age);
                   4935:        for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   4936:          for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   4937:            epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   4938:            /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   4939:          }
                   4940:          epj[nlstate+1] +=epj[j];
                   4941:        }
                   4942: 
                   4943:        for(i=1, vepp=0.;i <=nlstate;i++)
                   4944:          for(j=1;j <=nlstate;j++)
                   4945:            vepp += vareij[i][j][(int)age];
                   4946:        fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   4947:        for(j=1;j <=nlstate;j++){
                   4948:          fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   4949:        }
                   4950:        fprintf(ficrest,"\n");
                   4951:       }
1.59      brouard  4952:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   4953:       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   4954:       free_vector(epj,1,nlstate+1);
1.53      brouard  4955:     }
                   4956:   }
1.59      brouard  4957:   free_vector(weight,1,n);
                   4958:   free_imatrix(Tvard,1,15,1,2);
                   4959:   free_imatrix(s,1,maxwav+1,1,n);
                   4960:   free_matrix(anint,1,maxwav,1,n); 
                   4961:   free_matrix(mint,1,maxwav,1,n);
                   4962:   free_ivector(cod,1,n);
                   4963:   free_ivector(tab,1,NCOVMAX);
1.53      brouard  4964:   fclose(ficreseij);
                   4965:   fclose(ficresvij);
                   4966:   fclose(ficrest);
                   4967:   fclose(ficpar);
                   4968:   
1.54      brouard  4969:   /*------- Variance of stable prevalence------*/   
1.53      brouard  4970: 
                   4971:   strcpy(fileresvpl,"vpl");
                   4972:   strcat(fileresvpl,fileres);
                   4973:   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54      brouard  4974:     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
1.53      brouard  4975:     exit(0);
                   4976:   }
1.54      brouard  4977:   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53      brouard  4978: 
1.59      brouard  4979:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4980:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   4981:       k=k+1;
                   4982:       fprintf(ficresvpl,"\n#****** ");
                   4983:       for(j=1;j<=cptcoveff;j++) 
                   4984:        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4985:       fprintf(ficresvpl,"******\n");
                   4986:       
                   4987:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   4988:       oldm=oldms;savm=savms;
1.59      brouard  4989:       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
                   4990:       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53      brouard  4991:     }
1.59      brouard  4992:   }
1.53      brouard  4993: 
                   4994:   fclose(ficresvpl);
                   4995: 
                   4996:   /*---------- End : free ----------------*/
                   4997:   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
                   4998:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   4999:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   5000:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65      lievre   5001:   
                   5002:   free_matrix(covar,0,NCOVMAX,1,n);
1.53      brouard  5003:   free_matrix(matcov,1,npar,1,npar);
1.74      brouard  5004:   /*free_vector(delti,1,npar);*/
                   5005:   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
1.53      brouard  5006:   free_matrix(agev,1,maxwav,1,imx);
                   5007:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54      brouard  5008:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74      brouard  5009:   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   5010: 
1.59      brouard  5011:   free_ivector(ncodemax,1,8);
                   5012:   free_ivector(Tvar,1,15);
                   5013:   free_ivector(Tprod,1,15);
                   5014:   free_ivector(Tvaraff,1,15);
                   5015:   free_ivector(Tage,1,15);
                   5016:   free_ivector(Tcode,1,100);
1.53      brouard  5017: 
1.88      brouard  5018:   fflush(fichtm);
                   5019:   fflush(ficgp);
1.53      brouard  5020:   
                   5021: 
                   5022:   if(erreur >0){
                   5023:     printf("End of Imach with error or warning %d\n",erreur);
                   5024:     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
                   5025:   }else{
                   5026:    printf("End of Imach\n");
                   5027:    fprintf(ficlog,"End of Imach\n");
                   5028:   }
                   5029:   printf("See log file on %s\n",filelog);
                   5030:   fclose(ficlog);
                   5031:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
1.85      brouard  5032:   (void) gettimeofday(&end_time,&tzp);
                   5033:   tm = *localtime(&end_time.tv_sec);
                   5034:   tmg = *gmtime(&end_time.tv_sec);
1.88      brouard  5035:   strcpy(strtend,asctime(&tm));
                   5036:   printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
                   5037:   fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
1.85      brouard  5038:   /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
                   5039: 
                   5040:   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);
                   5041:   fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
                   5042:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
1.87      brouard  5043: /*   if(fileappend(fichtm,optionfilehtm)){ */
1.88      brouard  5044:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
1.87      brouard  5045:   fclose(fichtm);
1.88      brouard  5046:   fclose(ficgp);
1.53      brouard  5047:   /*------ End -----------*/
                   5048: 
1.59      brouard  5049:   end:
1.53      brouard  5050: #ifdef windows
                   5051:   /* chdir(pathcd);*/
                   5052: #endif 
1.88      brouard  5053:   chdir(path);
1.53      brouard  5054:  /*system("wgnuplot graph.plt");*/
                   5055:  /*system("../gp37mgw/wgnuplot graph.plt");*/
                   5056:  /*system("cd ../gp37mgw");*/
                   5057:  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59      brouard  5058:   strcpy(plotcmd,GNUPLOTPROGRAM);
                   5059:   strcat(plotcmd," ");
                   5060:   strcat(plotcmd,optionfilegnuplot);
1.75      brouard  5061:   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59      brouard  5062:   system(plotcmd);
1.75      brouard  5063:   printf(" Wait...");
1.53      brouard  5064: 
1.54      brouard  5065:  /*#ifdef windows*/
1.53      brouard  5066:   while (z[0] != 'q') {
                   5067:     /* chdir(path); */
                   5068:     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
                   5069:     scanf("%s",z);
                   5070:     if (z[0] == 'c') system("./imach");
                   5071:     else if (z[0] == 'e') system(optionfilehtm);
                   5072:     else if (z[0] == 'g') system(plotcmd);
                   5073:     else if (z[0] == 'q') exit(0);
                   5074:   }
1.54      brouard  5075:   /*#endif */
1.53      brouard  5076: }
1.88      brouard  5077: 
1.53      brouard  5078: 
                   5079: 

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