Annotation of imach096d/src/imach.c, revision 1.97

1.97    ! lievre      1: /* $Id: imach.c,v 1.96 2003/07/15 15:38:55 brouard Exp $
1.83      lievre      2:   $State: Exp $
                      3:   $Log: imach.c,v $
1.97    ! lievre      4:   Revision 1.96  2003/07/15 15:38:55  brouard
        !             5:   * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
        !             6:   rewritten within the same printf. Workaround: many printfs.
        !             7: 
1.96      brouard     8:   Revision 1.95  2003/07/08 07:54:34  brouard
                      9:   * imach.c (Repository):
                     10:   (Repository): Using imachwizard code to output a more meaningful covariance
                     11:   matrix (cov(a12,c31) instead of numbers.
                     12: 
1.95      brouard    13:   Revision 1.94  2003/06/27 13:00:02  brouard
                     14:   Just cleaning
                     15: 
1.94      brouard    16:   Revision 1.93  2003/06/25 16:33:55  brouard
                     17:   (Module): On windows (cygwin) function asctime_r doesn't
                     18:   exist so I changed back to asctime which exists.
                     19:   (Module): Version 0.96b
                     20: 
1.93      brouard    21:   Revision 1.92  2003/06/25 16:30:45  brouard
                     22:   (Module): On windows (cygwin) function asctime_r doesn't
                     23:   exist so I changed back to asctime which exists.
                     24: 
1.92      brouard    25:   Revision 1.91  2003/06/25 15:30:29  brouard
                     26:   * imach.c (Repository): Duplicated warning errors corrected.
                     27:   (Repository): Elapsed time after each iteration is now output. It
                     28:   helps to forecast when convergence will be reached. Elapsed time
                     29:   is stamped in powell.  We created a new html file for the graphs
                     30:   concerning matrix of covariance. It has extension -cov.htm.
                     31: 
1.91      brouard    32:   Revision 1.90  2003/06/24 12:34:15  brouard
                     33:   (Module): Some bugs corrected for windows. Also, when
                     34:   mle=-1 a template is output in file "or"mypar.txt with the design
                     35:   of the covariance matrix to be input.
                     36: 
1.90      brouard    37:   Revision 1.89  2003/06/24 12:30:52  brouard
                     38:   (Module): Some bugs corrected for windows. Also, when
                     39:   mle=-1 a template is output in file "or"mypar.txt with the design
                     40:   of the covariance matrix to be input.
                     41: 
1.89      brouard    42:   Revision 1.88  2003/06/23 17:54:56  brouard
                     43:   * 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.
                     44: 
1.88      brouard    45:   Revision 1.87  2003/06/18 12:26:01  brouard
                     46:   Version 0.96
                     47: 
1.87      brouard    48:   Revision 1.86  2003/06/17 20:04:08  brouard
                     49:   (Module): Change position of html and gnuplot routines and added
                     50:   routine fileappend.
                     51: 
1.86      brouard    52:   Revision 1.85  2003/06/17 13:12:43  brouard
                     53:   * imach.c (Repository): Check when date of death was earlier that
                     54:   current date of interview. It may happen when the death was just
                     55:   prior to the death. In this case, dh was negative and likelihood
                     56:   was wrong (infinity). We still send an "Error" but patch by
                     57:   assuming that the date of death was just one stepm after the
                     58:   interview.
                     59:   (Repository): Because some people have very long ID (first column)
                     60:   we changed int to long in num[] and we added a new lvector for
                     61:   memory allocation. But we also truncated to 8 characters (left
                     62:   truncation)
                     63:   (Repository): No more line truncation errors.
                     64: 
1.85      brouard    65:   Revision 1.84  2003/06/13 21:44:43  brouard
                     66:   * imach.c (Repository): Replace "freqsummary" at a correct
                     67:   place. It differs from routine "prevalence" which may be called
                     68:   many times. Probs is memory consuming and must be used with
                     69:   parcimony.
1.86      brouard    70:   Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85      brouard    71: 
1.84      brouard    72:   Revision 1.83  2003/06/10 13:39:11  lievre
                     73:   *** empty log message ***
                     74: 
1.83      lievre     75:   Revision 1.82  2003/06/05 15:57:20  brouard
                     76:   Add log in  imach.c and  fullversion number is now printed.
                     77: 
1.82      brouard    78: */
                     79: /*
1.53      brouard    80:    Interpolated Markov Chain
                     81: 
                     82:   Short summary of the programme:
                     83:   
                     84:   This program computes Healthy Life Expectancies from
                     85:   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
                     86:   first survey ("cross") where individuals from different ages are
                     87:   interviewed on their health status or degree of disability (in the
                     88:   case of a health survey which is our main interest) -2- at least a
                     89:   second wave of interviews ("longitudinal") which measure each change
                     90:   (if any) in individual health status.  Health expectancies are
                     91:   computed from the time spent in each health state according to a
                     92:   model. More health states you consider, more time is necessary to reach the
                     93:   Maximum Likelihood of the parameters involved in the model.  The
                     94:   simplest model is the multinomial logistic model where pij is the
                     95:   probability to be observed in state j at the second wave
                     96:   conditional to be observed in state i at the first wave. Therefore
                     97:   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
                     98:   'age' is age and 'sex' is a covariate. If you want to have a more
                     99:   complex model than "constant and age", you should modify the program
                    100:   where the markup *Covariates have to be included here again* invites
                    101:   you to do it.  More covariates you add, slower the
                    102:   convergence.
                    103: 
                    104:   The advantage of this computer programme, compared to a simple
                    105:   multinomial logistic model, is clear when the delay between waves is not
                    106:   identical for each individual. Also, if a individual missed an
                    107:   intermediate interview, the information is lost, but taken into
                    108:   account using an interpolation or extrapolation.  
                    109: 
                    110:   hPijx is the probability to be observed in state i at age x+h
                    111:   conditional to the observed state i at age x. The delay 'h' can be
                    112:   split into an exact number (nh*stepm) of unobserved intermediate
1.66      brouard   113:   states. This elementary transition (by month, quarter,
                    114:   semester or year) is modelled as a multinomial logistic.  The hPx
1.53      brouard   115:   matrix is simply the matrix product of nh*stepm elementary matrices
                    116:   and the contribution of each individual to the likelihood is simply
                    117:   hPijx.
                    118: 
                    119:   Also this programme outputs the covariance matrix of the parameters but also
1.54      brouard   120:   of the life expectancies. It also computes the stable prevalence. 
1.53      brouard   121:   
                    122:   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
                    123:            Institut national d'études démographiques, Paris.
                    124:   This software have been partly granted by Euro-REVES, a concerted action
                    125:   from the European Union.
                    126:   It is copyrighted identically to a GNU software product, ie programme and
                    127:   software can be distributed freely for non commercial use. Latest version
                    128:   can be accessed at http://euroreves.ined.fr/imach .
1.74      brouard   129: 
                    130:   Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
                    131:   or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
                    132:   
1.53      brouard   133:   **********************************************************************/
1.74      brouard   134: /*
                    135:   main
                    136:   read parameterfile
                    137:   read datafile
                    138:   concatwav
1.84      brouard   139:   freqsummary
1.74      brouard   140:   if (mle >= 1)
                    141:     mlikeli
                    142:   print results files
                    143:   if mle==1 
                    144:      computes hessian
                    145:   read end of parameter file: agemin, agemax, bage, fage, estepm
                    146:       begin-prev-date,...
                    147:   open gnuplot file
                    148:   open html file
                    149:   stable prevalence
                    150:    for age prevalim()
                    151:   h Pij x
                    152:   variance of p varprob
                    153:   forecasting if prevfcast==1 prevforecast call prevalence()
                    154:   health expectancies
                    155:   Variance-covariance of DFLE
                    156:   prevalence()
                    157:    movingaverage()
                    158:   varevsij() 
                    159:   if popbased==1 varevsij(,popbased)
                    160:   total life expectancies
                    161:   Variance of stable prevalence
                    162:  end
                    163: */
                    164: 
                    165: 
                    166: 
1.53      brouard   167:  
                    168: #include <math.h>
                    169: #include <stdio.h>
                    170: #include <stdlib.h>
                    171: #include <unistd.h>
                    172: 
1.86      brouard   173: #include <sys/time.h>
                    174: #include <time.h>
                    175: #include "timeval.h"
                    176: 
1.95      brouard   177: /* #include <libintl.h> */
                    178: /* #define _(String) gettext (String) */
                    179: 
1.53      brouard   180: #define MAXLINE 256
                    181: #define GNUPLOTPROGRAM "gnuplot"
                    182: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85      brouard   183: #define FILENAMELENGTH 132
1.53      brouard   184: /*#define DEBUG*/
1.85      brouard   185: /*#define windows*/
1.53      brouard   186: #define        GLOCK_ERROR_NOPATH              -1      /* empty path */
                    187: #define        GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
                    188: 
                    189: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
                    190: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
                    191: 
                    192: #define NINTERVMAX 8
                    193: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
                    194: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
                    195: #define NCOVMAX 8 /* Maximum number of covariates */
                    196: #define MAXN 20000
                    197: #define YEARM 12. /* Number of months per year */
                    198: #define AGESUP 130
                    199: #define AGEBASE 40
1.85      brouard   200: #ifdef unix
                    201: #define DIRSEPARATOR '/'
                    202: #define ODIRSEPARATOR '\\'
                    203: #else
1.53      brouard   204: #define DIRSEPARATOR '\\'
                    205: #define ODIRSEPARATOR '/'
                    206: #endif
                    207: 
1.97    ! lievre    208: /* $Id: imach.c,v 1.96 2003/07/15 15:38:55 brouard Exp $ */
1.81      brouard   209: /* $State: Exp $ */
1.80      brouard   210: 
1.97    ! lievre    211: char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
        !           212: char fullversion[]="$Revision: 1.96 $ $Date: 2003/07/15 15:38:55 $"; 
1.91      brouard   213: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
1.53      brouard   214: int nvar;
                    215: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
                    216: int npar=NPARMAX;
                    217: int nlstate=2; /* Number of live states */
                    218: int ndeath=1; /* Number of dead states */
                    219: int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
                    220: int popbased=0;
                    221: 
                    222: int *wav; /* Number of waves for this individuual 0 is possible */
                    223: int maxwav; /* Maxim number of waves */
                    224: int jmin, jmax; /* min, max spacing between 2 waves */
1.87      brouard   225: int gipmx, gsw; /* Global variables on the number of contributions 
                    226:                   to the likelihood and the sum of weights (done by funcone)*/
1.53      brouard   227: int mle, weightopt;
                    228: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
                    229: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59      brouard   230: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
                    231:           * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53      brouard   232: double jmean; /* Mean space between 2 waves */
                    233: double **oldm, **newm, **savm; /* Working pointers to matrices */
                    234: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
                    235: FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76      brouard   236: FILE *ficlog, *ficrespow;
1.85      brouard   237: int globpr; /* Global variable for printing or not */
                    238: double fretone; /* Only one call to likelihood */
                    239: long ipmx; /* Number of contributions */
                    240: double sw; /* Sum of weights */
                    241: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
                    242: FILE *ficresilk;
1.53      brouard   243: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
                    244: FILE *ficresprobmorprev;
1.91      brouard   245: FILE *fichtm, *fichtmcov; /* Html File */
1.53      brouard   246: FILE *ficreseij;
                    247: char filerese[FILENAMELENGTH];
                    248: FILE  *ficresvij;
                    249: char fileresv[FILENAMELENGTH];
                    250: FILE  *ficresvpl;
                    251: char fileresvpl[FILENAMELENGTH];
                    252: char title[MAXLINE];
                    253: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
                    254: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.96      brouard   255: char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
1.88      brouard   256: char command[FILENAMELENGTH];
                    257: int  outcmd=0;
1.53      brouard   258: 
                    259: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94      brouard   260: 
1.53      brouard   261: char filelog[FILENAMELENGTH]; /* Log file */
                    262: char filerest[FILENAMELENGTH];
                    263: char fileregp[FILENAMELENGTH];
                    264: char popfile[FILENAMELENGTH];
                    265: 
1.91      brouard   266: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
                    267: 
                    268: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
                    269: struct timezone tzp;
                    270: extern int gettimeofday();
                    271: struct tm tmg, tm, tmf, *gmtime(), *localtime();
                    272: long time_value;
                    273: extern long time();
                    274: char strcurr[80], strfor[80];
1.53      brouard   275: 
                    276: #define NR_END 1
                    277: #define FREE_ARG char*
                    278: #define FTOL 1.0e-10
                    279: 
                    280: #define NRANSI 
                    281: #define ITMAX 200 
                    282: 
                    283: #define TOL 2.0e-4 
                    284: 
                    285: #define CGOLD 0.3819660 
                    286: #define ZEPS 1.0e-10 
                    287: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
                    288: 
                    289: #define GOLD 1.618034 
                    290: #define GLIMIT 100.0 
                    291: #define TINY 1.0e-20 
                    292: 
                    293: static double maxarg1,maxarg2;
                    294: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
                    295: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                    296:   
                    297: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
                    298: #define rint(a) floor(a+0.5)
                    299: 
                    300: static double sqrarg;
                    301: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
                    302: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                    303: 
                    304: int imx; 
                    305: int stepm;
                    306: /* Stepm, step in month: minimum step interpolation*/
                    307: 
                    308: int estepm;
                    309: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
                    310: 
                    311: int m,nb;
1.85      brouard   312: long *num;
                    313: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53      brouard   314: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55      lievre    315: double **pmmij, ***probs;
1.53      brouard   316: double dateintmean=0;
                    317: 
                    318: double *weight;
                    319: int **s; /* Status */
                    320: double *agedc, **covar, idx;
                    321: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
                    322: 
                    323: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
                    324: double ftolhess; /* Tolerance for computing hessian */
                    325: 
                    326: /**************** split *************************/
                    327: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
                    328: {
1.59      brouard   329:   char *ss;                            /* pointer */
                    330:   int  l1, l2;                         /* length counters */
1.53      brouard   331: 
1.59      brouard   332:   l1 = strlen(path );                  /* length of path */
                    333:   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
                    334:   ss= strrchr( path, DIRSEPARATOR );           /* find last / */
                    335:   if ( ss == NULL ) {                  /* no directory, so use current */
                    336:     /*if(strrchr(path, ODIRSEPARATOR )==NULL)
                    337:       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74      brouard   338:     /* get current working directory */
                    339:     /*    extern  char* getcwd ( char *buf , int len);*/
1.59      brouard   340:     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
                    341:       return( GLOCK_ERROR_GETCWD );
                    342:     }
                    343:     strcpy( name, path );              /* we've got it */
                    344:   } else {                             /* strip direcotry from path */
                    345:     ss++;                              /* after this, the filename */
                    346:     l2 = strlen( ss );                 /* length of filename */
                    347:     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
                    348:     strcpy( name, ss );                /* save file name */
                    349:     strncpy( dirc, path, l1 - l2 );    /* now the directory */
                    350:     dirc[l1-l2] = 0;                   /* add zero */
                    351:   }
                    352:   l1 = strlen( dirc );                 /* length of directory */
1.85      brouard   353:   /*#ifdef windows
1.59      brouard   354:   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53      brouard   355: #else
1.59      brouard   356:   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53      brouard   357: #endif
1.85      brouard   358:   */
1.59      brouard   359:   ss = strrchr( name, '.' );           /* find last / */
                    360:   ss++;
                    361:   strcpy(ext,ss);                      /* save extension */
                    362:   l1= strlen( name);
                    363:   l2= strlen(ss)+1;
                    364:   strncpy( finame, name, l1-l2);
                    365:   finame[l1-l2]= 0;
                    366:   return( 0 );                         /* we're done */
1.53      brouard   367: }
                    368: 
                    369: 
                    370: /******************************************/
                    371: 
1.89      brouard   372: void replace_back_to_slash(char *s, char*t)
1.53      brouard   373: {
                    374:   int i;
1.89      brouard   375:   int lg=0;
1.53      brouard   376:   i=0;
                    377:   lg=strlen(t);
                    378:   for(i=0; i<= lg; i++) {
                    379:     (s[i] = t[i]);
                    380:     if (t[i]== '\\') s[i]='/';
                    381:   }
                    382: }
                    383: 
                    384: int nbocc(char *s, char occ)
                    385: {
                    386:   int i,j=0;
                    387:   int lg=20;
                    388:   i=0;
                    389:   lg=strlen(s);
                    390:   for(i=0; i<= lg; i++) {
                    391:   if  (s[i] == occ ) j++;
                    392:   }
                    393:   return j;
                    394: }
                    395: 
                    396: void cutv(char *u,char *v, char*t, char occ)
                    397: {
                    398:   /* cuts string t into u and v where u is ended by char occ excluding it
                    399:      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
                    400:      gives u="abcedf" and v="ghi2j" */
                    401:   int i,lg,j,p=0;
                    402:   i=0;
                    403:   for(j=0; j<=strlen(t)-1; j++) {
                    404:     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
                    405:   }
                    406: 
                    407:   lg=strlen(t);
                    408:   for(j=0; j<p; j++) {
                    409:     (u[j] = t[j]);
                    410:   }
                    411:      u[p]='\0';
                    412: 
                    413:    for(j=0; j<= lg; j++) {
                    414:     if (j>=(p+1))(v[j-p-1] = t[j]);
                    415:   }
                    416: }
                    417: 
                    418: /********************** nrerror ********************/
                    419: 
                    420: void nrerror(char error_text[])
                    421: {
                    422:   fprintf(stderr,"ERREUR ...\n");
                    423:   fprintf(stderr,"%s\n",error_text);
1.59      brouard   424:   exit(EXIT_FAILURE);
1.53      brouard   425: }
                    426: /*********************** vector *******************/
                    427: double *vector(int nl, int nh)
                    428: {
                    429:   double *v;
                    430:   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                    431:   if (!v) nrerror("allocation failure in vector");
                    432:   return v-nl+NR_END;
                    433: }
                    434: 
                    435: /************************ free vector ******************/
                    436: void free_vector(double*v, int nl, int nh)
                    437: {
                    438:   free((FREE_ARG)(v+nl-NR_END));
                    439: }
                    440: 
                    441: /************************ivector *******************************/
1.85      brouard   442: int *ivector(long nl,long nh)
1.76      brouard   443: {
1.85      brouard   444:   int *v;
                    445:   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                    446:   if (!v) nrerror("allocation failure in ivector");
1.76      brouard   447:   return v-nl+NR_END;
                    448: }
                    449: 
                    450: /******************free ivector **************************/
1.85      brouard   451: void free_ivector(int *v, long nl, long nh)
1.76      brouard   452: {
                    453:   free((FREE_ARG)(v+nl-NR_END));
                    454: }
                    455: 
1.85      brouard   456: /************************lvector *******************************/
                    457: long *lvector(long nl,long nh)
1.53      brouard   458: {
1.85      brouard   459:   long *v;
                    460:   v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53      brouard   461:   if (!v) nrerror("allocation failure in ivector");
                    462:   return v-nl+NR_END;
                    463: }
                    464: 
1.85      brouard   465: /******************free lvector **************************/
                    466: void free_lvector(long *v, long nl, long nh)
1.53      brouard   467: {
                    468:   free((FREE_ARG)(v+nl-NR_END));
                    469: }
                    470: 
                    471: /******************* imatrix *******************************/
                    472: int **imatrix(long nrl, long nrh, long ncl, long nch) 
                    473:      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
                    474: { 
                    475:   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
                    476:   int **m; 
                    477:   
                    478:   /* allocate pointers to rows */ 
                    479:   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
                    480:   if (!m) nrerror("allocation failure 1 in matrix()"); 
                    481:   m += NR_END; 
                    482:   m -= nrl; 
                    483:   
                    484:   
                    485:   /* allocate rows and set pointers to them */ 
                    486:   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
                    487:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
                    488:   m[nrl] += NR_END; 
                    489:   m[nrl] -= ncl; 
                    490:   
                    491:   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
                    492:   
                    493:   /* return pointer to array of pointers to rows */ 
                    494:   return m; 
                    495: } 
                    496: 
                    497: /****************** free_imatrix *************************/
                    498: void free_imatrix(m,nrl,nrh,ncl,nch)
                    499:       int **m;
                    500:       long nch,ncl,nrh,nrl; 
                    501:      /* free an int matrix allocated by imatrix() */ 
                    502: { 
                    503:   free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                    504:   free((FREE_ARG) (m+nrl-NR_END)); 
                    505: } 
                    506: 
                    507: /******************* matrix *******************************/
                    508: double **matrix(long nrl, long nrh, long ncl, long nch)
                    509: {
                    510:   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
                    511:   double **m;
                    512: 
                    513:   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    514:   if (!m) nrerror("allocation failure 1 in matrix()");
                    515:   m += NR_END;
                    516:   m -= nrl;
                    517: 
                    518:   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    519:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    520:   m[nrl] += NR_END;
                    521:   m[nrl] -= ncl;
                    522: 
                    523:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    524:   return m;
1.85      brouard   525:   /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
1.74      brouard   526:    */
1.53      brouard   527: }
                    528: 
                    529: /*************************free matrix ************************/
                    530: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                    531: {
                    532:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    533:   free((FREE_ARG)(m+nrl-NR_END));
                    534: }
                    535: 
                    536: /******************* ma3x *******************************/
                    537: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
                    538: {
                    539:   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
                    540:   double ***m;
                    541: 
                    542:   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                    543:   if (!m) nrerror("allocation failure 1 in matrix()");
                    544:   m += NR_END;
                    545:   m -= nrl;
                    546: 
                    547:   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                    548:   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                    549:   m[nrl] += NR_END;
                    550:   m[nrl] -= ncl;
                    551: 
                    552:   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
                    553: 
                    554:   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                    555:   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                    556:   m[nrl][ncl] += NR_END;
                    557:   m[nrl][ncl] -= nll;
                    558:   for (j=ncl+1; j<=nch; j++) 
                    559:     m[nrl][j]=m[nrl][j-1]+nlay;
                    560:   
                    561:   for (i=nrl+1; i<=nrh; i++) {
                    562:     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
                    563:     for (j=ncl+1; j<=nch; j++) 
                    564:       m[i][j]=m[i][j-1]+nlay;
                    565:   }
1.74      brouard   566:   return m; 
                    567:   /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                    568:            &(m[i][j][k]) <=> *((*(m+i) + j)+k)
                    569:   */
1.53      brouard   570: }
                    571: 
                    572: /*************************free ma3x ************************/
                    573: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
                    574: {
                    575:   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
                    576:   free((FREE_ARG)(m[nrl]+ncl-NR_END));
                    577:   free((FREE_ARG)(m+nrl-NR_END));
                    578: }
                    579: 
1.94      brouard   580: /*************** function subdirf ***********/
                    581: char *subdirf(char fileres[])
                    582: {
                    583:   /* Caution optionfilefiname is hidden */
                    584:   strcpy(tmpout,optionfilefiname);
                    585:   strcat(tmpout,"/"); /* Add to the right */
                    586:   strcat(tmpout,fileres);
                    587:   return tmpout;
                    588: }
                    589: 
                    590: /*************** function subdirf2 ***********/
                    591: char *subdirf2(char fileres[], char *preop)
                    592: {
                    593:   
                    594:   /* Caution optionfilefiname is hidden */
                    595:   strcpy(tmpout,optionfilefiname);
                    596:   strcat(tmpout,"/");
                    597:   strcat(tmpout,preop);
                    598:   strcat(tmpout,fileres);
                    599:   return tmpout;
                    600: }
                    601: 
                    602: /*************** function subdirf3 ***********/
                    603: char *subdirf3(char fileres[], char *preop, char *preop2)
                    604: {
                    605:   
                    606:   /* Caution optionfilefiname is hidden */
                    607:   strcpy(tmpout,optionfilefiname);
                    608:   strcat(tmpout,"/");
                    609:   strcat(tmpout,preop);
                    610:   strcat(tmpout,preop2);
                    611:   strcat(tmpout,fileres);
                    612:   return tmpout;
                    613: }
                    614: 
1.53      brouard   615: /***************** f1dim *************************/
                    616: extern int ncom; 
                    617: extern double *pcom,*xicom;
                    618: extern double (*nrfunc)(double []); 
                    619:  
                    620: double f1dim(double x) 
                    621: { 
                    622:   int j; 
                    623:   double f;
                    624:   double *xt; 
                    625:  
                    626:   xt=vector(1,ncom); 
                    627:   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
                    628:   f=(*nrfunc)(xt); 
                    629:   free_vector(xt,1,ncom); 
                    630:   return f; 
                    631: } 
                    632: 
                    633: /*****************brent *************************/
                    634: double brent(double ax, double bx, double cx, double (*f)(double), double tol,         double *xmin) 
                    635: { 
                    636:   int iter; 
                    637:   double a,b,d,etemp;
                    638:   double fu,fv,fw,fx;
                    639:   double ftemp;
                    640:   double p,q,r,tol1,tol2,u,v,w,x,xm; 
                    641:   double e=0.0; 
                    642:  
                    643:   a=(ax < cx ? ax : cx); 
                    644:   b=(ax > cx ? ax : cx); 
                    645:   x=w=v=bx; 
                    646:   fw=fv=fx=(*f)(x); 
                    647:   for (iter=1;iter<=ITMAX;iter++) { 
                    648:     xm=0.5*(a+b); 
                    649:     tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                    650:     /*         if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                    651:     printf(".");fflush(stdout);
                    652:     fprintf(ficlog,".");fflush(ficlog);
                    653: #ifdef DEBUG
                    654:     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);
                    655:     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);
                    656:     /*         if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                    657: #endif
                    658:     if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                    659:       *xmin=x; 
                    660:       return fx; 
                    661:     } 
                    662:     ftemp=fu;
                    663:     if (fabs(e) > tol1) { 
                    664:       r=(x-w)*(fx-fv); 
                    665:       q=(x-v)*(fx-fw); 
                    666:       p=(x-v)*q-(x-w)*r; 
                    667:       q=2.0*(q-r); 
                    668:       if (q > 0.0) p = -p; 
                    669:       q=fabs(q); 
                    670:       etemp=e; 
                    671:       e=d; 
                    672:       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
                    673:        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                    674:       else { 
                    675:        d=p/q; 
                    676:        u=x+d; 
                    677:        if (u-a < tol2 || b-u < tol2) 
                    678:          d=SIGN(tol1,xm-x); 
                    679:       } 
                    680:     } else { 
                    681:       d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
                    682:     } 
                    683:     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                    684:     fu=(*f)(u); 
                    685:     if (fu <= fx) { 
                    686:       if (u >= x) a=x; else b=x; 
                    687:       SHFT(v,w,x,u) 
                    688:        SHFT(fv,fw,fx,fu) 
                    689:        } else { 
                    690:          if (u < x) a=u; else b=u; 
                    691:          if (fu <= fw || w == x) { 
                    692:            v=w; 
                    693:            w=u; 
                    694:            fv=fw; 
                    695:            fw=fu; 
                    696:          } else if (fu <= fv || v == x || v == w) { 
                    697:            v=u; 
                    698:            fv=fu; 
                    699:          } 
                    700:        } 
                    701:   } 
                    702:   nrerror("Too many iterations in brent"); 
                    703:   *xmin=x; 
                    704:   return fx; 
                    705: } 
                    706: 
                    707: /****************** mnbrak ***********************/
                    708: 
                    709: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                    710:            double (*func)(double)) 
                    711: { 
                    712:   double ulim,u,r,q, dum;
                    713:   double fu; 
                    714:  
                    715:   *fa=(*func)(*ax); 
                    716:   *fb=(*func)(*bx); 
                    717:   if (*fb > *fa) { 
                    718:     SHFT(dum,*ax,*bx,dum) 
                    719:       SHFT(dum,*fb,*fa,dum) 
                    720:       } 
                    721:   *cx=(*bx)+GOLD*(*bx-*ax); 
                    722:   *fc=(*func)(*cx); 
                    723:   while (*fb > *fc) { 
                    724:     r=(*bx-*ax)*(*fb-*fc); 
                    725:     q=(*bx-*cx)*(*fb-*fa); 
                    726:     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                    727:       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
                    728:     ulim=(*bx)+GLIMIT*(*cx-*bx); 
                    729:     if ((*bx-u)*(u-*cx) > 0.0) { 
                    730:       fu=(*func)(u); 
                    731:     } else if ((*cx-u)*(u-ulim) > 0.0) { 
                    732:       fu=(*func)(u); 
                    733:       if (fu < *fc) { 
                    734:        SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                    735:          SHFT(*fb,*fc,fu,(*func)(u)) 
                    736:          } 
                    737:     } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                    738:       u=ulim; 
                    739:       fu=(*func)(u); 
                    740:     } else { 
                    741:       u=(*cx)+GOLD*(*cx-*bx); 
                    742:       fu=(*func)(u); 
                    743:     } 
                    744:     SHFT(*ax,*bx,*cx,u) 
                    745:       SHFT(*fa,*fb,*fc,fu) 
                    746:       } 
                    747: } 
                    748: 
                    749: /*************** linmin ************************/
                    750: 
                    751: int ncom; 
                    752: double *pcom,*xicom;
                    753: double (*nrfunc)(double []); 
                    754:  
                    755: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                    756: { 
                    757:   double brent(double ax, double bx, double cx, 
                    758:               double (*f)(double), double tol, double *xmin); 
                    759:   double f1dim(double x); 
                    760:   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                    761:              double *fc, double (*func)(double)); 
                    762:   int j; 
                    763:   double xx,xmin,bx,ax; 
                    764:   double fx,fb,fa;
                    765:  
                    766:   ncom=n; 
                    767:   pcom=vector(1,n); 
                    768:   xicom=vector(1,n); 
                    769:   nrfunc=func; 
                    770:   for (j=1;j<=n;j++) { 
                    771:     pcom[j]=p[j]; 
                    772:     xicom[j]=xi[j]; 
                    773:   } 
                    774:   ax=0.0; 
                    775:   xx=1.0; 
                    776:   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
                    777:   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
                    778: #ifdef DEBUG
                    779:   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                    780:   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                    781: #endif
                    782:   for (j=1;j<=n;j++) { 
                    783:     xi[j] *= xmin; 
                    784:     p[j] += xi[j]; 
                    785:   } 
                    786:   free_vector(xicom,1,n); 
                    787:   free_vector(pcom,1,n); 
                    788: } 
                    789: 
1.91      brouard   790: char *asc_diff_time(long time_sec, char ascdiff[])
                    791: {
                    792:   long sec_left, days, hours, minutes;
                    793:   days = (time_sec) / (60*60*24);
                    794:   sec_left = (time_sec) % (60*60*24);
                    795:   hours = (sec_left) / (60*60) ;
                    796:   sec_left = (sec_left) %(60*60);
                    797:   minutes = (sec_left) /60;
                    798:   sec_left = (sec_left) % (60);
                    799:   sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
                    800:   return ascdiff;
                    801: }
                    802: 
1.53      brouard   803: /*************** powell ************************/
                    804: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                    805:            double (*func)(double [])) 
                    806: { 
                    807:   void linmin(double p[], double xi[], int n, double *fret, 
                    808:              double (*func)(double [])); 
                    809:   int i,ibig,j; 
                    810:   double del,t,*pt,*ptt,*xit;
                    811:   double fp,fptt;
                    812:   double *xits;
1.91      brouard   813:   int niterf, itmp;
                    814: 
1.53      brouard   815:   pt=vector(1,n); 
                    816:   ptt=vector(1,n); 
                    817:   xit=vector(1,n); 
                    818:   xits=vector(1,n); 
                    819:   *fret=(*func)(p); 
                    820:   for (j=1;j<=n;j++) pt[j]=p[j]; 
                    821:   for (*iter=1;;++(*iter)) { 
                    822:     fp=(*fret); 
                    823:     ibig=0; 
                    824:     del=0.0; 
1.91      brouard   825:     last_time=curr_time;
                    826:     (void) gettimeofday(&curr_time,&tzp);
                    827:     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
                    828:     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
                    829:     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.76      brouard   830:     for (i=1;i<=n;i++) {
1.53      brouard   831:       printf(" %d %.12f",i, p[i]);
1.76      brouard   832:       fprintf(ficlog," %d %.12lf",i, p[i]);
                    833:       fprintf(ficrespow," %.12lf", p[i]);
                    834:     }
1.53      brouard   835:     printf("\n");
                    836:     fprintf(ficlog,"\n");
1.91      brouard   837:     fprintf(ficrespow,"\n");fflush(ficrespow);
                    838:     if(*iter <=3){
                    839:       tm = *localtime(&curr_time.tv_sec);
1.92      brouard   840:       strcpy(strcurr,asctime(&tmf));
                    841: /*       asctime_r(&tm,strcurr); */
1.91      brouard   842:       forecast_time=curr_time;
                    843:       itmp = strlen(strcurr);
                    844:       if(strcurr[itmp-1]=='\n')
                    845:        strcurr[itmp-1]='\0';
                    846:       printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                    847:       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                    848:       for(niterf=10;niterf<=30;niterf+=10){
                    849:        forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                    850:        tmf = *localtime(&forecast_time.tv_sec);
1.92      brouard   851: /*     asctime_r(&tmf,strfor); */
                    852:        strcpy(strfor,asctime(&tmf));
1.91      brouard   853:        itmp = strlen(strfor);
                    854:        if(strfor[itmp-1]=='\n')
                    855:        strfor[itmp-1]='\0';
                    856:        printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
                    857:        fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
                    858:       }
                    859:     }
1.53      brouard   860:     for (i=1;i<=n;i++) { 
                    861:       for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                    862:       fptt=(*fret); 
                    863: #ifdef DEBUG
                    864:       printf("fret=%lf \n",*fret);
                    865:       fprintf(ficlog,"fret=%lf \n",*fret);
                    866: #endif
                    867:       printf("%d",i);fflush(stdout);
                    868:       fprintf(ficlog,"%d",i);fflush(ficlog);
                    869:       linmin(p,xit,n,fret,func); 
                    870:       if (fabs(fptt-(*fret)) > del) { 
                    871:        del=fabs(fptt-(*fret)); 
                    872:        ibig=i; 
                    873:       } 
                    874: #ifdef DEBUG
                    875:       printf("%d %.12e",i,(*fret));
                    876:       fprintf(ficlog,"%d %.12e",i,(*fret));
                    877:       for (j=1;j<=n;j++) {
                    878:        xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                    879:        printf(" x(%d)=%.12e",j,xit[j]);
                    880:        fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                    881:       }
                    882:       for(j=1;j<=n;j++) {
                    883:        printf(" p=%.12e",p[j]);
                    884:        fprintf(ficlog," p=%.12e",p[j]);
                    885:       }
                    886:       printf("\n");
                    887:       fprintf(ficlog,"\n");
                    888: #endif
                    889:     } 
                    890:     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
                    891: #ifdef DEBUG
                    892:       int k[2],l;
                    893:       k[0]=1;
                    894:       k[1]=-1;
                    895:       printf("Max: %.12e",(*func)(p));
                    896:       fprintf(ficlog,"Max: %.12e",(*func)(p));
                    897:       for (j=1;j<=n;j++) {
                    898:        printf(" %.12e",p[j]);
                    899:        fprintf(ficlog," %.12e",p[j]);
                    900:       }
                    901:       printf("\n");
                    902:       fprintf(ficlog,"\n");
                    903:       for(l=0;l<=1;l++) {
                    904:        for (j=1;j<=n;j++) {
                    905:          ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                    906:          printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                    907:          fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                    908:        }
                    909:        printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                    910:        fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                    911:       }
                    912: #endif
                    913: 
                    914: 
                    915:       free_vector(xit,1,n); 
                    916:       free_vector(xits,1,n); 
                    917:       free_vector(ptt,1,n); 
                    918:       free_vector(pt,1,n); 
                    919:       return; 
                    920:     } 
                    921:     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
                    922:     for (j=1;j<=n;j++) { 
                    923:       ptt[j]=2.0*p[j]-pt[j]; 
                    924:       xit[j]=p[j]-pt[j]; 
                    925:       pt[j]=p[j]; 
                    926:     } 
                    927:     fptt=(*func)(ptt); 
                    928:     if (fptt < fp) { 
                    929:       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                    930:       if (t < 0.0) { 
                    931:        linmin(p,xit,n,fret,func); 
                    932:        for (j=1;j<=n;j++) { 
                    933:          xi[j][ibig]=xi[j][n]; 
                    934:          xi[j][n]=xit[j]; 
                    935:        }
                    936: #ifdef DEBUG
                    937:        printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                    938:        fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                    939:        for(j=1;j<=n;j++){
                    940:          printf(" %.12e",xit[j]);
                    941:          fprintf(ficlog," %.12e",xit[j]);
                    942:        }
                    943:        printf("\n");
                    944:        fprintf(ficlog,"\n");
                    945: #endif
1.54      brouard   946:       }
1.53      brouard   947:     } 
                    948:   } 
                    949: } 
                    950: 
1.54      brouard   951: /**** Prevalence limit (stable prevalence)  ****************/
1.53      brouard   952: 
                    953: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
                    954: {
                    955:   /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                    956:      matrix by transitions matrix until convergence is reached */
                    957: 
                    958:   int i, ii,j,k;
                    959:   double min, max, maxmin, maxmax,sumnew=0.;
                    960:   double **matprod2();
                    961:   double **out, cov[NCOVMAX], **pmij();
                    962:   double **newm;
                    963:   double agefin, delaymax=50 ; /* Max number of years to converge */
                    964: 
                    965:   for (ii=1;ii<=nlstate+ndeath;ii++)
                    966:     for (j=1;j<=nlstate+ndeath;j++){
                    967:       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    968:     }
                    969: 
                    970:    cov[1]=1.;
                    971:  
                    972:  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                    973:   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                    974:     newm=savm;
                    975:     /* Covariates have to be included here again */
                    976:      cov[2]=agefin;
                    977:   
                    978:       for (k=1; k<=cptcovn;k++) {
                    979:        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                    980:        /*      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]]);*/
                    981:       }
                    982:       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                    983:       for (k=1; k<=cptcovprod;k++)
                    984:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                    985: 
                    986:       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                    987:       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                    988:       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                    989:     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                    990: 
                    991:     savm=oldm;
                    992:     oldm=newm;
                    993:     maxmax=0.;
                    994:     for(j=1;j<=nlstate;j++){
                    995:       min=1.;
                    996:       max=0.;
                    997:       for(i=1; i<=nlstate; i++) {
                    998:        sumnew=0;
                    999:        for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                   1000:        prlim[i][j]= newm[i][j]/(1-sumnew);
                   1001:        max=FMAX(max,prlim[i][j]);
                   1002:        min=FMIN(min,prlim[i][j]);
                   1003:       }
                   1004:       maxmin=max-min;
                   1005:       maxmax=FMAX(maxmax,maxmin);
                   1006:     }
                   1007:     if(maxmax < ftolpl){
                   1008:       return prlim;
                   1009:     }
                   1010:   }
                   1011: }
                   1012: 
                   1013: /*************** transition probabilities ***************/ 
                   1014: 
                   1015: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                   1016: {
                   1017:   double s1, s2;
                   1018:   /*double t34;*/
                   1019:   int i,j,j1, nc, ii, jj;
                   1020: 
                   1021:     for(i=1; i<= nlstate; i++){
                   1022:     for(j=1; j<i;j++){
                   1023:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                   1024:        /*s2 += param[i][j][nc]*cov[nc];*/
                   1025:        s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                   1026:        /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
                   1027:       }
                   1028:       ps[i][j]=s2;
                   1029:       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
                   1030:     }
                   1031:     for(j=i+1; j<=nlstate+ndeath;j++){
                   1032:       for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                   1033:        s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                   1034:        /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
                   1035:       }
                   1036:       ps[i][j]=s2;
                   1037:     }
                   1038:   }
                   1039:     /*ps[3][2]=1;*/
                   1040: 
                   1041:   for(i=1; i<= nlstate; i++){
                   1042:      s1=0;
                   1043:     for(j=1; j<i; j++)
                   1044:       s1+=exp(ps[i][j]);
                   1045:     for(j=i+1; j<=nlstate+ndeath; j++)
                   1046:       s1+=exp(ps[i][j]);
                   1047:     ps[i][i]=1./(s1+1.);
                   1048:     for(j=1; j<i; j++)
                   1049:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1050:     for(j=i+1; j<=nlstate+ndeath; j++)
                   1051:       ps[i][j]= exp(ps[i][j])*ps[i][i];
                   1052:     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                   1053:   } /* end i */
                   1054: 
                   1055:   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   1056:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   1057:       ps[ii][jj]=0;
                   1058:       ps[ii][ii]=1;
                   1059:     }
                   1060:   }
                   1061: 
                   1062: 
                   1063:   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
                   1064:     for(jj=1; jj<= nlstate+ndeath; jj++){
                   1065:      printf("%lf ",ps[ii][jj]);
                   1066:    }
                   1067:     printf("\n ");
                   1068:     }
                   1069:     printf("\n ");printf("%lf ",cov[2]);*/
                   1070: /*
                   1071:   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   1072:   goto end;*/
                   1073:     return ps;
                   1074: }
                   1075: 
                   1076: /**************** Product of 2 matrices ******************/
                   1077: 
                   1078: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
                   1079: {
                   1080:   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                   1081:      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                   1082:   /* in, b, out are matrice of pointers which should have been initialized 
                   1083:      before: only the contents of out is modified. The function returns
                   1084:      a pointer to pointers identical to out */
                   1085:   long i, j, k;
                   1086:   for(i=nrl; i<= nrh; i++)
                   1087:     for(k=ncolol; k<=ncoloh; k++)
                   1088:       for(j=ncl,out[i][k]=0.; j<=nch; j++)
                   1089:        out[i][k] +=in[i][j]*b[j][k];
                   1090: 
                   1091:   return out;
                   1092: }
                   1093: 
                   1094: 
                   1095: /************* Higher Matrix Product ***************/
                   1096: 
                   1097: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                   1098: {
1.66      brouard  1099:   /* Computes the transition matrix starting at age 'age' over 
                   1100:      'nhstepm*hstepm*stepm' months (i.e. until
                   1101:      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
                   1102:      nhstepm*hstepm matrices. 
1.53      brouard  1103:      Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
1.66      brouard  1104:      (typically every 2 years instead of every month which is too big 
                   1105:      for the memory).
1.53      brouard  1106:      Model is determined by parameters x and covariates have to be 
                   1107:      included manually here. 
                   1108: 
                   1109:      */
                   1110: 
                   1111:   int i, j, d, h, k;
                   1112:   double **out, cov[NCOVMAX];
                   1113:   double **newm;
                   1114: 
                   1115:   /* Hstepm could be zero and should return the unit matrix */
                   1116:   for (i=1;i<=nlstate+ndeath;i++)
                   1117:     for (j=1;j<=nlstate+ndeath;j++){
                   1118:       oldm[i][j]=(i==j ? 1.0 : 0.0);
                   1119:       po[i][j][0]=(i==j ? 1.0 : 0.0);
                   1120:     }
                   1121:   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                   1122:   for(h=1; h <=nhstepm; h++){
                   1123:     for(d=1; d <=hstepm; d++){
                   1124:       newm=savm;
                   1125:       /* Covariates have to be included here again */
                   1126:       cov[1]=1.;
                   1127:       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                   1128:       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                   1129:       for (k=1; k<=cptcovage;k++)
                   1130:        cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   1131:       for (k=1; k<=cptcovprod;k++)
                   1132:        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   1133: 
                   1134: 
                   1135:       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                   1136:       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                   1137:       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                   1138:                   pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1139:       savm=oldm;
                   1140:       oldm=newm;
                   1141:     }
                   1142:     for(i=1; i<=nlstate+ndeath; i++)
                   1143:       for(j=1;j<=nlstate+ndeath;j++) {
                   1144:        po[i][j][h]=newm[i][j];
                   1145:        /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                   1146:         */
                   1147:       }
                   1148:   } /* end h */
                   1149:   return po;
                   1150: }
                   1151: 
                   1152: 
                   1153: /*************** log-likelihood *************/
                   1154: double func( double *x)
                   1155: {
                   1156:   int i, ii, j, k, mi, d, kk;
                   1157:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
                   1158:   double **out;
                   1159:   double sw; /* Sum of weights */
                   1160:   double lli; /* Individual log likelihood */
1.59      brouard  1161:   int s1, s2;
1.68      lievre   1162:   double bbh, survp;
1.53      brouard  1163:   long ipmx;
                   1164:   /*extern weight */
                   1165:   /* We are differentiating ll according to initial status */
                   1166:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1167:   /*for(i=1;i<imx;i++) 
                   1168:     printf(" %d\n",s[4][i]);
                   1169:   */
                   1170:   cov[1]=1.;
                   1171: 
                   1172:   for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61      brouard  1173: 
                   1174:   if(mle==1){
                   1175:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1176:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1177:       for(mi=1; mi<= wav[i]-1; mi++){
                   1178:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1179:          for (j=1;j<=nlstate+ndeath;j++){
                   1180:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1181:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1182:          }
                   1183:        for(d=0; d<dh[mi][i]; d++){
                   1184:          newm=savm;
                   1185:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1186:          for (kk=1; kk<=cptcovage;kk++) {
                   1187:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1188:          }
                   1189:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1190:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1191:          savm=oldm;
                   1192:          oldm=newm;
                   1193:        } /* end mult */
1.53      brouard  1194:       
1.61      brouard  1195:        /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                   1196:        /* But now since version 0.9 we anticipate for bias and large stepm.
                   1197:         * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   1198:         * (in months) between two waves is not a multiple of stepm, we rounded to 
                   1199:         * the nearest (and in case of equal distance, to the lowest) interval but now
                   1200:         * we keep into memory the bias bh[mi][i] and also the previous matrix product
                   1201:         * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
                   1202:         * probability in order to take into account the bias as a fraction of the way
                   1203:         * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                   1204:         * -stepm/2 to stepm/2 .
                   1205:         * For stepm=1 the results are the same as for previous versions of Imach.
                   1206:         * For stepm > 1 the results are less biased than in previous versions. 
                   1207:         */
                   1208:        s1=s[mw[mi][i]][i];
                   1209:        s2=s[mw[mi+1][i]][i];
1.64      lievre   1210:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1211:        /* bias is positive if real duration
                   1212:         * is higher than the multiple of stepm and negative otherwise.
                   1213:         */
                   1214:        /* 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  1215:        if( s2 > nlstate){ 
                   1216:          /* i.e. if s2 is a death state and if the date of death is known then the contribution
                   1217:             to the likelihood is the probability to die between last step unit time and current 
                   1218:             step unit time, which is also the differences between probability to die before dh 
                   1219:             and probability to die before dh-stepm . 
                   1220:             In version up to 0.92 likelihood was computed
                   1221:        as if date of death was unknown. Death was treated as any other
                   1222:        health state: the date of the interview describes the actual state
                   1223:        and not the date of a change in health state. The former idea was
                   1224:        to consider that at each interview the state was recorded
                   1225:        (healthy, disable or death) and IMaCh was corrected; but when we
                   1226:        introduced the exact date of death then we should have modified
                   1227:        the contribution of an exact death to the likelihood. This new
                   1228:        contribution is smaller and very dependent of the step unit
                   1229:        stepm. It is no more the probability to die between last interview
                   1230:        and month of death but the probability to survive from last
                   1231:        interview up to one month before death multiplied by the
                   1232:        probability to die within a month. Thanks to Chris
                   1233:        Jackson for correcting this bug.  Former versions increased
                   1234:        mortality artificially. The bad side is that we add another loop
                   1235:        which slows down the processing. The difference can be up to 10%
                   1236:        lower mortality.
                   1237:          */
                   1238:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1239:        }else{
                   1240:          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1241:          /*  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 */
                   1242:        } 
1.64      lievre   1243:        /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                   1244:        /*if(lli ==000.0)*/
                   1245:        /*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  1246:        ipmx +=1;
1.64      lievre   1247:        sw += weight[i];
                   1248:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1249:       } /* end of wave */
                   1250:     } /* end of individual */
                   1251:   }  else if(mle==2){
                   1252:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1253:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1254:       for(mi=1; mi<= wav[i]-1; mi++){
                   1255:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1256:          for (j=1;j<=nlstate+ndeath;j++){
                   1257:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1258:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1259:          }
                   1260:        for(d=0; d<=dh[mi][i]; d++){
                   1261:          newm=savm;
                   1262:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1263:          for (kk=1; kk<=cptcovage;kk++) {
                   1264:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1265:          }
                   1266:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1267:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1268:          savm=oldm;
                   1269:          oldm=newm;
                   1270:        } /* end mult */
                   1271:       
                   1272:        s1=s[mw[mi][i]][i];
                   1273:        s2=s[mw[mi+1][i]][i];
                   1274:        bbh=(double)bh[mi][i]/(double)stepm; 
1.63      lievre   1275:        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   1276:        ipmx +=1;
                   1277:        sw += weight[i];
                   1278:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1279:       } /* end of wave */
                   1280:     } /* end of individual */
                   1281:   }  else if(mle==3){  /* exponential inter-extrapolation */
                   1282:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1283:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1284:       for(mi=1; mi<= wav[i]-1; mi++){
                   1285:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1286:          for (j=1;j<=nlstate+ndeath;j++){
                   1287:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1288:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1289:          }
                   1290:        for(d=0; d<dh[mi][i]; d++){
                   1291:          newm=savm;
                   1292:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1293:          for (kk=1; kk<=cptcovage;kk++) {
                   1294:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1295:          }
                   1296:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1297:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1298:          savm=oldm;
                   1299:          oldm=newm;
                   1300:        } /* end mult */
                   1301:       
                   1302:        s1=s[mw[mi][i]][i];
                   1303:        s2=s[mw[mi+1][i]][i];
                   1304:        bbh=(double)bh[mi][i]/(double)stepm; 
                   1305:        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  1306:        ipmx +=1;
                   1307:        sw += weight[i];
                   1308:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1309:       } /* end of wave */
                   1310:     } /* end of individual */
1.84      brouard  1311:   }else if (mle==4){  /* ml=4 no inter-extrapolation */
1.61      brouard  1312:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1313:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1314:       for(mi=1; mi<= wav[i]-1; mi++){
                   1315:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1316:          for (j=1;j<=nlstate+ndeath;j++){
                   1317:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1318:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1319:          }
                   1320:        for(d=0; d<dh[mi][i]; d++){
                   1321:          newm=savm;
                   1322:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1323:          for (kk=1; kk<=cptcovage;kk++) {
                   1324:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1325:          }
                   1326:        
                   1327:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1328:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1329:          savm=oldm;
                   1330:          oldm=newm;
                   1331:        } /* end mult */
                   1332:       
1.84      brouard  1333:        s1=s[mw[mi][i]][i];
                   1334:        s2=s[mw[mi+1][i]][i];
                   1335:        if( s2 > nlstate){ 
                   1336:          lli=log(out[s1][s2] - savm[s1][s2]);
                   1337:        }else{
                   1338:          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1339:        }
                   1340:        ipmx +=1;
                   1341:        sw += weight[i];
                   1342:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85      brouard  1343: /*     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  1344:       } /* end of wave */
                   1345:     } /* end of individual */
                   1346:   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                   1347:     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1348:       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1349:       for(mi=1; mi<= wav[i]-1; mi++){
                   1350:        for (ii=1;ii<=nlstate+ndeath;ii++)
                   1351:          for (j=1;j<=nlstate+ndeath;j++){
                   1352:            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1353:            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1354:          }
                   1355:        for(d=0; d<dh[mi][i]; d++){
                   1356:          newm=savm;
                   1357:          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1358:          for (kk=1; kk<=cptcovage;kk++) {
                   1359:            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1360:          }
                   1361:        
                   1362:          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1363:                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1364:          savm=oldm;
                   1365:          oldm=newm;
                   1366:        } /* end mult */
                   1367:       
                   1368:        s1=s[mw[mi][i]][i];
                   1369:        s2=s[mw[mi+1][i]][i];
1.61      brouard  1370:        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                   1371:        ipmx +=1;
                   1372:        sw += weight[i];
                   1373:        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84      brouard  1374:        /*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  1375:       } /* end of wave */
                   1376:     } /* end of individual */
                   1377:   } /* End of if */
1.53      brouard  1378:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1379:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1380:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85      brouard  1381:   return -l;
                   1382: }
                   1383: 
                   1384: /*************** log-likelihood *************/
                   1385: double funcone( double *x)
                   1386: {
1.87      brouard  1387:   /* Same as likeli but slower because of a lot of printf and if */
1.85      brouard  1388:   int i, ii, j, k, mi, d, kk;
                   1389:   double l, ll[NLSTATEMAX], cov[NCOVMAX];
                   1390:   double **out;
                   1391:   double lli; /* Individual log likelihood */
1.87      brouard  1392:   double llt;
1.85      brouard  1393:   int s1, s2;
                   1394:   double bbh, survp;
                   1395:   /*extern weight */
                   1396:   /* We are differentiating ll according to initial status */
                   1397:   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                   1398:   /*for(i=1;i<imx;i++) 
                   1399:     printf(" %d\n",s[4][i]);
                   1400:   */
                   1401:   cov[1]=1.;
                   1402: 
                   1403:   for(k=1; k<=nlstate; k++) ll[k]=0.;
                   1404: 
                   1405:   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   1406:     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   1407:     for(mi=1; mi<= wav[i]-1; mi++){
                   1408:       for (ii=1;ii<=nlstate+ndeath;ii++)
                   1409:        for (j=1;j<=nlstate+ndeath;j++){
                   1410:          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1411:          savm[ii][j]=(ii==j ? 1.0 : 0.0);
                   1412:        }
                   1413:       for(d=0; d<dh[mi][i]; d++){
                   1414:        newm=savm;
                   1415:        cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                   1416:        for (kk=1; kk<=cptcovage;kk++) {
                   1417:          cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   1418:        }
                   1419:        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                   1420:                     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   1421:        savm=oldm;
                   1422:        oldm=newm;
                   1423:       } /* end mult */
                   1424:       
                   1425:       s1=s[mw[mi][i]][i];
                   1426:       s2=s[mw[mi+1][i]][i];
                   1427:       bbh=(double)bh[mi][i]/(double)stepm; 
                   1428:       /* bias is positive if real duration
                   1429:        * is higher than the multiple of stepm and negative otherwise.
                   1430:        */
                   1431:       if( s2 > nlstate && (mle <5) ){  /* Jackson */
                   1432:        lli=log(out[s1][s2] - savm[s1][s2]);
                   1433:       } else if (mle==1){
                   1434:        lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                   1435:       } else if(mle==2){
                   1436:        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 */
                   1437:       } else if(mle==3){  /* exponential inter-extrapolation */
                   1438:        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 */
                   1439:       } else if (mle==4){  /* mle=4 no inter-extrapolation */
                   1440:        lli=log(out[s1][s2]); /* Original formula */
                   1441:       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
                   1442:        lli=log(out[s1][s2]); /* Original formula */
                   1443:       } /* End of if */
                   1444:       ipmx +=1;
                   1445:       sw += weight[i];
                   1446:       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                   1447: /*       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]); */
                   1448:       if(globpr){
1.88      brouard  1449:        fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86      brouard  1450:  %10.6f %10.6f %10.6f ", \
                   1451:                num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   1452:                2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87      brouard  1453:        for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   1454:          llt +=ll[k]*gipmx/gsw;
                   1455:          fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
                   1456:        }
                   1457:        fprintf(ficresilk," %10.6f\n", -llt);
1.85      brouard  1458:       }
                   1459:     } /* end of wave */
                   1460:   } /* end of individual */
                   1461:   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
                   1462:   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
                   1463:   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87      brouard  1464:   if(globpr==0){ /* First time we count the contributions and weights */
                   1465:     gipmx=ipmx;
                   1466:     gsw=sw;
                   1467:   }
1.53      brouard  1468:   return -l;
                   1469: }
                   1470: 
                   1471: 
1.94      brouard  1472: /*************** function likelione ***********/
1.87      brouard  1473: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85      brouard  1474: {
1.87      brouard  1475:   /* This routine should help understanding what is done with 
                   1476:      the selection of individuals/waves and
1.85      brouard  1477:      to check the exact contribution to the likelihood.
                   1478:      Plotting could be done.
                   1479:    */
                   1480:   int k;
1.87      brouard  1481: 
1.88      brouard  1482:   if(*globpri !=0){ /* Just counts and sums, no printings */
1.85      brouard  1483:     strcpy(fileresilk,"ilk"); 
                   1484:     strcat(fileresilk,fileres);
                   1485:     if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                   1486:       printf("Problem with resultfile: %s\n", fileresilk);
                   1487:       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                   1488:     }
1.87      brouard  1489:     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  1490:     fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85      brouard  1491:     /*         i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   1492:     for(k=1; k<=nlstate; k++) 
1.87      brouard  1493:       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   1494:     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85      brouard  1495:   }
                   1496: 
                   1497:   *fretone=(*funcone)(p);
1.87      brouard  1498:   if(*globpri !=0){
1.85      brouard  1499:     fclose(ficresilk);
1.88      brouard  1500:     fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87      brouard  1501:     fflush(fichtm); 
                   1502:   } 
1.85      brouard  1503:   return;
                   1504: }
                   1505: 
1.88      brouard  1506: 
1.53      brouard  1507: /*********** Maximum Likelihood Estimation ***************/
                   1508: 
                   1509: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                   1510: {
                   1511:   int i,j, iter;
1.74      brouard  1512:   double **xi;
1.53      brouard  1513:   double fret;
1.85      brouard  1514:   double fretone; /* Only one call to likelihood */
1.76      brouard  1515:   char filerespow[FILENAMELENGTH];
1.53      brouard  1516:   xi=matrix(1,npar,1,npar);
                   1517:   for (i=1;i<=npar;i++)
                   1518:     for (j=1;j<=npar;j++)
                   1519:       xi[i][j]=(i==j ? 1.0 : 0.0);
                   1520:   printf("Powell\n");  fprintf(ficlog,"Powell\n");
1.76      brouard  1521:   strcpy(filerespow,"pow"); 
                   1522:   strcat(filerespow,fileres);
                   1523:   if((ficrespow=fopen(filerespow,"w"))==NULL) {
                   1524:     printf("Problem with resultfile: %s\n", filerespow);
                   1525:     fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
                   1526:   }
                   1527:   fprintf(ficrespow,"# Powell\n# iter -2*LL");
                   1528:   for (i=1;i<=nlstate;i++)
                   1529:     for(j=1;j<=nlstate+ndeath;j++)
                   1530:       if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
                   1531:   fprintf(ficrespow,"\n");
1.85      brouard  1532: 
1.53      brouard  1533:   powell(p,xi,npar,ftol,&iter,&fret,func);
                   1534: 
1.76      brouard  1535:   fclose(ficrespow);
                   1536:   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65      lievre   1537:   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53      brouard  1538:   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
                   1539: 
                   1540: }
                   1541: 
                   1542: /**** Computes Hessian and covariance matrix ***/
                   1543: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                   1544: {
                   1545:   double  **a,**y,*x,pd;
                   1546:   double **hess;
                   1547:   int i, j,jk;
                   1548:   int *indx;
                   1549: 
                   1550:   double hessii(double p[], double delta, int theta, double delti[]);
                   1551:   double hessij(double p[], double delti[], int i, int j);
                   1552:   void lubksb(double **a, int npar, int *indx, double b[]) ;
                   1553:   void ludcmp(double **a, int npar, int *indx, double *d) ;
                   1554: 
                   1555:   hess=matrix(1,npar,1,npar);
                   1556: 
                   1557:   printf("\nCalculation of the hessian matrix. Wait...\n");
                   1558:   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                   1559:   for (i=1;i<=npar;i++){
                   1560:     printf("%d",i);fflush(stdout);
                   1561:     fprintf(ficlog,"%d",i);fflush(ficlog);
                   1562:     hess[i][i]=hessii(p,ftolhess,i,delti);
                   1563:     /*printf(" %f ",p[i]);*/
                   1564:     /*printf(" %lf ",hess[i][i]);*/
                   1565:   }
                   1566:   
                   1567:   for (i=1;i<=npar;i++) {
                   1568:     for (j=1;j<=npar;j++)  {
                   1569:       if (j>i) { 
                   1570:        printf(".%d%d",i,j);fflush(stdout);
                   1571:        fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                   1572:        hess[i][j]=hessij(p,delti,i,j);
                   1573:        hess[j][i]=hess[i][j];    
                   1574:        /*printf(" %lf ",hess[i][j]);*/
                   1575:       }
                   1576:     }
                   1577:   }
                   1578:   printf("\n");
                   1579:   fprintf(ficlog,"\n");
                   1580: 
                   1581:   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
                   1582:   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
                   1583:   
                   1584:   a=matrix(1,npar,1,npar);
                   1585:   y=matrix(1,npar,1,npar);
                   1586:   x=vector(1,npar);
                   1587:   indx=ivector(1,npar);
                   1588:   for (i=1;i<=npar;i++)
                   1589:     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   1590:   ludcmp(a,npar,indx,&pd);
                   1591: 
                   1592:   for (j=1;j<=npar;j++) {
                   1593:     for (i=1;i<=npar;i++) x[i]=0;
                   1594:     x[j]=1;
                   1595:     lubksb(a,npar,indx,x);
                   1596:     for (i=1;i<=npar;i++){ 
                   1597:       matcov[i][j]=x[i];
                   1598:     }
                   1599:   }
                   1600: 
                   1601:   printf("\n#Hessian matrix#\n");
                   1602:   fprintf(ficlog,"\n#Hessian matrix#\n");
                   1603:   for (i=1;i<=npar;i++) { 
                   1604:     for (j=1;j<=npar;j++) { 
                   1605:       printf("%.3e ",hess[i][j]);
                   1606:       fprintf(ficlog,"%.3e ",hess[i][j]);
                   1607:     }
                   1608:     printf("\n");
                   1609:     fprintf(ficlog,"\n");
                   1610:   }
                   1611: 
                   1612:   /* Recompute Inverse */
                   1613:   for (i=1;i<=npar;i++)
                   1614:     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
                   1615:   ludcmp(a,npar,indx,&pd);
                   1616: 
                   1617:   /*  printf("\n#Hessian matrix recomputed#\n");
                   1618: 
                   1619:   for (j=1;j<=npar;j++) {
                   1620:     for (i=1;i<=npar;i++) x[i]=0;
                   1621:     x[j]=1;
                   1622:     lubksb(a,npar,indx,x);
                   1623:     for (i=1;i<=npar;i++){ 
                   1624:       y[i][j]=x[i];
                   1625:       printf("%.3e ",y[i][j]);
                   1626:       fprintf(ficlog,"%.3e ",y[i][j]);
                   1627:     }
                   1628:     printf("\n");
                   1629:     fprintf(ficlog,"\n");
                   1630:   }
                   1631:   */
                   1632: 
                   1633:   free_matrix(a,1,npar,1,npar);
                   1634:   free_matrix(y,1,npar,1,npar);
                   1635:   free_vector(x,1,npar);
                   1636:   free_ivector(indx,1,npar);
                   1637:   free_matrix(hess,1,npar,1,npar);
                   1638: 
                   1639: 
                   1640: }
                   1641: 
                   1642: /*************** hessian matrix ****************/
                   1643: double hessii( double x[], double delta, int theta, double delti[])
                   1644: {
                   1645:   int i;
                   1646:   int l=1, lmax=20;
                   1647:   double k1,k2;
                   1648:   double p2[NPARMAX+1];
                   1649:   double res;
                   1650:   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   1651:   double fx;
                   1652:   int k=0,kmax=10;
                   1653:   double l1;
                   1654: 
                   1655:   fx=func(x);
                   1656:   for (i=1;i<=npar;i++) p2[i]=x[i];
                   1657:   for(l=0 ; l <=lmax; l++){
                   1658:     l1=pow(10,l);
                   1659:     delts=delt;
                   1660:     for(k=1 ; k <kmax; k=k+1){
                   1661:       delt = delta*(l1*k);
                   1662:       p2[theta]=x[theta] +delt;
                   1663:       k1=func(p2)-fx;
                   1664:       p2[theta]=x[theta]-delt;
                   1665:       k2=func(p2)-fx;
                   1666:       /*res= (k1-2.0*fx+k2)/delt/delt; */
                   1667:       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   1668:       
                   1669: #ifdef DEBUG
                   1670:       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);
                   1671:       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);
                   1672: #endif
                   1673:       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   1674:       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   1675:        k=kmax;
                   1676:       }
                   1677:       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                   1678:        k=kmax; l=lmax*10.;
                   1679:       }
                   1680:       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   1681:        delts=delt;
                   1682:       }
                   1683:     }
                   1684:   }
                   1685:   delti[theta]=delts;
                   1686:   return res; 
                   1687:   
                   1688: }
                   1689: 
                   1690: double hessij( double x[], double delti[], int thetai,int thetaj)
                   1691: {
                   1692:   int i;
                   1693:   int l=1, l1, lmax=20;
                   1694:   double k1,k2,k3,k4,res,fx;
                   1695:   double p2[NPARMAX+1];
                   1696:   int k;
                   1697: 
                   1698:   fx=func(x);
                   1699:   for (k=1; k<=2; k++) {
                   1700:     for (i=1;i<=npar;i++) p2[i]=x[i];
                   1701:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   1702:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   1703:     k1=func(p2)-fx;
                   1704:   
                   1705:     p2[thetai]=x[thetai]+delti[thetai]/k;
                   1706:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   1707:     k2=func(p2)-fx;
                   1708:   
                   1709:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   1710:     p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   1711:     k3=func(p2)-fx;
                   1712:   
                   1713:     p2[thetai]=x[thetai]-delti[thetai]/k;
                   1714:     p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   1715:     k4=func(p2)-fx;
                   1716:     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   1717: #ifdef DEBUG
                   1718:     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);
                   1719:     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);
                   1720: #endif
                   1721:   }
                   1722:   return res;
                   1723: }
                   1724: 
                   1725: /************** Inverse of matrix **************/
                   1726: void ludcmp(double **a, int n, int *indx, double *d) 
                   1727: { 
                   1728:   int i,imax,j,k; 
                   1729:   double big,dum,sum,temp; 
                   1730:   double *vv; 
                   1731:  
                   1732:   vv=vector(1,n); 
                   1733:   *d=1.0; 
                   1734:   for (i=1;i<=n;i++) { 
                   1735:     big=0.0; 
                   1736:     for (j=1;j<=n;j++) 
                   1737:       if ((temp=fabs(a[i][j])) > big) big=temp; 
                   1738:     if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   1739:     vv[i]=1.0/big; 
                   1740:   } 
                   1741:   for (j=1;j<=n;j++) { 
                   1742:     for (i=1;i<j;i++) { 
                   1743:       sum=a[i][j]; 
                   1744:       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   1745:       a[i][j]=sum; 
                   1746:     } 
                   1747:     big=0.0; 
                   1748:     for (i=j;i<=n;i++) { 
                   1749:       sum=a[i][j]; 
                   1750:       for (k=1;k<j;k++) 
                   1751:        sum -= a[i][k]*a[k][j]; 
                   1752:       a[i][j]=sum; 
                   1753:       if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   1754:        big=dum; 
                   1755:        imax=i; 
                   1756:       } 
                   1757:     } 
                   1758:     if (j != imax) { 
                   1759:       for (k=1;k<=n;k++) { 
                   1760:        dum=a[imax][k]; 
                   1761:        a[imax][k]=a[j][k]; 
                   1762:        a[j][k]=dum; 
                   1763:       } 
                   1764:       *d = -(*d); 
                   1765:       vv[imax]=vv[j]; 
                   1766:     } 
                   1767:     indx[j]=imax; 
                   1768:     if (a[j][j] == 0.0) a[j][j]=TINY; 
                   1769:     if (j != n) { 
                   1770:       dum=1.0/(a[j][j]); 
                   1771:       for (i=j+1;i<=n;i++) a[i][j] *= dum; 
                   1772:     } 
                   1773:   } 
                   1774:   free_vector(vv,1,n);  /* Doesn't work */
                   1775: ;
                   1776: } 
                   1777: 
                   1778: void lubksb(double **a, int n, int *indx, double b[]) 
                   1779: { 
                   1780:   int i,ii=0,ip,j; 
                   1781:   double sum; 
                   1782:  
                   1783:   for (i=1;i<=n;i++) { 
                   1784:     ip=indx[i]; 
                   1785:     sum=b[ip]; 
                   1786:     b[ip]=b[i]; 
                   1787:     if (ii) 
                   1788:       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
                   1789:     else if (sum) ii=i; 
                   1790:     b[i]=sum; 
                   1791:   } 
                   1792:   for (i=n;i>=1;i--) { 
                   1793:     sum=b[i]; 
                   1794:     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
                   1795:     b[i]=sum/a[i][i]; 
                   1796:   } 
                   1797: } 
                   1798: 
                   1799: /************ Frequencies ********************/
1.84      brouard  1800: 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  1801: {  /* Some frequencies */
                   1802:   
                   1803:   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
                   1804:   int first;
                   1805:   double ***freq; /* Frequencies */
1.73      lievre   1806:   double *pp, **prop;
                   1807:   double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53      brouard  1808:   FILE *ficresp;
                   1809:   char fileresp[FILENAMELENGTH];
                   1810:   
                   1811:   pp=vector(1,nlstate);
1.74      brouard  1812:   prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53      brouard  1813:   strcpy(fileresp,"p");
                   1814:   strcat(fileresp,fileres);
                   1815:   if((ficresp=fopen(fileresp,"w"))==NULL) {
                   1816:     printf("Problem with prevalence resultfile: %s\n", fileresp);
                   1817:     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                   1818:     exit(0);
                   1819:   }
1.74      brouard  1820:   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53      brouard  1821:   j1=0;
                   1822:   
                   1823:   j=cptcoveff;
                   1824:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   1825: 
                   1826:   first=1;
                   1827: 
                   1828:   for(k1=1; k1<=j;k1++){
                   1829:     for(i1=1; i1<=ncodemax[k1];i1++){
                   1830:       j1++;
                   1831:       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                   1832:        scanf("%d", i);*/
                   1833:       for (i=-1; i<=nlstate+ndeath; i++)  
                   1834:        for (jk=-1; jk<=nlstate+ndeath; jk++)  
1.74      brouard  1835:          for(m=iagemin; m <= iagemax+3; m++)
1.53      brouard  1836:            freq[i][jk][m]=0;
1.73      lievre   1837: 
                   1838:     for (i=1; i<=nlstate; i++)  
1.74      brouard  1839:       for(m=iagemin; m <= iagemax+3; m++)
1.73      lievre   1840:        prop[i][m]=0;
1.53      brouard  1841:       
                   1842:       dateintsum=0;
                   1843:       k2cpt=0;
                   1844:       for (i=1; i<=imx; i++) {
                   1845:        bool=1;
                   1846:        if  (cptcovn>0) {
                   1847:          for (z1=1; z1<=cptcoveff; z1++) 
                   1848:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   1849:              bool=0;
                   1850:        }
1.58      lievre   1851:        if (bool==1){
1.53      brouard  1852:          for(m=firstpass; m<=lastpass; m++){
                   1853:            k2=anint[m][i]+(mint[m][i]/12.);
1.84      brouard  1854:            /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74      brouard  1855:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   1856:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73      lievre   1857:              if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53      brouard  1858:              if (m<lastpass) {
                   1859:                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74      brouard  1860:                freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53      brouard  1861:              }
                   1862:              
1.74      brouard  1863:              if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53      brouard  1864:                dateintsum=dateintsum+k2;
                   1865:                k2cpt++;
                   1866:              }
1.84      brouard  1867:              /*}*/
1.53      brouard  1868:          }
                   1869:        }
                   1870:       }
                   1871:        
1.84      brouard  1872:       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53      brouard  1873: 
                   1874:       if  (cptcovn>0) {
                   1875:        fprintf(ficresp, "\n#********** Variable "); 
                   1876:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   1877:        fprintf(ficresp, "**********\n#");
                   1878:       }
                   1879:       for(i=1; i<=nlstate;i++) 
                   1880:        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                   1881:       fprintf(ficresp, "\n");
                   1882:       
1.74      brouard  1883:       for(i=iagemin; i <= iagemax+3; i++){
                   1884:        if(i==iagemax+3){
1.53      brouard  1885:          fprintf(ficlog,"Total");
                   1886:        }else{
                   1887:          if(first==1){
                   1888:            first=0;
                   1889:            printf("See log file for details...\n");
                   1890:          }
                   1891:          fprintf(ficlog,"Age %d", i);
                   1892:        }
                   1893:        for(jk=1; jk <=nlstate ; jk++){
                   1894:          for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                   1895:            pp[jk] += freq[jk][m][i]; 
                   1896:        }
                   1897:        for(jk=1; jk <=nlstate ; jk++){
                   1898:          for(m=-1, pos=0; m <=0 ; m++)
                   1899:            pos += freq[jk][m][i];
                   1900:          if(pp[jk]>=1.e-10){
                   1901:            if(first==1){
                   1902:            printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   1903:            }
                   1904:            fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   1905:          }else{
                   1906:            if(first==1)
                   1907:              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   1908:            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   1909:          }
                   1910:        }
                   1911: 
                   1912:        for(jk=1; jk <=nlstate ; jk++){
                   1913:          for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                   1914:            pp[jk] += freq[jk][m][i];
1.73      lievre   1915:        }       
                   1916:        for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                   1917:          pos += pp[jk];
                   1918:          posprop += prop[jk][i];
1.53      brouard  1919:        }
                   1920:        for(jk=1; jk <=nlstate ; jk++){
                   1921:          if(pos>=1.e-5){
                   1922:            if(first==1)
                   1923:              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   1924:            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                   1925:          }else{
                   1926:            if(first==1)
                   1927:              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   1928:            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                   1929:          }
1.74      brouard  1930:          if( i <= iagemax){
1.53      brouard  1931:            if(pos>=1.e-5){
1.73      lievre   1932:              fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84      brouard  1933:              /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53      brouard  1934:              /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                   1935:            }
                   1936:            else
1.73      lievre   1937:              fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53      brouard  1938:          }
                   1939:        }
                   1940:        
1.69      brouard  1941:        for(jk=-1; jk <=nlstate+ndeath; jk++)
                   1942:          for(m=-1; m <=nlstate+ndeath; m++)
1.53      brouard  1943:            if(freq[jk][m][i] !=0 ) {
                   1944:            if(first==1)
                   1945:              printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                   1946:              fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                   1947:            }
1.74      brouard  1948:        if(i <= iagemax)
1.53      brouard  1949:          fprintf(ficresp,"\n");
                   1950:        if(first==1)
                   1951:          printf("Others in log...\n");
                   1952:        fprintf(ficlog,"\n");
                   1953:       }
                   1954:     }
                   1955:   }
                   1956:   dateintmean=dateintsum/k2cpt; 
                   1957:  
                   1958:   fclose(ficresp);
1.74      brouard  1959:   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53      brouard  1960:   free_vector(pp,1,nlstate);
1.74      brouard  1961:   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53      brouard  1962:   /* End of Freq */
                   1963: }
                   1964: 
                   1965: /************ Prevalence ********************/
1.84      brouard  1966: 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  1967: {  
                   1968:   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   1969:      in each health status at the date of interview (if between dateprev1 and dateprev2).
                   1970:      We still use firstpass and lastpass as another selection.
                   1971:   */
1.53      brouard  1972:  
                   1973:   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
                   1974:   double ***freq; /* Frequencies */
1.73      lievre   1975:   double *pp, **prop;
                   1976:   double pos,posprop; 
1.69      brouard  1977:   double  y2; /* in fractional years */
1.74      brouard  1978:   int iagemin, iagemax;
1.53      brouard  1979: 
1.74      brouard  1980:   iagemin= (int) agemin;
                   1981:   iagemax= (int) agemax;
                   1982:   /*pp=vector(1,nlstate);*/
                   1983:   prop=matrix(1,nlstate,iagemin,iagemax+3); 
                   1984:   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53      brouard  1985:   j1=0;
                   1986:   
                   1987:   j=cptcoveff;
                   1988:   if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   1989:   
                   1990:   for(k1=1; k1<=j;k1++){
                   1991:     for(i1=1; i1<=ncodemax[k1];i1++){
                   1992:       j1++;
                   1993:       
1.73      lievre   1994:       for (i=1; i<=nlstate; i++)  
1.74      brouard  1995:        for(m=iagemin; m <= iagemax+3; m++)
                   1996:          prop[i][m]=0.0;
1.53      brouard  1997:      
1.69      brouard  1998:       for (i=1; i<=imx; i++) { /* Each individual */
1.53      brouard  1999:        bool=1;
                   2000:        if  (cptcovn>0) {
                   2001:          for (z1=1; z1<=cptcoveff; z1++) 
                   2002:            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                   2003:              bool=0;
                   2004:        } 
                   2005:        if (bool==1) { 
1.69      brouard  2006:          for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                   2007:            y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   2008:            if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74      brouard  2009:              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   2010:              if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   2011:              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); 
                   2012:              if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   2013:                /*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]]);*/
                   2014:                prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   2015:                prop[s[m][i]][iagemax+3] += weight[i]; 
                   2016:              } 
1.53      brouard  2017:            }
1.69      brouard  2018:          } /* end selection of waves */
1.53      brouard  2019:        }
                   2020:       }
1.74      brouard  2021:       for(i=iagemin; i <= iagemax+3; i++){  
1.53      brouard  2022:        
1.74      brouard  2023:        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                   2024:          posprop += prop[jk][i]; 
                   2025:        } 
                   2026: 
                   2027:        for(jk=1; jk <=nlstate ; jk++){     
                   2028:          if( i <=  iagemax){ 
                   2029:            if(posprop>=1.e-5){ 
                   2030:              probs[i][jk][j1]= prop[jk][i]/posprop;
                   2031:            } 
                   2032:          } 
                   2033:        }/* end jk */ 
                   2034:       }/* end i */ 
1.53      brouard  2035:     } /* end i1 */
                   2036:   } /* end k1 */
                   2037:   
1.74      brouard  2038:   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
                   2039:   /*free_vector(pp,1,nlstate);*/
                   2040:   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                   2041: }  /* End of prevalence */
1.53      brouard  2042: 
                   2043: /************* Waves Concatenation ***************/
                   2044: 
1.59      brouard  2045: 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  2046: {
                   2047:   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
                   2048:      Death is a valid wave (if date is known).
                   2049:      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
1.59      brouard  2050:      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53      brouard  2051:      and mw[mi+1][i]. dh depends on stepm.
                   2052:      */
                   2053: 
                   2054:   int i, mi, m;
                   2055:   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                   2056:      double sum=0., jmean=0.;*/
                   2057:   int first;
                   2058:   int j, k=0,jk, ju, jl;
                   2059:   double sum=0.;
                   2060:   first=0;
                   2061:   jmin=1e+5;
                   2062:   jmax=-1;
                   2063:   jmean=0.;
                   2064:   for(i=1; i<=imx; i++){
                   2065:     mi=0;
                   2066:     m=firstpass;
                   2067:     while(s[m][i] <= nlstate){
1.69      brouard  2068:       if(s[m][i]>=1)
1.53      brouard  2069:        mw[++mi][i]=m;
                   2070:       if(m >=lastpass)
                   2071:        break;
                   2072:       else
                   2073:        m++;
                   2074:     }/* end while */
                   2075:     if (s[m][i] > nlstate){
                   2076:       mi++;    /* Death is another wave */
                   2077:       /* if(mi==0)  never been interviewed correctly before death */
                   2078:         /* Only death is a correct wave */
                   2079:       mw[mi][i]=m;
                   2080:     }
                   2081: 
                   2082:     wav[i]=mi;
                   2083:     if(mi==0){
1.91      brouard  2084:       nbwarn++;
1.53      brouard  2085:       if(first==0){
1.85      brouard  2086:        printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53      brouard  2087:        first=1;
                   2088:       }
                   2089:       if(first==1){
1.85      brouard  2090:        fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53      brouard  2091:       }
                   2092:     } /* end mi==0 */
1.77      brouard  2093:   } /* End individuals */
1.53      brouard  2094: 
                   2095:   for(i=1; i<=imx; i++){
                   2096:     for(mi=1; mi<wav[i];mi++){
                   2097:       if (stepm <=0)
                   2098:        dh[mi][i]=1;
                   2099:       else{
1.77      brouard  2100:        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53      brouard  2101:          if (agedc[i] < 2*AGESUP) {
1.85      brouard  2102:            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   2103:            if(j==0) j=1;  /* Survives at least one month after exam */
                   2104:            else if(j<0){
1.91      brouard  2105:              nberr++;
1.85      brouard  2106:              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]);
1.91      brouard  2107:              j=1; /* Temporary Dangerous patch */
1.86      brouard  2108:              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);
1.91      brouard  2109:              fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
1.85      brouard  2110:              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);
                   2111:            }
                   2112:            k=k+1;
                   2113:            if (j >= jmax) jmax=j;
                   2114:            if (j <= jmin) jmin=j;
                   2115:            sum=sum+j;
                   2116:            /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   2117:            /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53      brouard  2118:          }
                   2119:        }
                   2120:        else{
                   2121:          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68      lievre   2122:          /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53      brouard  2123:          k=k+1;
                   2124:          if (j >= jmax) jmax=j;
                   2125:          else if (j <= jmin)jmin=j;
                   2126:          /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73      lievre   2127:          /*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  2128:          if(j<0){
1.91      brouard  2129:            nberr++;
1.85      brouard  2130:            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]);
                   2131:            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]);
                   2132:          }
1.53      brouard  2133:          sum=sum+j;
                   2134:        }
                   2135:        jk= j/stepm;
                   2136:        jl= j -jk*stepm;
                   2137:        ju= j -(jk+1)*stepm;
1.85      brouard  2138:        if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64      lievre   2139:          if(jl==0){
                   2140:            dh[mi][i]=jk;
                   2141:            bh[mi][i]=0;
                   2142:          }else{ /* We want a negative bias in order to only have interpolation ie
                   2143:                  * at the price of an extra matrix product in likelihood */
                   2144:            dh[mi][i]=jk+1;
                   2145:            bh[mi][i]=ju;
                   2146:          }
                   2147:        }else{
                   2148:          if(jl <= -ju){
                   2149:            dh[mi][i]=jk;
                   2150:            bh[mi][i]=jl;       /* bias is positive if real duration
                   2151:                                 * is higher than the multiple of stepm and negative otherwise.
                   2152:                                 */
                   2153:          }
                   2154:          else{
                   2155:            dh[mi][i]=jk+1;
                   2156:            bh[mi][i]=ju;
                   2157:          }
                   2158:          if(dh[mi][i]==0){
                   2159:            dh[mi][i]=1; /* At least one step */
                   2160:            bh[mi][i]=ju; /* At least one step */
1.71      brouard  2161:            /*  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   2162:          }
1.85      brouard  2163:        } /* end if mle */
                   2164:       }
1.64      lievre   2165:     } /* end wave */
1.53      brouard  2166:   }
                   2167:   jmean=sum/k;
                   2168:   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   2169:   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   2170:  }
                   2171: 
                   2172: /*********** Tricode ****************************/
                   2173: void tricode(int *Tvar, int **nbcode, int imx)
                   2174: {
1.58      lievre   2175:   
                   2176:   int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53      brouard  2177:   int cptcode=0;
                   2178:   cptcoveff=0; 
                   2179:  
1.58      lievre   2180:   for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53      brouard  2181:   for (k=1; k<=7; k++) ncodemax[k]=0;
                   2182: 
                   2183:   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58      lievre   2184:     for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                   2185:                               modality*/ 
                   2186:       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   2187:       Ndum[ij]++; /*store the modality */
1.53      brouard  2188:       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58      lievre   2189:       if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                   2190:                                       Tvar[j]. If V=sex and male is 0 and 
                   2191:                                       female is 1, then  cptcode=1.*/
1.53      brouard  2192:     }
                   2193: 
                   2194:     for (i=0; i<=cptcode; i++) {
1.58      lievre   2195:       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  2196:     }
1.58      lievre   2197: 
1.53      brouard  2198:     ij=1; 
                   2199:     for (i=1; i<=ncodemax[j]; i++) {
1.58      lievre   2200:       for (k=0; k<= maxncov; k++) {
1.53      brouard  2201:        if (Ndum[k] != 0) {
                   2202:          nbcode[Tvar[j]][ij]=k; 
1.58      lievre   2203:          /* 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  2204:          
                   2205:          ij++;
                   2206:        }
                   2207:        if (ij > ncodemax[j]) break; 
                   2208:       }  
                   2209:     } 
                   2210:   }  
                   2211: 
1.58      lievre   2212:  for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53      brouard  2213: 
1.58      lievre   2214:  for (i=1; i<=ncovmodel-2; i++) { 
                   2215:    /* 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  2216:    ij=Tvar[i];
1.58      lievre   2217:    Ndum[ij]++;
1.53      brouard  2218:  }
                   2219: 
                   2220:  ij=1;
1.58      lievre   2221:  for (i=1; i<= maxncov; i++) {
1.53      brouard  2222:    if((Ndum[i]!=0) && (i<=ncovcol)){
1.58      lievre   2223:      Tvaraff[ij]=i; /*For printing */
1.53      brouard  2224:      ij++;
                   2225:    }
                   2226:  }
                   2227:  
1.58      lievre   2228:  cptcoveff=ij-1; /*Number of simple covariates*/
1.53      brouard  2229: }
                   2230: 
                   2231: /*********** Health Expectancies ****************/
                   2232: 
                   2233: 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 )
                   2234: 
                   2235: {
                   2236:   /* Health expectancies */
                   2237:   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                   2238:   double age, agelim, hf;
                   2239:   double ***p3mat,***varhe;
                   2240:   double **dnewm,**doldm;
                   2241:   double *xp;
                   2242:   double **gp, **gm;
                   2243:   double ***gradg, ***trgradg;
                   2244:   int theta;
                   2245: 
1.74      brouard  2246:   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53      brouard  2247:   xp=vector(1,npar);
1.74      brouard  2248:   dnewm=matrix(1,nlstate*nlstate,1,npar);
                   2249:   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53      brouard  2250:   
                   2251:   fprintf(ficreseij,"# Health expectancies\n");
                   2252:   fprintf(ficreseij,"# Age");
                   2253:   for(i=1; i<=nlstate;i++)
                   2254:     for(j=1; j<=nlstate;j++)
                   2255:       fprintf(ficreseij," %1d-%1d (SE)",i,j);
                   2256:   fprintf(ficreseij,"\n");
                   2257: 
                   2258:   if(estepm < stepm){
                   2259:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2260:   }
                   2261:   else  hstepm=estepm;   
                   2262:   /* We compute the life expectancy from trapezoids spaced every estepm months
                   2263:    * This is mainly to measure the difference between two models: for example
                   2264:    * if stepm=24 months pijx are given only every 2 years and by summing them
                   2265:    * we are calculating an estimate of the Life Expectancy assuming a linear 
1.66      brouard  2266:    * progression in between and thus overestimating or underestimating according
1.53      brouard  2267:    * to the curvature of the survival function. If, for the same date, we 
                   2268:    * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   2269:    * to compare the new estimate of Life expectancy with the same linear 
                   2270:    * hypothesis. A more precise result, taking into account a more precise
                   2271:    * curvature will be obtained if estepm is as small as stepm. */
                   2272: 
                   2273:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2274:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2275:      nhstepm is the number of hstepm from age to agelim 
                   2276:      nstepm is the number of stepm from age to agelin. 
                   2277:      Look at hpijx to understand the reason of that which relies in memory size
                   2278:      and note for a fixed period like estepm months */
                   2279:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2280:      survival function given by stepm (the optimization length). Unfortunately it
                   2281:      means that if the survival funtion is printed only each two years of age and if
                   2282:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2283:      results. So we changed our mind and took the option of the best precision.
                   2284:   */
                   2285:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2286: 
                   2287:   agelim=AGESUP;
                   2288:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2289:     /* nhstepm age range expressed in number of stepm */
                   2290:     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
                   2291:     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   2292:     /* if (stepm >= YEARM) hstepm=1;*/
                   2293:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2294:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74      brouard  2295:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   2296:     gp=matrix(0,nhstepm,1,nlstate*nlstate);
                   2297:     gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53      brouard  2298: 
                   2299:     /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   2300:        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   2301:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
                   2302:  
                   2303: 
                   2304:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2305: 
1.95      brouard  2306:     /* Computing  Variances of health expectancies */
1.53      brouard  2307: 
                   2308:      for(theta=1; theta <=npar; theta++){
                   2309:       for(i=1; i<=npar; i++){ 
                   2310:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2311:       }
                   2312:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2313:   
                   2314:       cptj=0;
                   2315:       for(j=1; j<= nlstate; j++){
                   2316:        for(i=1; i<=nlstate; i++){
                   2317:          cptj=cptj+1;
                   2318:          for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                   2319:            gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   2320:          }
                   2321:        }
                   2322:       }
                   2323:      
                   2324:      
                   2325:       for(i=1; i<=npar; i++) 
                   2326:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2327:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2328:       
                   2329:       cptj=0;
                   2330:       for(j=1; j<= nlstate; j++){
                   2331:        for(i=1;i<=nlstate;i++){
                   2332:          cptj=cptj+1;
                   2333:          for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77      brouard  2334: 
1.53      brouard  2335:            gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                   2336:          }
                   2337:        }
                   2338:       }
1.74      brouard  2339:       for(j=1; j<= nlstate*nlstate; j++)
1.53      brouard  2340:        for(h=0; h<=nhstepm-1; h++){
                   2341:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   2342:        }
                   2343:      } 
                   2344:    
                   2345: /* End theta */
                   2346: 
1.74      brouard  2347:      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53      brouard  2348: 
                   2349:      for(h=0; h<=nhstepm-1; h++)
1.74      brouard  2350:       for(j=1; j<=nlstate*nlstate;j++)
1.53      brouard  2351:        for(theta=1; theta <=npar; theta++)
                   2352:          trgradg[h][j][theta]=gradg[h][theta][j];
                   2353:      
                   2354: 
1.74      brouard  2355:      for(i=1;i<=nlstate*nlstate;i++)
                   2356:       for(j=1;j<=nlstate*nlstate;j++)
1.53      brouard  2357:        varhe[i][j][(int)age] =0.;
                   2358: 
                   2359:      printf("%d|",(int)age);fflush(stdout);
                   2360:      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                   2361:      for(h=0;h<=nhstepm-1;h++){
                   2362:       for(k=0;k<=nhstepm-1;k++){
1.74      brouard  2363:        matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                   2364:        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                   2365:        for(i=1;i<=nlstate*nlstate;i++)
                   2366:          for(j=1;j<=nlstate*nlstate;j++)
1.53      brouard  2367:            varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                   2368:       }
                   2369:     }
                   2370:     /* Computing expectancies */
                   2371:     for(i=1; i<=nlstate;i++)
                   2372:       for(j=1; j<=nlstate;j++)
                   2373:        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                   2374:          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   2375:          
                   2376: /* 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]);*/
                   2377: 
                   2378:        }
                   2379: 
                   2380:     fprintf(ficreseij,"%3.0f",age );
                   2381:     cptj=0;
                   2382:     for(i=1; i<=nlstate;i++)
                   2383:       for(j=1; j<=nlstate;j++){
                   2384:        cptj++;
                   2385:        fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
                   2386:       }
                   2387:     fprintf(ficreseij,"\n");
                   2388:    
1.74      brouard  2389:     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   2390:     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   2391:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   2392:     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53      brouard  2393:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2394:   }
                   2395:   printf("\n");
                   2396:   fprintf(ficlog,"\n");
                   2397: 
                   2398:   free_vector(xp,1,npar);
1.74      brouard  2399:   free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   2400:   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   2401:   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53      brouard  2402: }
                   2403: 
                   2404: /************ Variance ******************/
                   2405: 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)
                   2406: {
                   2407:   /* Variance of health expectancies */
                   2408:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   2409:   /* double **newm;*/
                   2410:   double **dnewm,**doldm;
                   2411:   double **dnewmp,**doldmp;
                   2412:   int i, j, nhstepm, hstepm, h, nstepm ;
                   2413:   int k, cptcode;
                   2414:   double *xp;
                   2415:   double **gp, **gm;  /* for var eij */
                   2416:   double ***gradg, ***trgradg; /*for var eij */
                   2417:   double **gradgp, **trgradgp; /* for var p point j */
                   2418:   double *gpp, *gmp; /* for var p point j */
                   2419:   double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                   2420:   double ***p3mat;
                   2421:   double age,agelim, hf;
                   2422:   double ***mobaverage;
                   2423:   int theta;
                   2424:   char digit[4];
1.55      lievre   2425:   char digitp[25];
1.53      brouard  2426: 
                   2427:   char fileresprobmorprev[FILENAMELENGTH];
                   2428: 
1.55      lievre   2429:   if(popbased==1){
1.58      lievre   2430:     if(mobilav!=0)
1.55      lievre   2431:       strcpy(digitp,"-populbased-mobilav-");
                   2432:     else strcpy(digitp,"-populbased-nomobil-");
                   2433:   }
                   2434:   else 
1.53      brouard  2435:     strcpy(digitp,"-stablbased-");
1.56      lievre   2436: 
1.54      brouard  2437:   if (mobilav!=0) {
1.53      brouard  2438:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  2439:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   2440:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   2441:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   2442:     }
1.53      brouard  2443:   }
                   2444: 
                   2445:   strcpy(fileresprobmorprev,"prmorprev"); 
                   2446:   sprintf(digit,"%-d",ij);
                   2447:   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   2448:   strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   2449:   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   2450:   strcat(fileresprobmorprev,fileres);
                   2451:   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   2452:     printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   2453:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   2454:   }
                   2455:   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   2456:   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66      brouard  2457:   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  2458:   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   2459:   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   2460:     fprintf(ficresprobmorprev," p.%-d SE",j);
                   2461:     for(i=1; i<=nlstate;i++)
                   2462:       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                   2463:   }  
                   2464:   fprintf(ficresprobmorprev,"\n");
1.88      brouard  2465:   fprintf(ficgp,"\n# Routine varevsij");
1.87      brouard  2466:   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");
                   2467:   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   2468: /*   } */
1.53      brouard  2469:   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2470: 
                   2471:   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");
                   2472:   fprintf(ficresvij,"# Age");
                   2473:   for(i=1; i<=nlstate;i++)
                   2474:     for(j=1; j<=nlstate;j++)
                   2475:       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                   2476:   fprintf(ficresvij,"\n");
                   2477: 
                   2478:   xp=vector(1,npar);
                   2479:   dnewm=matrix(1,nlstate,1,npar);
                   2480:   doldm=matrix(1,nlstate,1,nlstate);
                   2481:   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   2482:   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2483: 
                   2484:   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                   2485:   gpp=vector(nlstate+1,nlstate+ndeath);
                   2486:   gmp=vector(nlstate+1,nlstate+ndeath);
                   2487:   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   2488:   
                   2489:   if(estepm < stepm){
                   2490:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   2491:   }
                   2492:   else  hstepm=estepm;   
                   2493:   /* For example we decided to compute the life expectancy with the smallest unit */
                   2494:   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   2495:      nhstepm is the number of hstepm from age to agelim 
                   2496:      nstepm is the number of stepm from age to agelin. 
                   2497:      Look at hpijx to understand the reason of that which relies in memory size
                   2498:      and note for a fixed period like k years */
                   2499:   /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   2500:      survival function given by stepm (the optimization length). Unfortunately it
1.66      brouard  2501:      means that if the survival funtion is printed every two years of age and if
1.53      brouard  2502:      you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   2503:      results. So we changed our mind and took the option of the best precision.
                   2504:   */
                   2505:   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   2506:   agelim = AGESUP;
                   2507:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2508:     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   2509:     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   2510:     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2511:     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                   2512:     gp=matrix(0,nhstepm,1,nlstate);
                   2513:     gm=matrix(0,nhstepm,1,nlstate);
                   2514: 
                   2515: 
                   2516:     for(theta=1; theta <=npar; theta++){
1.66      brouard  2517:       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53      brouard  2518:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2519:       }
                   2520:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2521:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2522: 
                   2523:       if (popbased==1) {
1.54      brouard  2524:        if(mobilav ==0){
1.53      brouard  2525:          for(i=1; i<=nlstate;i++)
                   2526:            prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2527:        }else{ /* mobilav */ 
1.53      brouard  2528:          for(i=1; i<=nlstate;i++)
                   2529:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   2530:        }
                   2531:       }
                   2532:   
                   2533:       for(j=1; j<= nlstate; j++){
                   2534:        for(h=0; h<=nhstepm; h++){
                   2535:          for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                   2536:            gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   2537:        }
                   2538:       }
1.66      brouard  2539:       /* This for computing probability of death (h=1 means
                   2540:          computed over hstepm matrices product = hstepm*stepm months) 
                   2541:          as a weighted average of prlim.
                   2542:       */
1.69      brouard  2543:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68      lievre   2544:        for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53      brouard  2545:          gpp[j] += prlim[i][i]*p3mat[i][j][1];
                   2546:       }    
1.66      brouard  2547:       /* end probability of death */
1.53      brouard  2548: 
1.66      brouard  2549:       for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53      brouard  2550:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2551:       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   2552:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2553:  
                   2554:       if (popbased==1) {
1.54      brouard  2555:        if(mobilav ==0){
1.53      brouard  2556:          for(i=1; i<=nlstate;i++)
                   2557:            prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2558:        }else{ /* mobilav */ 
1.53      brouard  2559:          for(i=1; i<=nlstate;i++)
                   2560:            prlim[i][i]=mobaverage[(int)age][i][ij];
                   2561:        }
                   2562:       }
                   2563: 
                   2564:       for(j=1; j<= nlstate; j++){
                   2565:        for(h=0; h<=nhstepm; h++){
                   2566:          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                   2567:            gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                   2568:        }
                   2569:       }
1.66      brouard  2570:       /* This for computing probability of death (h=1 means
                   2571:          computed over hstepm matrices product = hstepm*stepm months) 
                   2572:          as a weighted average of prlim.
                   2573:       */
1.69      brouard  2574:       for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68      lievre   2575:        for(i=1,gmp[j]=0.; i<= nlstate; i++)
                   2576:          gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53      brouard  2577:       }    
1.66      brouard  2578:       /* end probability of death */
1.53      brouard  2579: 
                   2580:       for(j=1; j<= nlstate; j++) /* vareij */
                   2581:        for(h=0; h<=nhstepm; h++){
                   2582:          gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   2583:        }
1.68      lievre   2584: 
1.53      brouard  2585:       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                   2586:        gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                   2587:       }
                   2588: 
                   2589:     } /* End theta */
                   2590: 
                   2591:     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   2592: 
                   2593:     for(h=0; h<=nhstepm; h++) /* veij */
                   2594:       for(j=1; j<=nlstate;j++)
                   2595:        for(theta=1; theta <=npar; theta++)
                   2596:          trgradg[h][j][theta]=gradg[h][theta][j];
                   2597: 
                   2598:     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69      brouard  2599:       for(theta=1; theta <=npar; theta++)
1.53      brouard  2600:        trgradgp[j][theta]=gradgp[theta][j];
1.69      brouard  2601:   
1.53      brouard  2602: 
                   2603:     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   2604:     for(i=1;i<=nlstate;i++)
                   2605:       for(j=1;j<=nlstate;j++)
                   2606:        vareij[i][j][(int)age] =0.;
                   2607: 
                   2608:     for(h=0;h<=nhstepm;h++){
                   2609:       for(k=0;k<=nhstepm;k++){
                   2610:        matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                   2611:        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                   2612:        for(i=1;i<=nlstate;i++)
                   2613:          for(j=1;j<=nlstate;j++)
                   2614:            vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                   2615:       }
                   2616:     }
1.70      brouard  2617:   
1.53      brouard  2618:     /* pptj */
                   2619:     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                   2620:     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70      brouard  2621:     for(j=nlstate+1;j<=nlstate+ndeath;j++)
                   2622:       for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53      brouard  2623:        varppt[j][i]=doldmp[j][i];
                   2624:     /* end ppptj */
1.66      brouard  2625:     /*  x centered again */
1.53      brouard  2626:     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   2627:     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                   2628:  
                   2629:     if (popbased==1) {
1.54      brouard  2630:       if(mobilav ==0){
1.53      brouard  2631:        for(i=1; i<=nlstate;i++)
                   2632:          prlim[i][i]=probs[(int)age][i][ij];
1.54      brouard  2633:       }else{ /* mobilav */ 
1.53      brouard  2634:        for(i=1; i<=nlstate;i++)
                   2635:          prlim[i][i]=mobaverage[(int)age][i][ij];
                   2636:       }
                   2637:     }
1.70      brouard  2638:              
1.66      brouard  2639:     /* This for computing probability of death (h=1 means
                   2640:        computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   2641:        as a weighted average of prlim.
                   2642:     */
1.68      lievre   2643:     for(j=nlstate+1;j<=nlstate+ndeath;j++){
                   2644:       for(i=1,gmp[j]=0.;i<= nlstate; i++) 
1.53      brouard  2645:        gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                   2646:     }    
1.66      brouard  2647:     /* end probability of death */
1.53      brouard  2648: 
                   2649:     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   2650:     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   2651:       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                   2652:       for(i=1; i<=nlstate;i++){
                   2653:        fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                   2654:       }
                   2655:     } 
                   2656:     fprintf(ficresprobmorprev,"\n");
                   2657: 
                   2658:     fprintf(ficresvij,"%.0f ",age );
                   2659:     for(i=1; i<=nlstate;i++)
                   2660:       for(j=1; j<=nlstate;j++){
                   2661:        fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
                   2662:       }
                   2663:     fprintf(ficresvij,"\n");
                   2664:     free_matrix(gp,0,nhstepm,1,nlstate);
                   2665:     free_matrix(gm,0,nhstepm,1,nlstate);
                   2666:     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
                   2667:     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                   2668:     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   2669:   } /* End age */
                   2670:   free_vector(gpp,nlstate+1,nlstate+ndeath);
                   2671:   free_vector(gmp,nlstate+1,nlstate+ndeath);
                   2672:   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
                   2673:   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                   2674:   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
                   2675:   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
                   2676:   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67      brouard  2677: /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
                   2678: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
                   2679: /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88      brouard  2680:   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
                   2681:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
                   2682:   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
                   2683:   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                   2684:   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  2685:   /*  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);
                   2686: */
1.88      brouard  2687: /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89      brouard  2688:   fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53      brouard  2689: 
                   2690:   free_vector(xp,1,npar);
                   2691:   free_matrix(doldm,1,nlstate,1,nlstate);
                   2692:   free_matrix(dnewm,1,nlstate,1,npar);
                   2693:   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   2694:   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
                   2695:   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55      lievre   2696:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  2697:   fclose(ficresprobmorprev);
1.88      brouard  2698:   fflush(ficgp);
                   2699:   fflush(fichtm); 
1.84      brouard  2700: }  /* end varevsij */
1.53      brouard  2701: 
                   2702: /************ Variance of prevlim ******************/
                   2703: 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)
                   2704: {
                   2705:   /* Variance of prevalence limit */
1.59      brouard  2706:   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53      brouard  2707:   double **newm;
                   2708:   double **dnewm,**doldm;
                   2709:   int i, j, nhstepm, hstepm;
                   2710:   int k, cptcode;
                   2711:   double *xp;
                   2712:   double *gp, *gm;
                   2713:   double **gradg, **trgradg;
                   2714:   double age,agelim;
                   2715:   int theta;
                   2716:    
1.54      brouard  2717:   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53      brouard  2718:   fprintf(ficresvpl,"# Age");
                   2719:   for(i=1; i<=nlstate;i++)
                   2720:       fprintf(ficresvpl," %1d-%1d",i,i);
                   2721:   fprintf(ficresvpl,"\n");
                   2722: 
                   2723:   xp=vector(1,npar);
                   2724:   dnewm=matrix(1,nlstate,1,npar);
                   2725:   doldm=matrix(1,nlstate,1,nlstate);
                   2726:   
                   2727:   hstepm=1*YEARM; /* Every year of age */
                   2728:   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                   2729:   agelim = AGESUP;
                   2730:   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   2731:     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   2732:     if (stepm >= YEARM) hstepm=1;
                   2733:     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   2734:     gradg=matrix(1,npar,1,nlstate);
                   2735:     gp=vector(1,nlstate);
                   2736:     gm=vector(1,nlstate);
                   2737: 
                   2738:     for(theta=1; theta <=npar; theta++){
                   2739:       for(i=1; i<=npar; i++){ /* Computes gradient */
                   2740:        xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   2741:       }
                   2742:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2743:       for(i=1;i<=nlstate;i++)
                   2744:        gp[i] = prlim[i][i];
                   2745:     
                   2746:       for(i=1; i<=npar; i++) /* Computes gradient */
                   2747:        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   2748:       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   2749:       for(i=1;i<=nlstate;i++)
                   2750:        gm[i] = prlim[i][i];
                   2751: 
                   2752:       for(i=1;i<=nlstate;i++)
                   2753:        gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                   2754:     } /* End theta */
                   2755: 
                   2756:     trgradg =matrix(1,nlstate,1,npar);
                   2757: 
                   2758:     for(j=1; j<=nlstate;j++)
                   2759:       for(theta=1; theta <=npar; theta++)
                   2760:        trgradg[j][theta]=gradg[theta][j];
                   2761: 
                   2762:     for(i=1;i<=nlstate;i++)
                   2763:       varpl[i][(int)age] =0.;
                   2764:     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   2765:     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                   2766:     for(i=1;i<=nlstate;i++)
                   2767:       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
                   2768: 
                   2769:     fprintf(ficresvpl,"%.0f ",age );
                   2770:     for(i=1; i<=nlstate;i++)
                   2771:       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                   2772:     fprintf(ficresvpl,"\n");
                   2773:     free_vector(gp,1,nlstate);
                   2774:     free_vector(gm,1,nlstate);
                   2775:     free_matrix(gradg,1,npar,1,nlstate);
                   2776:     free_matrix(trgradg,1,nlstate,1,npar);
                   2777:   } /* End age */
                   2778: 
                   2779:   free_vector(xp,1,npar);
                   2780:   free_matrix(doldm,1,nlstate,1,npar);
                   2781:   free_matrix(dnewm,1,nlstate,1,nlstate);
                   2782: 
                   2783: }
                   2784: 
                   2785: /************ Variance of one-step probabilities  ******************/
                   2786: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
                   2787: {
                   2788:   int i, j=0,  i1, k1, l1, t, tj;
                   2789:   int k2, l2, j1,  z1;
                   2790:   int k=0,l, cptcode;
                   2791:   int first=1, first1;
                   2792:   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                   2793:   double **dnewm,**doldm;
                   2794:   double *xp;
                   2795:   double *gp, *gm;
                   2796:   double **gradg, **trgradg;
                   2797:   double **mu;
                   2798:   double age,agelim, cov[NCOVMAX];
                   2799:   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   2800:   int theta;
                   2801:   char fileresprob[FILENAMELENGTH];
                   2802:   char fileresprobcov[FILENAMELENGTH];
                   2803:   char fileresprobcor[FILENAMELENGTH];
                   2804: 
                   2805:   double ***varpij;
                   2806: 
                   2807:   strcpy(fileresprob,"prob"); 
                   2808:   strcat(fileresprob,fileres);
                   2809:   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                   2810:     printf("Problem with resultfile: %s\n", fileresprob);
                   2811:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                   2812:   }
                   2813:   strcpy(fileresprobcov,"probcov"); 
                   2814:   strcat(fileresprobcov,fileres);
                   2815:   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   2816:     printf("Problem with resultfile: %s\n", fileresprobcov);
                   2817:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
                   2818:   }
                   2819:   strcpy(fileresprobcor,"probcor"); 
                   2820:   strcat(fileresprobcor,fileres);
                   2821:   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
                   2822:     printf("Problem with resultfile: %s\n", fileresprobcor);
                   2823:     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
                   2824:   }
                   2825:   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   2826:   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                   2827:   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   2828:   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                   2829:   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   2830:   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                   2831:   
                   2832:   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
                   2833:   fprintf(ficresprob,"# Age");
                   2834:   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
                   2835:   fprintf(ficresprobcov,"# Age");
                   2836:   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
                   2837:   fprintf(ficresprobcov,"# Age");
                   2838: 
                   2839: 
                   2840:   for(i=1; i<=nlstate;i++)
                   2841:     for(j=1; j<=(nlstate+ndeath);j++){
                   2842:       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
                   2843:       fprintf(ficresprobcov," p%1d-%1d ",i,j);
                   2844:       fprintf(ficresprobcor," p%1d-%1d ",i,j);
                   2845:     }  
1.69      brouard  2846:  /* fprintf(ficresprob,"\n");
1.53      brouard  2847:   fprintf(ficresprobcov,"\n");
                   2848:   fprintf(ficresprobcor,"\n");
1.69      brouard  2849:  */
                   2850:  xp=vector(1,npar);
1.53      brouard  2851:   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   2852:   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
                   2853:   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                   2854:   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                   2855:   first=1;
1.88      brouard  2856:   fprintf(ficgp,"\n# Routine varprob");
                   2857:   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   2858:   fprintf(fichtm,"\n");
                   2859: 
1.95      brouard  2860:   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
                   2861:   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91      brouard  2862:   file %s<br>\n",optionfilehtmcov);
                   2863:   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
                   2864: and drawn. It helps understanding how is the covariance between two incidences.\
                   2865:  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                   2866:   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
                   2867: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
                   2868: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
                   2869: standard deviations wide on each axis. <br>\
                   2870:  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
                   2871:  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
                   2872: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
1.53      brouard  2873: 
                   2874:   cov[1]=1;
                   2875:   tj=cptcoveff;
                   2876:   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   2877:   j1=0;
                   2878:   for(t=1; t<=tj;t++){
                   2879:     for(i1=1; i1<=ncodemax[t];i1++){ 
                   2880:       j1++;
                   2881:       if  (cptcovn>0) {
                   2882:        fprintf(ficresprob, "\n#********** Variable "); 
                   2883:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2884:        fprintf(ficresprob, "**********\n#\n");
1.53      brouard  2885:        fprintf(ficresprobcov, "\n#********** Variable "); 
                   2886:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2887:        fprintf(ficresprobcov, "**********\n#\n");
1.53      brouard  2888:        
                   2889:        fprintf(ficgp, "\n#********** Variable "); 
1.69      brouard  2890:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                   2891:        fprintf(ficgp, "**********\n#\n");
1.53      brouard  2892:        
                   2893:        
1.96      brouard  2894:        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
1.53      brouard  2895:        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96      brouard  2896:        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53      brouard  2897:        
                   2898:        fprintf(ficresprobcor, "\n#********** Variable ");    
                   2899:        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69      brouard  2900:        fprintf(ficresprobcor, "**********\n#");    
1.53      brouard  2901:       }
                   2902:       
                   2903:       for (age=bage; age<=fage; age ++){ 
                   2904:        cov[2]=age;
                   2905:        for (k=1; k<=cptcovn;k++) {
                   2906:          cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                   2907:        }
                   2908:        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                   2909:        for (k=1; k<=cptcovprod;k++)
                   2910:          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   2911:        
                   2912:        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                   2913:        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                   2914:        gp=vector(1,(nlstate)*(nlstate+ndeath));
                   2915:        gm=vector(1,(nlstate)*(nlstate+ndeath));
                   2916:     
                   2917:        for(theta=1; theta <=npar; theta++){
                   2918:          for(i=1; i<=npar; i++)
1.74      brouard  2919:            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53      brouard  2920:          
                   2921:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   2922:          
                   2923:          k=0;
                   2924:          for(i=1; i<= (nlstate); i++){
                   2925:            for(j=1; j<=(nlstate+ndeath);j++){
                   2926:              k=k+1;
                   2927:              gp[k]=pmmij[i][j];
                   2928:            }
                   2929:          }
                   2930:          
                   2931:          for(i=1; i<=npar; i++)
1.74      brouard  2932:            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53      brouard  2933:     
                   2934:          pmij(pmmij,cov,ncovmodel,xp,nlstate);
                   2935:          k=0;
                   2936:          for(i=1; i<=(nlstate); i++){
                   2937:            for(j=1; j<=(nlstate+ndeath);j++){
                   2938:              k=k+1;
                   2939:              gm[k]=pmmij[i][j];
                   2940:            }
                   2941:          }
                   2942:      
                   2943:          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
1.74      brouard  2944:            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
1.53      brouard  2945:        }
                   2946: 
                   2947:        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                   2948:          for(theta=1; theta <=npar; theta++)
                   2949:            trgradg[j][theta]=gradg[theta][j];
                   2950:        
                   2951:        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                   2952:        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59      brouard  2953:        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                   2954:        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                   2955:        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   2956:        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                   2957: 
1.53      brouard  2958:        pmij(pmmij,cov,ncovmodel,x,nlstate);
                   2959:        
                   2960:        k=0;
                   2961:        for(i=1; i<=(nlstate); i++){
                   2962:          for(j=1; j<=(nlstate+ndeath);j++){
                   2963:            k=k+1;
                   2964:            mu[k][(int) age]=pmmij[i][j];
                   2965:          }
                   2966:        }
                   2967:        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                   2968:          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   2969:            varpij[i][j][(int)age] = doldm[i][j];
                   2970: 
                   2971:        /*printf("\n%d ",(int)age);
1.59      brouard  2972:          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   2973:          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   2974:          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                   2975:          }*/
1.53      brouard  2976: 
                   2977:        fprintf(ficresprob,"\n%d ",(int)age);
                   2978:        fprintf(ficresprobcov,"\n%d ",(int)age);
                   2979:        fprintf(ficresprobcor,"\n%d ",(int)age);
                   2980: 
                   2981:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                   2982:          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   2983:        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                   2984:          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   2985:          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                   2986:        }
                   2987:        i=0;
                   2988:        for (k=1; k<=(nlstate);k++){
                   2989:          for (l=1; l<=(nlstate+ndeath);l++){ 
                   2990:            i=i++;
                   2991:            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                   2992:            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                   2993:            for (j=1; j<=i;j++){
                   2994:              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                   2995:              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                   2996:            }
                   2997:          }
                   2998:        }/* end of loop for state */
                   2999:       } /* end of loop for age */
                   3000: 
                   3001:       /* Confidence intervalle of pij  */
                   3002:       /*
1.59      brouard  3003:        fprintf(ficgp,"\nset noparametric;unset label");
                   3004:        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                   3005:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                   3006:        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);
                   3007:        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                   3008:        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                   3009:        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53      brouard  3010:       */
                   3011: 
                   3012:       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                   3013:       first1=1;
                   3014:       for (k2=1; k2<=(nlstate);k2++){
                   3015:        for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                   3016:          if(l2==k2) continue;
                   3017:          j=(k2-1)*(nlstate+ndeath)+l2;
                   3018:          for (k1=1; k1<=(nlstate);k1++){
                   3019:            for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                   3020:              if(l1==k1) continue;
                   3021:              i=(k1-1)*(nlstate+ndeath)+l1;
                   3022:              if(i<=j) continue;
                   3023:              for (age=bage; age<=fage; age ++){ 
                   3024:                if ((int)age %5==0){
                   3025:                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                   3026:                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   3027:                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                   3028:                  mu1=mu[i][(int) age]/stepm*YEARM ;
                   3029:                  mu2=mu[j][(int) age]/stepm*YEARM;
                   3030:                  c12=cv12/sqrt(v1*v2);
                   3031:                  /* Computing eigen value of matrix of covariance */
                   3032:                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   3033:                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                   3034:                  /* Eigen vectors */
                   3035:                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   3036:                  /*v21=sqrt(1.-v11*v11); *//* error */
                   3037:                  v21=(lc1-v1)/cv12*v11;
                   3038:                  v12=-v21;
                   3039:                  v22=v11;
                   3040:                  tnalp=v21/v11;
                   3041:                  if(first1==1){
                   3042:                    first1=0;
                   3043:                    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);
                   3044:                  }
                   3045:                  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);
                   3046:                  /*printf(fignu*/
                   3047:                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                   3048:                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                   3049:                  if(first==1){
                   3050:                    first=0;
                   3051:                    fprintf(ficgp,"\nset parametric;unset label");
                   3052:                    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);
                   3053:                    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91      brouard  3054:                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88      brouard  3055:  :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                   3056: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                   3057:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                   3058:                            subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91      brouard  3059:                    fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                   3060:                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88      brouard  3061:                    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53      brouard  3062:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3063:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3064:                    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",\
                   3065:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3066:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3067:                  }else{
                   3068:                    first=0;
1.91      brouard  3069:                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53      brouard  3070:                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                   3071:                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                   3072:                    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",\
                   3073:                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                   3074:                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   3075:                  }/* if first */
                   3076:                } /* age mod 5 */
                   3077:              } /* end loop age */
1.88      brouard  3078:              fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53      brouard  3079:              first=1;
                   3080:            } /*l12 */
                   3081:          } /* k12 */
                   3082:        } /*l1 */
                   3083:       }/* k1 */
                   3084:     } /* loop covariates */
                   3085:   }
1.59      brouard  3086:   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
                   3087:   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53      brouard  3088:   free_vector(xp,1,npar);
                   3089:   fclose(ficresprob);
                   3090:   fclose(ficresprobcov);
                   3091:   fclose(ficresprobcor);
1.91      brouard  3092:   fflush(ficgp);
                   3093:   fflush(fichtmcov);
1.53      brouard  3094: }
                   3095: 
                   3096: 
                   3097: /******************* Printing html file ***********/
                   3098: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                   3099:                  int lastpass, int stepm, int weightopt, char model[],\
                   3100:                  int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   3101:                  int popforecast, int estepm ,\
                   3102:                  double jprev1, double mprev1,double anprev1, \
                   3103:                  double jprev2, double mprev2,double anprev2){
                   3104:   int jj1, k1, i1, cpt;
                   3105: 
1.85      brouard  3106:    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
1.96      brouard  3107:  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
                   3108:           jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
                   3109:    fprintf(fichtm,"\
                   3110:  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
                   3111:           stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
                   3112:    fprintf(fichtm,"\
                   3113:  - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
                   3114:           subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
                   3115:    fprintf(fichtm,"\
1.85      brouard  3116:  - Life expectancies by age and initial health status (estepm=%2d months): \
1.96      brouard  3117:    <a href=\"%s\">%s</a> <br>\n</li>",
1.88      brouard  3118:           estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53      brouard  3119: 
                   3120: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
                   3121: 
                   3122:  m=cptcoveff;
                   3123:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3124: 
                   3125:  jj1=0;
                   3126:  for(k1=1; k1<=m;k1++){
                   3127:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3128:      jj1++;
                   3129:      if (cptcovn > 0) {
                   3130:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3131:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3132:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3133:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3134:      }
                   3135:      /* Pij */
1.88      brouard  3136:      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> \
                   3137: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
1.53      brouard  3138:      /* Quasi-incidences */
1.85      brouard  3139:      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88      brouard  3140:  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
                   3141: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
1.53      brouard  3142:        /* Stable prevalence in each health state */
                   3143:        for(cpt=1; cpt<nlstate;cpt++){
1.85      brouard  3144:         fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88      brouard  3145: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53      brouard  3146:        }
                   3147:      for(cpt=1; cpt<=nlstate;cpt++) {
1.88      brouard  3148:         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89      brouard  3149: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53      brouard  3150:      }
                   3151:    } /* end i1 */
                   3152:  }/* End k1 */
                   3153:  fprintf(fichtm,"</ul>");
                   3154: 
                   3155: 
1.96      brouard  3156:  fprintf(fichtm,"\
                   3157: \n<br><li><h4> Result files (second order: variances)</h4>\n\
                   3158:  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
                   3159: 
                   3160:  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3161:         subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
                   3162:  fprintf(fichtm,"\
                   3163:  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3164:         subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
                   3165: 
                   3166:  fprintf(fichtm,"\
                   3167:  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                   3168:         subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
                   3169:  fprintf(fichtm,"\
                   3170:  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
                   3171:         estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
                   3172:  fprintf(fichtm,"\
                   3173:  - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
                   3174:         subdirf2(fileres,"t"),subdirf2(fileres,"t"));
                   3175:  fprintf(fichtm,"\
1.88      brouard  3176:  - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
                   3177:         subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53      brouard  3178: 
1.76      brouard  3179: /*  if(popforecast==1) fprintf(fichtm,"\n */
                   3180: /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
                   3181: /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
                   3182: /*     <br>",fileres,fileres,fileres,fileres); */
                   3183: /*  else  */
                   3184: /*    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); */
1.96      brouard  3185:  fflush(fichtm);
                   3186:  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53      brouard  3187: 
                   3188:  m=cptcoveff;
                   3189:  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
                   3190: 
                   3191:  jj1=0;
                   3192:  for(k1=1; k1<=m;k1++){
                   3193:    for(i1=1; i1<=ncodemax[k1];i1++){
                   3194:      jj1++;
                   3195:      if (cptcovn > 0) {
                   3196:        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                   3197:        for (cpt=1; cpt<=cptcoveff;cpt++) 
                   3198:         fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                   3199:        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                   3200:      }
                   3201:      for(cpt=1; cpt<=nlstate;cpt++) {
1.95      brouard  3202:        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
                   3203: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90      brouard  3204: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
1.53      brouard  3205:      }
1.96      brouard  3206:      fprintf(fichtm,"\n<br>- Total life expectancy by age and \
                   3207: health expectancies in states (1) and (2): %s%d.png<br>\
                   3208: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53      brouard  3209:    } /* end i1 */
                   3210:  }/* End k1 */
                   3211:  fprintf(fichtm,"</ul>");
1.87      brouard  3212:  fflush(fichtm);
1.53      brouard  3213: }
                   3214: 
                   3215: /******************* Gnuplot file **************/
1.89      brouard  3216: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53      brouard  3217: 
1.88      brouard  3218:   char dirfileres[132],optfileres[132];
1.53      brouard  3219:   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
                   3220:   int ng;
1.88      brouard  3221: /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
                   3222: /*     printf("Problem with file %s",optionfilegnuplot); */
                   3223: /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                   3224: /*   } */
1.53      brouard  3225: 
1.54      brouard  3226:   /*#ifdef windows */
1.89      brouard  3227:   fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54      brouard  3228:     /*#endif */
1.88      brouard  3229:   m=pow(2,cptcoveff);
                   3230: 
                   3231:   strcpy(dirfileres,optionfilefiname);
                   3232:   strcpy(optfileres,"vpl");
1.53      brouard  3233:  /* 1eme*/
                   3234:   for (cpt=1; cpt<= nlstate ; cpt ++) {
                   3235:    for (k1=1; k1<= m ; k1 ++) {
1.88      brouard  3236:      fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
                   3237:      fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
                   3238:      fprintf(ficgp,"set xlabel \"Age\" \n\
                   3239: set ylabel \"Probability\" \n\
                   3240: set ter png small\n\
                   3241: set size 0.65,0.65\n\
                   3242: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53      brouard  3243: 
                   3244:      for (i=1; i<= nlstate ; i ++) {
                   3245:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3246:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3247:      }
1.88      brouard  3248:      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  3249:      for (i=1; i<= nlstate ; i ++) {
                   3250:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3251:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3252:      } 
1.88      brouard  3253:      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
1.53      brouard  3254:      for (i=1; i<= nlstate ; i ++) {
                   3255:        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                   3256:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3257:      }  
1.88      brouard  3258:      fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53      brouard  3259:    }
                   3260:   }
                   3261:   /*2 eme*/
                   3262:   
                   3263:   for (k1=1; k1<= m ; k1 ++) { 
1.88      brouard  3264:     fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53      brouard  3265:     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
                   3266:     
                   3267:     for (i=1; i<= nlstate+1 ; i ++) {
                   3268:       k=2*i;
1.88      brouard  3269:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3270:       for (j=1; j<= nlstate+1 ; j ++) {
                   3271:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3272:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3273:       }   
                   3274:       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
                   3275:       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88      brouard  3276:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3277:       for (j=1; j<= nlstate+1 ; j ++) {
                   3278:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3279:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3280:       }   
                   3281:       fprintf(ficgp,"\" t\"\" w l 0,");
1.88      brouard  3282:       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53      brouard  3283:       for (j=1; j<= nlstate+1 ; j ++) {
                   3284:        if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                   3285:        else fprintf(ficgp," \%%*lf (\%%*lf)");
                   3286:       }   
                   3287:       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                   3288:       else fprintf(ficgp,"\" t\"\" w l 0,");
                   3289:     }
                   3290:   }
                   3291:   
                   3292:   /*3eme*/
                   3293:   
                   3294:   for (k1=1; k1<= m ; k1 ++) { 
                   3295:     for (cpt=1; cpt<= nlstate ; cpt ++) {
                   3296:       k=2+nlstate*(2*cpt-2);
1.88      brouard  3297:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
                   3298:       fprintf(ficgp,"set ter png small\n\
                   3299: set size 0.65,0.65\n\
                   3300: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53      brouard  3301:       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   3302:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   3303:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   3304:        fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                   3305:        for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                   3306:        fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                   3307:        
                   3308:       */
                   3309:       for (i=1; i< nlstate ; i ++) {
1.88      brouard  3310:        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  3311:        
                   3312:       } 
                   3313:     }
                   3314:   }
                   3315:   
1.76      brouard  3316:   /* CV preval stable (period) */
1.53      brouard  3317:   for (k1=1; k1<= m ; k1 ++) { 
1.76      brouard  3318:     for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53      brouard  3319:       k=3;
1.88      brouard  3320:       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
                   3321:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
                   3322: set ter png small\nset size 0.65,0.65\n\
1.89      brouard  3323: unset log y\n\
1.88      brouard  3324: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53      brouard  3325:       
1.83      lievre   3326:       for (i=1; i< nlstate ; i ++)
1.53      brouard  3327:        fprintf(ficgp,"+$%d",k+i+1);
                   3328:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
                   3329:       
                   3330:       l=3+(nlstate+ndeath)*cpt;
1.88      brouard  3331:       fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53      brouard  3332:       for (i=1; i< nlstate ; i ++) {
                   3333:        l=3+(nlstate+ndeath)*cpt;
                   3334:        fprintf(ficgp,"+$%d",l+i+1);
                   3335:       }
                   3336:       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
                   3337:     } 
                   3338:   }  
                   3339:   
                   3340:   /* proba elementaires */
                   3341:   for(i=1,jk=1; i <=nlstate; i++){
                   3342:     for(k=1; k <=(nlstate+ndeath); k++){
                   3343:       if (k != i) {
                   3344:        for(j=1; j <=ncovmodel; j++){
                   3345:          fprintf(ficgp,"p%d=%f ",jk,p[jk]);
                   3346:          jk++; 
                   3347:          fprintf(ficgp,"\n");
                   3348:        }
                   3349:       }
                   3350:     }
                   3351:    }
                   3352: 
                   3353:    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
                   3354:      for(jk=1; jk <=m; jk++) {
1.88      brouard  3355:        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
1.53      brouard  3356:        if (ng==2)
                   3357:         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
                   3358:        else
                   3359:         fprintf(ficgp,"\nset title \"Probability\"\n");
                   3360:        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
                   3361:        i=1;
                   3362:        for(k2=1; k2<=nlstate; k2++) {
                   3363:         k3=i;
                   3364:         for(k=1; k<=(nlstate+ndeath); k++) {
                   3365:           if (k != k2){
                   3366:             if(ng==2)
                   3367:               fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                   3368:             else
                   3369:               fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   3370:             ij=1;
                   3371:             for(j=3; j <=ncovmodel; j++) {
                   3372:               if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                   3373:                 fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                   3374:                 ij++;
                   3375:               }
                   3376:               else
                   3377:                 fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   3378:             }
                   3379:             fprintf(ficgp,")/(1");
                   3380:             
                   3381:             for(k1=1; k1 <=nlstate; k1++){   
                   3382:               fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                   3383:               ij=1;
                   3384:               for(j=3; j <=ncovmodel; j++){
                   3385:                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                   3386:                   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                   3387:                   ij++;
                   3388:                 }
                   3389:                 else
                   3390:                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   3391:               }
                   3392:               fprintf(ficgp,")");
                   3393:             }
                   3394:             fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                   3395:             if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                   3396:             i=i+ncovmodel;
                   3397:           }
                   3398:         } /* end k */
                   3399:        } /* end k2 */
                   3400:      } /* end jk */
                   3401:    } /* end ng */
1.88      brouard  3402:    fflush(ficgp); 
1.53      brouard  3403: }  /* end gnuplot */
                   3404: 
                   3405: 
                   3406: /*************** Moving average **************/
1.54      brouard  3407: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53      brouard  3408: 
                   3409:   int i, cpt, cptcod;
1.58      lievre   3410:   int modcovmax =1;
1.54      brouard  3411:   int mobilavrange, mob;
1.53      brouard  3412:   double age;
1.58      lievre   3413: 
                   3414:   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                   3415:                           a covariate has 2 modalities */
                   3416:   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
                   3417: 
1.54      brouard  3418:   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
                   3419:     if(mobilav==1) mobilavrange=5; /* default */
                   3420:     else mobilavrange=mobilav;
                   3421:     for (age=bage; age<=fage; age++)
                   3422:       for (i=1; i<=nlstate;i++)
1.58      lievre   3423:        for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54      brouard  3424:          mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
                   3425:     /* We keep the original values on the extreme ages bage, fage and for 
                   3426:        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
                   3427:        we use a 5 terms etc. until the borders are no more concerned. 
                   3428:     */ 
                   3429:     for (mob=3;mob <=mobilavrange;mob=mob+2){
                   3430:       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                   3431:        for (i=1; i<=nlstate;i++){
1.58      lievre   3432:          for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54      brouard  3433:            mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                   3434:              for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   3435:                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   3436:                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                   3437:              }
                   3438:            mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                   3439:          }
1.53      brouard  3440:        }
1.54      brouard  3441:       }/* end age */
                   3442:     }/* end mob */
                   3443:   }else return -1;
                   3444:   return 0;
                   3445: }/* End movingaverage */
1.53      brouard  3446: 
                   3447: 
                   3448: /************** Forecasting ******************/
1.70      brouard  3449: 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  3450:   /* proj1, year, month, day of starting projection 
                   3451:      agemin, agemax range of age
                   3452:      dateprev1 dateprev2 range of dates during which prevalence is computed
1.70      brouard  3453:      anproj2 year of en of projection (same day and month as proj1).
1.69      brouard  3454:   */
1.73      lievre   3455:   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53      brouard  3456:   int *popage;
1.70      brouard  3457:   double agec; /* generic age */
                   3458:   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53      brouard  3459:   double *popeffectif,*popcount;
                   3460:   double ***p3mat;
1.55      lievre   3461:   double ***mobaverage;
1.53      brouard  3462:   char fileresf[FILENAMELENGTH];
                   3463: 
1.69      brouard  3464:   agelim=AGESUP;
1.84      brouard  3465:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53      brouard  3466:  
                   3467:   strcpy(fileresf,"f"); 
                   3468:   strcat(fileresf,fileres);
                   3469:   if((ficresf=fopen(fileresf,"w"))==NULL) {
                   3470:     printf("Problem with forecast resultfile: %s\n", fileresf);
                   3471:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
                   3472:   }
                   3473:   printf("Computing forecasting: result on file '%s' \n", fileresf);
                   3474:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                   3475: 
                   3476:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   3477: 
1.54      brouard  3478:   if (mobilav!=0) {
1.53      brouard  3479:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  3480:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   3481:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3482:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3483:     }
1.53      brouard  3484:   }
                   3485: 
                   3486:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   3487:   if (stepm<=12) stepsize=1;
1.74      brouard  3488:   if(estepm < stepm){
                   3489:     printf ("Problem %d lower than %d\n",estepm, stepm);
                   3490:   }
                   3491:   else  hstepm=estepm;   
                   3492: 
1.53      brouard  3493:   hstepm=hstepm/stepm; 
1.69      brouard  3494:   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                   3495:                                fractional in yp1 */
1.53      brouard  3496:   anprojmean=yp;
                   3497:   yp2=modf((yp1*12),&yp);
                   3498:   mprojmean=yp;
                   3499:   yp1=modf((yp2*30.5),&yp);
                   3500:   jprojmean=yp;
                   3501:   if(jprojmean==0) jprojmean=1;
                   3502:   if(mprojmean==0) jprojmean=1;
1.73      lievre   3503: 
                   3504:   i1=cptcoveff;
                   3505:   if (cptcovn < 1){i1=1;}
1.53      brouard  3506:   
1.70      brouard  3507:   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
1.53      brouard  3508:   
1.70      brouard  3509:   fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73      lievre   3510: 
1.75      brouard  3511: /*           if (h==(int)(YEARM*yearp)){ */
1.73      lievre   3512:   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53      brouard  3513:     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   3514:       k=k+1;
                   3515:       fprintf(ficresf,"\n#******");
                   3516:       for(j=1;j<=cptcoveff;j++) {
1.70      brouard  3517:        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  3518:       }
                   3519:       fprintf(ficresf,"******\n");
1.70      brouard  3520:       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
                   3521:       for(j=1; j<=nlstate+ndeath;j++){ 
                   3522:        for(i=1; i<=nlstate;i++)              
                   3523:           fprintf(ficresf," p%d%d",i,j);
                   3524:        fprintf(ficresf," p.%d",j);
                   3525:       }
1.74      brouard  3526:       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
1.53      brouard  3527:        fprintf(ficresf,"\n");
1.70      brouard  3528:        fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
1.53      brouard  3529: 
1.71      brouard  3530:        for (agec=fage; agec>=(ageminpar-1); agec--){ 
1.70      brouard  3531:          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
1.53      brouard  3532:          nhstepm = nhstepm/hstepm; 
                   3533:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3534:          oldm=oldms;savm=savms;
1.70      brouard  3535:          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
1.53      brouard  3536:        
                   3537:          for (h=0; h<=nhstepm; h++){
1.75      brouard  3538:            if (h*hstepm/YEARM*stepm ==yearp) {
1.69      brouard  3539:               fprintf(ficresf,"\n");
                   3540:               for(j=1;j<=cptcoveff;j++) 
                   3541:                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70      brouard  3542:              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53      brouard  3543:            } 
                   3544:            for(j=1; j<=nlstate+ndeath;j++) {
1.70      brouard  3545:              ppij=0.;
1.71      brouard  3546:              for(i=1; i<=nlstate;i++) {
1.53      brouard  3547:                if (mobilav==1) 
1.71      brouard  3548:                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53      brouard  3549:                else {
1.71      brouard  3550:                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53      brouard  3551:                }
1.75      brouard  3552:                if (h*hstepm/YEARM*stepm== yearp) {
1.70      brouard  3553:                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75      brouard  3554:                }
                   3555:              } /* end i */
                   3556:              if (h*hstepm/YEARM*stepm==yearp) {
1.70      brouard  3557:                fprintf(ficresf," %.3f", ppij);
1.53      brouard  3558:              }
1.75      brouard  3559:            }/* end j */
                   3560:          } /* end h */
1.53      brouard  3561:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75      brouard  3562:        } /* end agec */
                   3563:       } /* end yearp */
                   3564:     } /* end cptcod */
                   3565:   } /* end  cptcov */
1.53      brouard  3566:        
1.54      brouard  3567:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  3568: 
                   3569:   fclose(ficresf);
                   3570: }
1.70      brouard  3571: 
                   3572: /************** Forecasting *****not tested NB*************/
1.53      brouard  3573: 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){
                   3574:   
                   3575:   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
                   3576:   int *popage;
1.69      brouard  3577:   double calagedatem, agelim, kk1, kk2;
1.53      brouard  3578:   double *popeffectif,*popcount;
                   3579:   double ***p3mat,***tabpop,***tabpopprev;
1.55      lievre   3580:   double ***mobaverage;
1.53      brouard  3581:   char filerespop[FILENAMELENGTH];
                   3582: 
                   3583:   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3584:   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3585:   agelim=AGESUP;
1.69      brouard  3586:   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53      brouard  3587:   
1.84      brouard  3588:   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53      brouard  3589:   
                   3590:   
                   3591:   strcpy(filerespop,"pop"); 
                   3592:   strcat(filerespop,fileres);
                   3593:   if((ficrespop=fopen(filerespop,"w"))==NULL) {
                   3594:     printf("Problem with forecast resultfile: %s\n", filerespop);
                   3595:     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
                   3596:   }
                   3597:   printf("Computing forecasting: result on file '%s' \n", filerespop);
                   3598:   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
                   3599: 
                   3600:   if (cptcoveff==0) ncodemax[cptcoveff]=1;
                   3601: 
1.54      brouard  3602:   if (mobilav!=0) {
1.53      brouard  3603:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  3604:     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
                   3605:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   3606:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   3607:     }
1.53      brouard  3608:   }
                   3609: 
                   3610:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   3611:   if (stepm<=12) stepsize=1;
                   3612:   
                   3613:   agelim=AGESUP;
                   3614:   
                   3615:   hstepm=1;
                   3616:   hstepm=hstepm/stepm; 
                   3617:   
                   3618:   if (popforecast==1) {
                   3619:     if((ficpop=fopen(popfile,"r"))==NULL) {
                   3620:       printf("Problem with population file : %s\n",popfile);exit(0);
                   3621:       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
                   3622:     } 
                   3623:     popage=ivector(0,AGESUP);
                   3624:     popeffectif=vector(0,AGESUP);
                   3625:     popcount=vector(0,AGESUP);
                   3626:     
                   3627:     i=1;   
                   3628:     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
                   3629:    
                   3630:     imx=i;
                   3631:     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
                   3632:   }
                   3633: 
1.69      brouard  3634:   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53      brouard  3635:    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                   3636:       k=k+1;
                   3637:       fprintf(ficrespop,"\n#******");
                   3638:       for(j=1;j<=cptcoveff;j++) {
                   3639:        fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   3640:       }
                   3641:       fprintf(ficrespop,"******\n");
                   3642:       fprintf(ficrespop,"# Age");
                   3643:       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
                   3644:       if (popforecast==1)  fprintf(ficrespop," [Population]");
                   3645:       
                   3646:       for (cpt=0; cpt<=0;cpt++) { 
                   3647:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
                   3648:        
1.69      brouard  3649:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
1.53      brouard  3650:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   3651:          nhstepm = nhstepm/hstepm; 
                   3652:          
                   3653:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3654:          oldm=oldms;savm=savms;
                   3655:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   3656:        
                   3657:          for (h=0; h<=nhstepm; h++){
1.69      brouard  3658:            if (h==(int) (calagedatem+YEARM*cpt)) {
1.53      brouard  3659:              fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   3660:            } 
                   3661:            for(j=1; j<=nlstate+ndeath;j++) {
                   3662:              kk1=0.;kk2=0;
                   3663:              for(i=1; i<=nlstate;i++) {              
                   3664:                if (mobilav==1) 
                   3665:                  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   3666:                else {
                   3667:                  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   3668:                }
                   3669:              }
1.69      brouard  3670:              if (h==(int)(calagedatem+12*cpt)){
1.53      brouard  3671:                tabpop[(int)(agedeb)][j][cptcod]=kk1;
                   3672:                  /*fprintf(ficrespop," %.3f", kk1);
                   3673:                    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                   3674:              }
                   3675:            }
                   3676:            for(i=1; i<=nlstate;i++){
                   3677:              kk1=0.;
                   3678:                for(j=1; j<=nlstate;j++){
                   3679:                  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   3680:                }
1.69      brouard  3681:                  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53      brouard  3682:            }
                   3683: 
1.69      brouard  3684:            if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
1.53      brouard  3685:              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
                   3686:          }
                   3687:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3688:        }
                   3689:       }
                   3690:  
                   3691:   /******/
                   3692: 
                   3693:       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
                   3694:        fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
1.69      brouard  3695:        for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
1.53      brouard  3696:          nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
                   3697:          nhstepm = nhstepm/hstepm; 
                   3698:          
                   3699:          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3700:          oldm=oldms;savm=savms;
                   3701:          hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
                   3702:          for (h=0; h<=nhstepm; h++){
1.69      brouard  3703:            if (h==(int) (calagedatem+YEARM*cpt)) {
1.53      brouard  3704:              fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                   3705:            } 
                   3706:            for(j=1; j<=nlstate+ndeath;j++) {
                   3707:              kk1=0.;kk2=0;
                   3708:              for(i=1; i<=nlstate;i++) {              
                   3709:                kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                   3710:              }
1.69      brouard  3711:              if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
1.53      brouard  3712:            }
                   3713:          }
                   3714:          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   3715:        }
                   3716:       }
                   3717:    } 
                   3718:   }
                   3719:  
1.54      brouard  3720:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53      brouard  3721: 
                   3722:   if (popforecast==1) {
                   3723:     free_ivector(popage,0,AGESUP);
                   3724:     free_vector(popeffectif,0,AGESUP);
                   3725:     free_vector(popcount,0,AGESUP);
                   3726:   }
                   3727:   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3728:   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   3729:   fclose(ficrespop);
1.84      brouard  3730: } /* End of popforecast */
1.53      brouard  3731: 
1.87      brouard  3732: int fileappend(FILE *fichier, char *optionfich)
1.86      brouard  3733: {
1.87      brouard  3734:   if((fichier=fopen(optionfich,"a"))==NULL) {
                   3735:     printf("Problem with file: %s\n", optionfich);
                   3736:     fprintf(ficlog,"Problem with file: %s\n", optionfich);
                   3737:     return (0);
1.86      brouard  3738:   }
1.87      brouard  3739:   fflush(fichier);
                   3740:   return (1);
1.86      brouard  3741: }
1.94      brouard  3742: 
                   3743: 
                   3744: /**************** function prwizard **********************/
1.88      brouard  3745: void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
                   3746: {
                   3747: 
1.94      brouard  3748:   /* Wizard to print covariance matrix template */
                   3749: 
1.88      brouard  3750:   char ca[32], cb[32], cc[32];
                   3751:   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
                   3752:   int numlinepar;
                   3753: 
                   3754:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   3755:   fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   3756:   for(i=1; i <=nlstate; i++){
                   3757:     jj=0;
                   3758:     for(j=1; j <=nlstate+ndeath; j++){
                   3759:       if(j==i) continue;
                   3760:       jj++;
                   3761:       /*ca[0]= k+'a'-1;ca[1]='\0';*/
                   3762:       printf("%1d%1d",i,j);
                   3763:       fprintf(ficparo,"%1d%1d",i,j);
                   3764:       for(k=1; k<=ncovmodel;k++){
                   3765:        /*        printf(" %lf",param[i][j][k]); */
                   3766:        /*        fprintf(ficparo," %lf",param[i][j][k]); */
                   3767:        printf(" 0.");
                   3768:        fprintf(ficparo," 0.");
                   3769:       }
                   3770:       printf("\n");
                   3771:       fprintf(ficparo,"\n");
                   3772:     }
                   3773:   }
                   3774:   printf("# Scales (for hessian or gradient estimation)\n");
                   3775:   fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
                   3776:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
                   3777:   for(i=1; i <=nlstate; i++){
                   3778:     jj=0;
                   3779:     for(j=1; j <=nlstate+ndeath; j++){
                   3780:       if(j==i) continue;
                   3781:       jj++;
                   3782:       fprintf(ficparo,"%1d%1d",i,j);
                   3783:       printf("%1d%1d",i,j);
                   3784:       fflush(stdout);
                   3785:       for(k=1; k<=ncovmodel;k++){
                   3786:        /*      printf(" %le",delti3[i][j][k]); */
                   3787:        /*      fprintf(ficparo," %le",delti3[i][j][k]); */
                   3788:        printf(" 0.");
                   3789:        fprintf(ficparo," 0.");
                   3790:       }
                   3791:       numlinepar++;
                   3792:       printf("\n");
                   3793:       fprintf(ficparo,"\n");
                   3794:     }
                   3795:   }
                   3796:   printf("# Covariance matrix\n");
                   3797: /* # 121 Var(a12)\n\ */
                   3798: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   3799: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   3800: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   3801: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   3802: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   3803: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   3804: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   3805:   fflush(stdout);
                   3806:   fprintf(ficparo,"# Covariance matrix\n");
                   3807:   /* # 121 Var(a12)\n\ */
                   3808:   /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   3809:   /* #   ...\n\ */
                   3810:   /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
                   3811:   
                   3812:   for(itimes=1;itimes<=2;itimes++){
                   3813:     jj=0;
                   3814:     for(i=1; i <=nlstate; i++){
                   3815:       for(j=1; j <=nlstate+ndeath; j++){
                   3816:        if(j==i) continue;
                   3817:        for(k=1; k<=ncovmodel;k++){
                   3818:          jj++;
                   3819:          ca[0]= k+'a'-1;ca[1]='\0';
                   3820:          if(itimes==1){
                   3821:            printf("#%1d%1d%d",i,j,k);
                   3822:            fprintf(ficparo,"#%1d%1d%d",i,j,k);
                   3823:          }else{
                   3824:            printf("%1d%1d%d",i,j,k);
                   3825:            fprintf(ficparo,"%1d%1d%d",i,j,k);
                   3826:            /*  printf(" %.5le",matcov[i][j]); */
                   3827:          }
                   3828:          ll=0;
                   3829:          for(li=1;li <=nlstate; li++){
                   3830:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   3831:              if(lj==li) continue;
                   3832:              for(lk=1;lk<=ncovmodel;lk++){
                   3833:                ll++;
                   3834:                if(ll<=jj){
                   3835:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   3836:                  if(ll<jj){
                   3837:                    if(itimes==1){
                   3838:                      printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   3839:                      fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   3840:                    }else{
                   3841:                      printf(" 0.");
                   3842:                      fprintf(ficparo," 0.");
                   3843:                    }
                   3844:                  }else{
                   3845:                    if(itimes==1){
                   3846:                      printf(" Var(%s%1d%1d)",ca,i,j);
                   3847:                      fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                   3848:                    }else{
                   3849:                      printf(" 0.");
                   3850:                      fprintf(ficparo," 0.");
                   3851:                    }
                   3852:                  }
                   3853:                }
                   3854:              } /* end lk */
                   3855:            } /* end lj */
                   3856:          } /* end li */
                   3857:          printf("\n");
                   3858:          fprintf(ficparo,"\n");
                   3859:          numlinepar++;
                   3860:        } /* end k*/
                   3861:       } /*end j */
                   3862:     } /* end i */
1.95      brouard  3863:   } /* end itimes */
1.88      brouard  3864: 
                   3865: } /* end of prwizard */
                   3866: 
1.91      brouard  3867: 
1.53      brouard  3868: /***********************************************/
                   3869: /**************** Main Program *****************/
                   3870: /***********************************************/
                   3871: 
                   3872: int main(int argc, char *argv[])
                   3873: {
1.61      brouard  3874:   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74      brouard  3875:   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.95      brouard  3876:   int jj, ll, li, lj, lk, imk;
1.85      brouard  3877:   int numlinepar=0; /* Current linenumber of parameter file */
1.95      brouard  3878:   int itimes;
                   3879: 
                   3880:   char ca[32], cb[32], cc[32];
1.87      brouard  3881:   /*  FILE *fichtm; *//* Html File */
                   3882:   /* FILE *ficgp;*/ /*Gnuplot File */
1.53      brouard  3883:   double agedeb, agefin,hf;
                   3884:   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
                   3885: 
                   3886:   double fret;
                   3887:   double **xi,tmp,delta;
                   3888: 
                   3889:   double dum; /* Dummy variable */
                   3890:   double ***p3mat;
                   3891:   double ***mobaverage;
                   3892:   int *indx;
                   3893:   char line[MAXLINE], linepar[MAXLINE];
1.88      brouard  3894:   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
                   3895:   char pathr[MAXLINE]; 
1.53      brouard  3896:   int firstobs=1, lastobs=10;
                   3897:   int sdeb, sfin; /* Status at beginning and end */
                   3898:   int c,  h , cpt,l;
                   3899:   int ju,jl, mi;
                   3900:   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59      brouard  3901:   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
1.69      brouard  3902:   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53      brouard  3903:   int mobilav=0,popforecast=0;
                   3904:   int hstepm, nhstepm;
1.74      brouard  3905:   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
                   3906:   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53      brouard  3907: 
                   3908:   double bage, fage, age, agelim, agebase;
                   3909:   double ftolpl=FTOL;
                   3910:   double **prlim;
                   3911:   double *severity;
                   3912:   double ***param; /* Matrix of parameters */
                   3913:   double  *p;
                   3914:   double **matcov; /* Matrix of covariance */
                   3915:   double ***delti3; /* Scale */
                   3916:   double *delti; /* Scale */
                   3917:   double ***eij, ***vareij;
                   3918:   double **varpl; /* Variances of prevalence limits by age */
                   3919:   double *epj, vepp;
                   3920:   double kk1, kk2;
1.74      brouard  3921:   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53      brouard  3922: 
                   3923:   char *alph[]={"a","a","b","c","d","e"}, str[4];
                   3924: 
                   3925: 
                   3926:   char z[1]="c", occ;
1.86      brouard  3927: 
1.53      brouard  3928:   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88      brouard  3929:   char strstart[80], *strt, strtend[80];
1.85      brouard  3930:   char *stratrunc;
                   3931:   int lstra;
                   3932: 
                   3933:   long total_usecs;
1.53      brouard  3934:  
1.95      brouard  3935: /*   setlocale (LC_ALL, ""); */
                   3936: /*   bindtextdomain (PACKAGE, LOCALEDIR); */
                   3937: /*   textdomain (PACKAGE); */
                   3938: /*   setlocale (LC_CTYPE, ""); */
                   3939: /*   setlocale (LC_MESSAGES, ""); */
                   3940: 
1.85      brouard  3941:   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
                   3942:   (void) gettimeofday(&start_time,&tzp);
1.91      brouard  3943:   curr_time=start_time;
1.85      brouard  3944:   tm = *localtime(&start_time.tv_sec);
                   3945:   tmg = *gmtime(&start_time.tv_sec);
1.88      brouard  3946:   strcpy(strstart,asctime(&tm));
1.86      brouard  3947: 
1.88      brouard  3948: /*  printf("Localtime (at start)=%s",strstart); */
1.85      brouard  3949: /*  tp.tv_sec = tp.tv_sec +86400; */
                   3950: /*  tm = *localtime(&start_time.tv_sec); */
                   3951: /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
                   3952: /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
                   3953: /*   tmg.tm_hour=tmg.tm_hour + 1; */
                   3954: /*   tp.tv_sec = mktime(&tmg); */
                   3955: /*   strt=asctime(&tmg); */
1.88      brouard  3956: /*   printf("Time(after) =%s",strstart);  */
1.85      brouard  3957: /*  (void) time (&time_value);
                   3958: *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
                   3959: *  tm = *localtime(&time_value);
1.88      brouard  3960: *  strstart=asctime(&tm);
                   3961: *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
1.85      brouard  3962: */
                   3963: 
1.91      brouard  3964:   nberr=0; /* Number of errors and warnings */
                   3965:   nbwarn=0;
1.53      brouard  3966:   getcwd(pathcd, size);
                   3967: 
1.81      brouard  3968:   printf("\n%s\n%s",version,fullversion);
1.53      brouard  3969:   if(argc <=1){
                   3970:     printf("\nEnter the parameter file name: ");
                   3971:     scanf("%s",pathtot);
                   3972:   }
                   3973:   else{
                   3974:     strcpy(pathtot,argv[1]);
                   3975:   }
1.88      brouard  3976:   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53      brouard  3977:   /*cygwin_split_path(pathtot,path,optionfile);
                   3978:     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
                   3979:   /* cutv(path,optionfile,pathtot,'\\');*/
                   3980: 
                   3981:   split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85      brouard  3982:   printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53      brouard  3983:   chdir(path);
1.88      brouard  3984:   strcpy(command,"mkdir ");
                   3985:   strcat(command,optionfilefiname);
                   3986:   if((outcmd=system(command)) != 0){
                   3987:     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
                   3988:     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
                   3989:     /* fclose(ficlog); */
                   3990: /*     exit(1); */
                   3991:   }
                   3992: /*   if((imk=mkdir(optionfilefiname))<0){ */
                   3993: /*     perror("mkdir"); */
                   3994: /*   } */
1.53      brouard  3995: 
1.59      brouard  3996:   /*-------- arguments in the command line --------*/
1.53      brouard  3997: 
                   3998:   /* Log file */
                   3999:   strcat(filelog, optionfilefiname);
                   4000:   strcat(filelog,".log");    /* */
                   4001:   if((ficlog=fopen(filelog,"w"))==NULL)    {
                   4002:     printf("Problem with logfile %s\n",filelog);
                   4003:     goto end;
                   4004:   }
                   4005:   fprintf(ficlog,"Log filename:%s\n",filelog);
1.85      brouard  4006:   fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53      brouard  4007:   fprintf(ficlog,"\nEnter the parameter file name: ");
1.88      brouard  4008:   fprintf(ficlog,"pathtot=%s\n\
                   4009:  path=%s \n\
                   4010:  optionfile=%s\n\
                   4011:  optionfilext=%s\n\
                   4012:  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86      brouard  4013: 
1.94      brouard  4014:   printf("Local time (at start):%s",strstart);
                   4015:   fprintf(ficlog,"Local time (at start): %s",strstart);
1.53      brouard  4016:   fflush(ficlog);
1.91      brouard  4017: /*   (void) gettimeofday(&curr_time,&tzp); */
                   4018: /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53      brouard  4019: 
                   4020:   /* */
                   4021:   strcpy(fileres,"r");
                   4022:   strcat(fileres, optionfilefiname);
                   4023:   strcat(fileres,".txt");    /* Other files have txt extension */
                   4024: 
                   4025:   /*---------arguments file --------*/
                   4026: 
                   4027:   if((ficpar=fopen(optionfile,"r"))==NULL)    {
                   4028:     printf("Problem with optionfile %s\n",optionfile);
                   4029:     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85      brouard  4030:     fflush(ficlog);
1.53      brouard  4031:     goto end;
                   4032:   }
                   4033: 
1.88      brouard  4034: 
                   4035: 
1.53      brouard  4036:   strcpy(filereso,"o");
                   4037:   strcat(filereso,fileres);
1.88      brouard  4038:   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53      brouard  4039:     printf("Problem with Output resultfile: %s\n", filereso);
                   4040:     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85      brouard  4041:     fflush(ficlog);
1.53      brouard  4042:     goto end;
                   4043:   }
                   4044: 
                   4045:   /* Reads comments: lines beginning with '#' */
1.85      brouard  4046:   numlinepar=0;
1.53      brouard  4047:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4048:     ungetc(c,ficpar);
                   4049:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4050:     numlinepar++;
1.53      brouard  4051:     puts(line);
                   4052:     fputs(line,ficparo);
1.85      brouard  4053:     fputs(line,ficlog);
1.53      brouard  4054:   }
                   4055:   ungetc(c,ficpar);
                   4056: 
                   4057:   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  4058:   numlinepar++;
1.53      brouard  4059:   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);
                   4060:   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  4061:   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);
                   4062:   fflush(ficlog);
1.59      brouard  4063:   while((c=getc(ficpar))=='#' && c!= EOF){
1.53      brouard  4064:     ungetc(c,ficpar);
                   4065:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4066:     numlinepar++;
1.53      brouard  4067:     puts(line);
                   4068:     fputs(line,ficparo);
1.85      brouard  4069:     fputs(line,ficlog);
1.53      brouard  4070:   }
                   4071:   ungetc(c,ficpar);
1.85      brouard  4072: 
1.53      brouard  4073:    
                   4074:   covar=matrix(0,NCOVMAX,1,n); 
1.58      lievre   4075:   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53      brouard  4076:   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
                   4077: 
1.58      lievre   4078:   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53      brouard  4079:   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.88      brouard  4080:  
                   4081:   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
                   4082:     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
                   4083:     printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   4084:     fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
                   4085:     fclose (ficparo);
                   4086:     fclose (ficlog);
                   4087:     exit(0);
                   4088:   }
1.53      brouard  4089:   /* Read guess parameters */
                   4090:   /* Reads comments: lines beginning with '#' */
                   4091:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4092:     ungetc(c,ficpar);
                   4093:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4094:     numlinepar++;
1.53      brouard  4095:     puts(line);
                   4096:     fputs(line,ficparo);
1.85      brouard  4097:     fputs(line,ficlog);
1.53      brouard  4098:   }
                   4099:   ungetc(c,ficpar);
1.85      brouard  4100: 
1.53      brouard  4101:   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85      brouard  4102:   for(i=1; i <=nlstate; i++){
                   4103:     j=0;
                   4104:     for(jj=1; jj <=nlstate+ndeath; jj++){
                   4105:       if(jj==i) continue;
                   4106:       j++;
1.53      brouard  4107:       fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85      brouard  4108:       if ((i1 != i) && (j1 != j)){
                   4109:        printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   4110:        exit(1);
                   4111:       }
1.53      brouard  4112:       fprintf(ficparo,"%1d%1d",i1,j1);
                   4113:       if(mle==1)
                   4114:        printf("%1d%1d",i,j);
                   4115:       fprintf(ficlog,"%1d%1d",i,j);
                   4116:       for(k=1; k<=ncovmodel;k++){
                   4117:        fscanf(ficpar," %lf",&param[i][j][k]);
                   4118:        if(mle==1){
                   4119:          printf(" %lf",param[i][j][k]);
                   4120:          fprintf(ficlog," %lf",param[i][j][k]);
                   4121:        }
                   4122:        else
                   4123:          fprintf(ficlog," %lf",param[i][j][k]);
                   4124:        fprintf(ficparo," %lf",param[i][j][k]);
                   4125:       }
                   4126:       fscanf(ficpar,"\n");
1.85      brouard  4127:       numlinepar++;
1.53      brouard  4128:       if(mle==1)
                   4129:        printf("\n");
                   4130:       fprintf(ficlog,"\n");
                   4131:       fprintf(ficparo,"\n");
                   4132:     }
1.85      brouard  4133:   }  
                   4134:   fflush(ficlog);
                   4135: 
1.59      brouard  4136:   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53      brouard  4137: 
                   4138:   p=param[1][1];
                   4139:   
                   4140:   /* Reads comments: lines beginning with '#' */
                   4141:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4142:     ungetc(c,ficpar);
                   4143:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4144:     numlinepar++;
1.53      brouard  4145:     puts(line);
                   4146:     fputs(line,ficparo);
1.85      brouard  4147:     fputs(line,ficlog);
1.53      brouard  4148:   }
                   4149:   ungetc(c,ficpar);
                   4150: 
                   4151:   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74      brouard  4152:   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53      brouard  4153:   for(i=1; i <=nlstate; i++){
                   4154:     for(j=1; j <=nlstate+ndeath-1; j++){
                   4155:       fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85      brouard  4156:       if ((i1-i)*(j1-j)!=0){
                   4157:        printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                   4158:        exit(1);
                   4159:       }
1.53      brouard  4160:       printf("%1d%1d",i,j);
                   4161:       fprintf(ficparo,"%1d%1d",i1,j1);
1.85      brouard  4162:       fprintf(ficlog,"%1d%1d",i1,j1);
1.53      brouard  4163:       for(k=1; k<=ncovmodel;k++){
                   4164:        fscanf(ficpar,"%le",&delti3[i][j][k]);
                   4165:        printf(" %le",delti3[i][j][k]);
                   4166:        fprintf(ficparo," %le",delti3[i][j][k]);
1.85      brouard  4167:        fprintf(ficlog," %le",delti3[i][j][k]);
1.53      brouard  4168:       }
                   4169:       fscanf(ficpar,"\n");
1.85      brouard  4170:       numlinepar++;
1.53      brouard  4171:       printf("\n");
                   4172:       fprintf(ficparo,"\n");
1.85      brouard  4173:       fprintf(ficlog,"\n");
1.53      brouard  4174:     }
                   4175:   }
1.85      brouard  4176:   fflush(ficlog);
                   4177: 
1.53      brouard  4178:   delti=delti3[1][1];
1.74      brouard  4179: 
                   4180: 
                   4181:   /* 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  4182:   
                   4183:   /* Reads comments: lines beginning with '#' */
                   4184:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4185:     ungetc(c,ficpar);
                   4186:     fgets(line, MAXLINE, ficpar);
1.85      brouard  4187:     numlinepar++;
1.53      brouard  4188:     puts(line);
                   4189:     fputs(line,ficparo);
1.85      brouard  4190:     fputs(line,ficlog);
1.53      brouard  4191:   }
                   4192:   ungetc(c,ficpar);
                   4193:   
                   4194:   matcov=matrix(1,npar,1,npar);
                   4195:   for(i=1; i <=npar; i++){
                   4196:     fscanf(ficpar,"%s",&str);
                   4197:     if(mle==1)
                   4198:       printf("%s",str);
                   4199:     fprintf(ficlog,"%s",str);
                   4200:     fprintf(ficparo,"%s",str);
                   4201:     for(j=1; j <=i; j++){
                   4202:       fscanf(ficpar," %le",&matcov[i][j]);
                   4203:       if(mle==1){
                   4204:        printf(" %.5le",matcov[i][j]);
                   4205:       }
1.85      brouard  4206:       fprintf(ficlog," %.5le",matcov[i][j]);
1.53      brouard  4207:       fprintf(ficparo," %.5le",matcov[i][j]);
                   4208:     }
                   4209:     fscanf(ficpar,"\n");
1.85      brouard  4210:     numlinepar++;
1.53      brouard  4211:     if(mle==1)
                   4212:       printf("\n");
                   4213:     fprintf(ficlog,"\n");
                   4214:     fprintf(ficparo,"\n");
                   4215:   }
                   4216:   for(i=1; i <=npar; i++)
                   4217:     for(j=i+1;j<=npar;j++)
                   4218:       matcov[i][j]=matcov[j][i];
                   4219:    
                   4220:   if(mle==1)
                   4221:     printf("\n");
                   4222:   fprintf(ficlog,"\n");
                   4223: 
1.85      brouard  4224:   fflush(ficlog);
1.53      brouard  4225: 
1.59      brouard  4226:   /*-------- Rewriting paramater file ----------*/
                   4227:   strcpy(rfileres,"r");    /* "Rparameterfile */
                   4228:   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
                   4229:   strcat(rfileres,".");    /* */
                   4230:   strcat(rfileres,optionfilext);    /* Other files have txt extension */
                   4231:   if((ficres =fopen(rfileres,"w"))==NULL) {
                   4232:     printf("Problem writing new parameter file: %s\n", fileres);goto end;
                   4233:     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
                   4234:   }
                   4235:   fprintf(ficres,"#%s\n",version);
1.53      brouard  4236:     
1.59      brouard  4237:   /*-------- data file ----------*/
                   4238:   if((fic=fopen(datafile,"r"))==NULL)    {
                   4239:     printf("Problem with datafile: %s\n", datafile);goto end;
                   4240:     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
                   4241:   }
                   4242: 
                   4243:   n= lastobs;
                   4244:   severity = vector(1,maxwav);
                   4245:   outcome=imatrix(1,maxwav+1,1,n);
1.85      brouard  4246:   num=lvector(1,n);
1.59      brouard  4247:   moisnais=vector(1,n);
                   4248:   annais=vector(1,n);
                   4249:   moisdc=vector(1,n);
                   4250:   andc=vector(1,n);
                   4251:   agedc=vector(1,n);
                   4252:   cod=ivector(1,n);
                   4253:   weight=vector(1,n);
                   4254:   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
                   4255:   mint=matrix(1,maxwav,1,n);
                   4256:   anint=matrix(1,maxwav,1,n);
                   4257:   s=imatrix(1,maxwav+1,1,n);
                   4258:   tab=ivector(1,NCOVMAX);
                   4259:   ncodemax=ivector(1,8);
                   4260: 
                   4261:   i=1;
                   4262:   while (fgets(line, MAXLINE, fic) != NULL)    {
                   4263:     if ((i >= firstobs) && (i <=lastobs)) {
1.53      brouard  4264:        
1.59      brouard  4265:       for (j=maxwav;j>=1;j--){
                   4266:        cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
                   4267:        strcpy(line,stra);
                   4268:        cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4269:        cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4270:       }
1.53      brouard  4271:        
1.59      brouard  4272:       cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4273:       cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53      brouard  4274: 
1.59      brouard  4275:       cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4276:       cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53      brouard  4277: 
1.59      brouard  4278:       cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
                   4279:       for (j=ncovcol;j>=1;j--){
                   4280:        cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
                   4281:       } 
1.85      brouard  4282:       lstra=strlen(stra);
                   4283:       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
                   4284:        stratrunc = &(stra[lstra-9]);
                   4285:        num[i]=atol(stratrunc);
                   4286:       }
                   4287:       else
                   4288:        num[i]=atol(stra);
1.53      brouard  4289:        
1.59      brouard  4290:       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85      brouard  4291:        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  4292: 
1.59      brouard  4293:       i=i+1;
                   4294:     }
                   4295:   }
                   4296:   /* printf("ii=%d", ij);
                   4297:      scanf("%d",i);*/
1.53      brouard  4298:   imx=i-1; /* Number of individuals */
                   4299: 
                   4300:   /* for (i=1; i<=imx; i++){
                   4301:     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
                   4302:     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
                   4303:     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
                   4304:     }*/
                   4305:    /*  for (i=1; i<=imx; i++){
                   4306:      if (s[4][i]==9)  s[4][i]=-1; 
1.85      brouard  4307:      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  4308:   
1.71      brouard  4309:  for (i=1; i<=imx; i++)
1.53      brouard  4310:  
1.71      brouard  4311:    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
                   4312:      else weight[i]=1;*/
                   4313: 
1.53      brouard  4314:   /* Calculation of the number of parameter from char model*/
                   4315:   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
                   4316:   Tprod=ivector(1,15); 
                   4317:   Tvaraff=ivector(1,15); 
                   4318:   Tvard=imatrix(1,15,1,2);
                   4319:   Tage=ivector(1,15);      
                   4320:    
1.58      lievre   4321:   if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53      brouard  4322:     j=0, j1=0, k1=1, k2=1;
1.58      lievre   4323:     j=nbocc(model,'+'); /* j=Number of '+' */
                   4324:     j1=nbocc(model,'*'); /* j1=Number of '*' */
                   4325:     cptcovn=j+1; 
                   4326:     cptcovprod=j1; /*Number of products */
1.53      brouard  4327:     
                   4328:     strcpy(modelsav,model); 
                   4329:     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
                   4330:       printf("Error. Non available option model=%s ",model);
                   4331:       fprintf(ficlog,"Error. Non available option model=%s ",model);
                   4332:       goto end;
                   4333:     }
                   4334:     
1.59      brouard  4335:     /* This loop fills the array Tvar from the string 'model'.*/
1.58      lievre   4336: 
1.53      brouard  4337:     for(i=(j+1); i>=1;i--){
                   4338:       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
1.59      brouard  4339:       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53      brouard  4340:       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
                   4341:       /*scanf("%d",i);*/
                   4342:       if (strchr(strb,'*')) {  /* Model includes a product */
                   4343:        cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
                   4344:        if (strcmp(strc,"age")==0) { /* Vn*age */
                   4345:          cptcovprod--;
                   4346:          cutv(strb,stre,strd,'V');
                   4347:          Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
                   4348:          cptcovage++;
                   4349:            Tage[cptcovage]=i;
                   4350:            /*printf("stre=%s ", stre);*/
                   4351:        }
                   4352:        else if (strcmp(strd,"age")==0) { /* or age*Vn */
                   4353:          cptcovprod--;
                   4354:          cutv(strb,stre,strc,'V');
                   4355:          Tvar[i]=atoi(stre);
                   4356:          cptcovage++;
                   4357:          Tage[cptcovage]=i;
                   4358:        }
                   4359:        else {  /* Age is not in the model */
                   4360:          cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
                   4361:          Tvar[i]=ncovcol+k1;
                   4362:          cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
                   4363:          Tprod[k1]=i;
                   4364:          Tvard[k1][1]=atoi(strc); /* m*/
                   4365:          Tvard[k1][2]=atoi(stre); /* n */
                   4366:          Tvar[cptcovn+k2]=Tvard[k1][1];
                   4367:          Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
                   4368:          for (k=1; k<=lastobs;k++) 
                   4369:            covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
                   4370:          k1++;
                   4371:          k2=k2+2;
                   4372:        }
                   4373:       }
                   4374:       else { /* no more sum */
                   4375:        /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
                   4376:        /*  scanf("%d",i);*/
                   4377:       cutv(strd,strc,strb,'V');
                   4378:       Tvar[i]=atoi(strc);
                   4379:       }
                   4380:       strcpy(modelsav,stra);  
                   4381:       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                   4382:        scanf("%d",i);*/
                   4383:     } /* end of loop + */
                   4384:   } /* end model */
                   4385:   
1.58      lievre   4386:   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
                   4387:     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
                   4388: 
1.53      brouard  4389:   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
                   4390:   printf("cptcovprod=%d ", cptcovprod);
                   4391:   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58      lievre   4392: 
                   4393:   scanf("%d ",i);
                   4394:   fclose(fic);*/
1.53      brouard  4395: 
                   4396:     /*  if(mle==1){*/
1.59      brouard  4397:   if (weightopt != 1) { /* Maximisation without weights*/
                   4398:     for(i=1;i<=n;i++) weight[i]=1.0;
                   4399:   }
1.53      brouard  4400:     /*-calculation of age at interview from date of interview and age at death -*/
1.59      brouard  4401:   agev=matrix(1,maxwav,1,imx);
1.53      brouard  4402: 
1.59      brouard  4403:   for (i=1; i<=imx; i++) {
                   4404:     for(m=2; (m<= maxwav); m++) {
1.76      brouard  4405:       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59      brouard  4406:        anint[m][i]=9999;
                   4407:        s[m][i]=-1;
                   4408:       }
1.76      brouard  4409:       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91      brouard  4410:        nberr++;
1.85      brouard  4411:        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);
                   4412:        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  4413:        s[m][i]=-1;
                   4414:       }
                   4415:       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91      brouard  4416:        nberr++;
1.85      brouard  4417:        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]); 
                   4418:        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  4419:        s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76      brouard  4420:       }
1.53      brouard  4421:     }
1.59      brouard  4422:   }
1.53      brouard  4423: 
1.59      brouard  4424:   for (i=1; i<=imx; i++)  {
                   4425:     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71      brouard  4426:     for(m=firstpass; (m<= lastpass); m++){
1.69      brouard  4427:       if(s[m][i] >0){
1.59      brouard  4428:        if (s[m][i] >= nlstate+1) {
                   4429:          if(agedc[i]>0)
1.76      brouard  4430:            if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69      brouard  4431:              agev[m][i]=agedc[i];
1.59      brouard  4432:          /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
                   4433:            else {
1.76      brouard  4434:              if ((int)andc[i]!=9999){
1.91      brouard  4435:                nbwarn++;
1.85      brouard  4436:                printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   4437:                fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59      brouard  4438:                agev[m][i]=-1;
1.53      brouard  4439:              }
                   4440:            }
1.70      brouard  4441:        }
1.69      brouard  4442:        else if(s[m][i] !=9){ /* Standard case, age in fractional
                   4443:                                 years but with the precision of a
                   4444:                                 month */
1.59      brouard  4445:          agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76      brouard  4446:          if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59      brouard  4447:            agev[m][i]=1;
                   4448:          else if(agev[m][i] <agemin){ 
                   4449:            agemin=agev[m][i];
                   4450:            /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53      brouard  4451:          }
1.59      brouard  4452:          else if(agev[m][i] >agemax){
                   4453:            agemax=agev[m][i];
                   4454:            /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53      brouard  4455:          }
1.59      brouard  4456:          /*agev[m][i]=anint[m][i]-annais[i];*/
                   4457:          /*     agev[m][i] = age[i]+2*m;*/
1.53      brouard  4458:        }
1.59      brouard  4459:        else { /* =9 */
1.53      brouard  4460:          agev[m][i]=1;
1.59      brouard  4461:          s[m][i]=-1;
                   4462:        }
1.53      brouard  4463:       }
1.59      brouard  4464:       else /*= 0 Unknown */
                   4465:        agev[m][i]=1;
                   4466:     }
1.53      brouard  4467:     
1.59      brouard  4468:   }
                   4469:   for (i=1; i<=imx; i++)  {
1.71      brouard  4470:     for(m=firstpass; (m<=lastpass); m++){
1.59      brouard  4471:       if (s[m][i] > (nlstate+ndeath)) {
1.91      brouard  4472:        nberr++;
1.59      brouard  4473:        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);     
                   4474:        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);     
                   4475:        goto end;
1.53      brouard  4476:       }
                   4477:     }
1.59      brouard  4478:   }
1.53      brouard  4479: 
1.71      brouard  4480:   /*for (i=1; i<=imx; i++){
                   4481:   for (m=firstpass; (m<lastpass); m++){
1.85      brouard  4482:      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  4483: }
                   4484: 
                   4485: }*/
                   4486: 
1.97    ! lievre   4487: 
1.59      brouard  4488:   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
                   4489:   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
                   4490: 
                   4491:   free_vector(severity,1,maxwav);
                   4492:   free_imatrix(outcome,1,maxwav+1,1,n);
                   4493:   free_vector(moisnais,1,n);
                   4494:   free_vector(annais,1,n);
                   4495:   /* free_matrix(mint,1,maxwav,1,n);
                   4496:      free_matrix(anint,1,maxwav,1,n);*/
                   4497:   free_vector(moisdc,1,n);
                   4498:   free_vector(andc,1,n);
1.53      brouard  4499: 
                   4500:    
1.59      brouard  4501:   wav=ivector(1,imx);
                   4502:   dh=imatrix(1,lastpass-firstpass+1,1,imx);
                   4503:   bh=imatrix(1,lastpass-firstpass+1,1,imx);
                   4504:   mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69      brouard  4505:    
1.59      brouard  4506:   /* Concatenates waves */
                   4507:   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
1.53      brouard  4508: 
1.59      brouard  4509:   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53      brouard  4510: 
1.59      brouard  4511:   Tcode=ivector(1,100);
                   4512:   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
                   4513:   ncodemax[1]=1;
                   4514:   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53      brouard  4515:       
1.59      brouard  4516:   codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                   4517:                                 the estimations*/
                   4518:   h=0;
                   4519:   m=pow(2,cptcoveff);
1.53      brouard  4520:  
1.59      brouard  4521:   for(k=1;k<=cptcoveff; k++){
                   4522:     for(i=1; i <=(m/pow(2,k));i++){
                   4523:       for(j=1; j <= ncodemax[k]; j++){
                   4524:        for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
                   4525:          h++;
                   4526:          if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
                   4527:          /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
                   4528:        } 
                   4529:       }
                   4530:     }
                   4531:   } 
                   4532:   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
                   4533:      codtab[1][2]=1;codtab[2][2]=2; */
                   4534:   /* for(i=1; i <=m ;i++){ 
                   4535:      for(k=1; k <=cptcovn; k++){
                   4536:      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
                   4537:      }
                   4538:      printf("\n");
1.53      brouard  4539:      }
1.59      brouard  4540:      scanf("%d",i);*/
1.53      brouard  4541:     
1.86      brouard  4542:   /*------------ gnuplot -------------*/
                   4543:   strcpy(optionfilegnuplot,optionfilefiname);
                   4544:   strcat(optionfilegnuplot,".gp");
                   4545:   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
                   4546:     printf("Problem with file %s",optionfilegnuplot);
                   4547:   }
                   4548:   else{
                   4549:     fprintf(ficgp,"\n# %s\n", version); 
                   4550:     fprintf(ficgp,"# %s\n", optionfilegnuplot); 
                   4551:     fprintf(ficgp,"set missing 'NaNq'\n");
                   4552:   }
1.88      brouard  4553:   /*  fclose(ficgp);*/
1.86      brouard  4554:   /*--------- index.htm --------*/
                   4555: 
1.91      brouard  4556:   strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.86      brouard  4557:   strcat(optionfilehtm,".htm");
                   4558:   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
                   4559:     printf("Problem with %s \n",optionfilehtm), exit(0);
                   4560:   }
                   4561: 
1.91      brouard  4562:   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
                   4563:   strcat(optionfilehtmcov,"-cov.htm");
                   4564:   if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
                   4565:     printf("Problem with %s \n",optionfilehtmcov), exit(0);
                   4566:   }
                   4567:   else{
                   4568:   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
                   4569: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   4570: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
                   4571:          fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
                   4572:   }
                   4573: 
1.87      brouard  4574:   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86      brouard  4575: <hr size=\"2\" color=\"#EC5E5E\"> \n\
                   4576: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
                   4577: \n\
                   4578: <hr  size=\"2\" color=\"#EC5E5E\">\
                   4579:  <ul><li><h4>Parameter files</h4>\n\
                   4580:  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
                   4581:  - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87      brouard  4582:  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86      brouard  4583:  - Date and time at start: %s</ul>\n",\
1.91      brouard  4584:          fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
                   4585:          fileres,fileres,\
1.88      brouard  4586:          filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87      brouard  4587:   fflush(fichtm);
1.86      brouard  4588: 
1.88      brouard  4589:   strcpy(pathr,path);
                   4590:   strcat(pathr,optionfilefiname);
                   4591:   chdir(optionfilefiname); /* Move to directory named optionfile */
                   4592:   
1.59      brouard  4593:   /* Calculates basic frequencies. Computes observed prevalence at single age
                   4594:      and prints on file fileres'p'. */
1.84      brouard  4595:   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53      brouard  4596: 
1.88      brouard  4597:   fprintf(fichtm,"\n");
                   4598:   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86      brouard  4599: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
                   4600: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88      brouard  4601:          imx,agemin,agemax,jmin,jmax,jmean);
                   4602:   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60      brouard  4603:     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4604:     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4605:     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
                   4606:     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53      brouard  4607:     
                   4608:    
1.59      brouard  4609:   /* For Powell, parameters are in a vector p[] starting at p[1]
                   4610:      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
                   4611:   p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53      brouard  4612: 
1.86      brouard  4613:   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85      brouard  4614:   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   4615:   printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   4616:   for (k=1; k<=npar;k++)
                   4617:     printf(" %d %8.5f",k,p[k]);
                   4618:   printf("\n");
                   4619:   globpr=1; /* to print the contributions */
                   4620:   likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
                   4621:   printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
                   4622:   for (k=1; k<=npar;k++)
                   4623:     printf(" %d %8.5f",k,p[k]);
                   4624:   printf("\n");
1.61      brouard  4625:   if(mle>=1){ /* Could be 1 or 2 */
1.53      brouard  4626:     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59      brouard  4627:   }
1.53      brouard  4628:     
1.59      brouard  4629:   /*--------- results files --------------*/
                   4630:   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  4631:   
                   4632: 
1.59      brouard  4633:   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4634:   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4635:   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
                   4636:   for(i=1,jk=1; i <=nlstate; i++){
                   4637:     for(k=1; k <=(nlstate+ndeath); k++){
1.95      brouard  4638:       if (k != i) {
                   4639:        printf("%d%d ",i,k);
                   4640:        fprintf(ficlog,"%d%d ",i,k);
                   4641:        fprintf(ficres,"%1d%1d ",i,k);
                   4642:        for(j=1; j <=ncovmodel; j++){
                   4643:          printf("%f ",p[jk]);
                   4644:          fprintf(ficlog,"%f ",p[jk]);
                   4645:          fprintf(ficres,"%f ",p[jk]);
                   4646:          jk++; 
1.59      brouard  4647:        }
1.95      brouard  4648:        printf("\n");
                   4649:        fprintf(ficlog,"\n");
                   4650:        fprintf(ficres,"\n");
                   4651:       }
1.59      brouard  4652:     }
                   4653:   }
1.84      brouard  4654:   if(mle!=0){
1.59      brouard  4655:     /* Computing hessian and covariance matrix */
                   4656:     ftolhess=ftol; /* Usually correct */
                   4657:     hesscov(matcov, p, npar, delti, ftolhess, func);
                   4658:   }
                   4659:   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
                   4660:   printf("# Scales (for hessian or gradient estimation)\n");
                   4661:   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
                   4662:   for(i=1,jk=1; i <=nlstate; i++){
                   4663:     for(j=1; j <=nlstate+ndeath; j++){
                   4664:       if (j!=i) {
                   4665:        fprintf(ficres,"%1d%1d",i,j);
                   4666:        printf("%1d%1d",i,j);
                   4667:        fprintf(ficlog,"%1d%1d",i,j);
                   4668:        for(k=1; k<=ncovmodel;k++){
                   4669:          printf(" %.5e",delti[jk]);
                   4670:          fprintf(ficlog," %.5e",delti[jk]);
                   4671:          fprintf(ficres," %.5e",delti[jk]);
                   4672:          jk++;
                   4673:        }
                   4674:        printf("\n");
                   4675:        fprintf(ficlog,"\n");
                   4676:        fprintf(ficres,"\n");
                   4677:       }
                   4678:     }
                   4679:   }
1.53      brouard  4680:    
1.59      brouard  4681:   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");
1.95      brouard  4682:   if(mle>=1)
1.59      brouard  4683:     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");
                   4684:   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");
1.95      brouard  4685: /* # 121 Var(a12)\n\ */
                   4686: /* # 122 Cov(b12,a12) Var(b12)\n\ */
                   4687: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
                   4688: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
                   4689: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
                   4690: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
                   4691: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
                   4692: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
                   4693: 
                   4694: 
                   4695: /* Just to have a covariance matrix which will be more understandable
                   4696:    even is we still don't want to manage dictionary of variables
                   4697: */
                   4698:   for(itimes=1;itimes<=2;itimes++){
                   4699:     jj=0;
                   4700:     for(i=1; i <=nlstate; i++){
                   4701:       for(j=1; j <=nlstate+ndeath; j++){
                   4702:        if(j==i) continue;
                   4703:        for(k=1; k<=ncovmodel;k++){
                   4704:          jj++;
                   4705:          ca[0]= k+'a'-1;ca[1]='\0';
                   4706:          if(itimes==1){
                   4707:            if(mle>=1)
                   4708:              printf("#%1d%1d%d",i,j,k);
                   4709:            fprintf(ficlog,"#%1d%1d%d",i,j,k);
                   4710:            fprintf(ficres,"#%1d%1d%d",i,j,k);
                   4711:          }else{
                   4712:            if(mle>=1)
                   4713:              printf("%1d%1d%d",i,j,k);
                   4714:            fprintf(ficlog,"%1d%1d%d",i,j,k);
                   4715:            fprintf(ficres,"%1d%1d%d",i,j,k);
                   4716:          }
                   4717:          ll=0;
                   4718:          for(li=1;li <=nlstate; li++){
                   4719:            for(lj=1;lj <=nlstate+ndeath; lj++){
                   4720:              if(lj==li) continue;
                   4721:              for(lk=1;lk<=ncovmodel;lk++){
                   4722:                ll++;
                   4723:                if(ll<=jj){
                   4724:                  cb[0]= lk +'a'-1;cb[1]='\0';
                   4725:                  if(ll<jj){
                   4726:                    if(itimes==1){
                   4727:                      if(mle>=1)
                   4728:                        printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4729:                      fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4730:                      fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                   4731:                    }else{
                   4732:                      if(mle>=1)
                   4733:                        printf(" %.5e",matcov[jj][ll]); 
                   4734:                      fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   4735:                      fprintf(ficres," %.5e",matcov[jj][ll]); 
                   4736:                    }
                   4737:                  }else{
                   4738:                    if(itimes==1){
                   4739:                      if(mle>=1)
                   4740:                        printf(" Var(%s%1d%1d)",ca,i,j);
                   4741:                      fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                   4742:                      fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                   4743:                    }else{
                   4744:                      if(mle>=1)
                   4745:                        printf(" %.5e",matcov[jj][ll]); 
                   4746:                      fprintf(ficlog," %.5e",matcov[jj][ll]); 
                   4747:                      fprintf(ficres," %.5e",matcov[jj][ll]); 
                   4748:                    }
                   4749:                  }
                   4750:                }
                   4751:              } /* end lk */
                   4752:            } /* end lj */
                   4753:          } /* end li */
                   4754:          if(mle>=1)
                   4755:            printf("\n");
                   4756:          fprintf(ficlog,"\n");
                   4757:          fprintf(ficres,"\n");
                   4758:          numlinepar++;
                   4759:        } /* end k*/
                   4760:       } /*end j */
                   4761:     } /* end i */
                   4762:   } /* end itimes */
                   4763: 
                   4764:   fflush(ficlog);
                   4765:   fflush(ficres);
                   4766: 
1.59      brouard  4767:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4768:     ungetc(c,ficpar);
                   4769:     fgets(line, MAXLINE, ficpar);
                   4770:     puts(line);
                   4771:     fputs(line,ficparo);
                   4772:   }
                   4773:   ungetc(c,ficpar);
                   4774: 
                   4775:   estepm=0;
                   4776:   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
                   4777:   if (estepm==0 || estepm < stepm) estepm=stepm;
                   4778:   if (fage <= 2) {
                   4779:     bage = ageminpar;
                   4780:     fage = agemaxpar;
                   4781:   }
1.53      brouard  4782:    
1.59      brouard  4783:   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
                   4784:   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
                   4785:   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53      brouard  4786:    
1.59      brouard  4787:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4788:     ungetc(c,ficpar);
                   4789:     fgets(line, MAXLINE, ficpar);
                   4790:     puts(line);
                   4791:     fputs(line,ficparo);
                   4792:   }
                   4793:   ungetc(c,ficpar);
1.53      brouard  4794:   
1.59      brouard  4795:   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);
                   4796:   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);
                   4797:   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  4798:   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
                   4799:   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  4800:    
1.59      brouard  4801:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4802:     ungetc(c,ficpar);
                   4803:     fgets(line, MAXLINE, ficpar);
                   4804:     puts(line);
                   4805:     fputs(line,ficparo);
                   4806:   }
                   4807:   ungetc(c,ficpar);
1.53      brouard  4808:  
                   4809: 
1.70      brouard  4810:   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
                   4811:   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53      brouard  4812: 
                   4813:   fscanf(ficpar,"pop_based=%d\n",&popbased);
                   4814:   fprintf(ficparo,"pop_based=%d\n",popbased);   
                   4815:   fprintf(ficres,"pop_based=%d\n",popbased);   
                   4816:   
                   4817:   while((c=getc(ficpar))=='#' && c!= EOF){
                   4818:     ungetc(c,ficpar);
                   4819:     fgets(line, MAXLINE, ficpar);
                   4820:     puts(line);
                   4821:     fputs(line,ficparo);
                   4822:   }
                   4823:   ungetc(c,ficpar);
                   4824: 
1.69      brouard  4825:   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  4826:   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  4827:   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);
                   4828:   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);
                   4829:   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  4830:   /* day and month of proj2 are not used but only year anproj2.*/
1.53      brouard  4831: 
1.59      brouard  4832:   while((c=getc(ficpar))=='#' && c!= EOF){
1.53      brouard  4833:     ungetc(c,ficpar);
                   4834:     fgets(line, MAXLINE, ficpar);
                   4835:     puts(line);
                   4836:     fputs(line,ficparo);
                   4837:   }
                   4838:   ungetc(c,ficpar);
                   4839: 
1.97    ! lievre   4840:   /*  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
1.53      brouard  4841:   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
1.97    ! lievre   4842:   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);*/
1.53      brouard  4843: 
1.86      brouard  4844:   /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84      brouard  4845:   /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58      lievre   4846: 
1.89      brouard  4847:   replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
                   4848:   printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.53      brouard  4849: 
1.85      brouard  4850:   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                   4851:               model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                   4852:               jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53      brouard  4853:  
1.59      brouard  4854:   /*------------ free_vector  -------------*/
1.88      brouard  4855:   /*  chdir(path); */
1.53      brouard  4856:  
1.59      brouard  4857:   free_ivector(wav,1,imx);
                   4858:   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
                   4859:   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
                   4860:   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
1.85      brouard  4861:   free_lvector(num,1,n);
1.59      brouard  4862:   free_vector(agedc,1,n);
1.65      lievre   4863:   /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59      brouard  4864:   /*free_matrix(covar,1,NCOVMAX,1,n);*/
                   4865:   fclose(ficparo);
                   4866:   fclose(ficres);
1.53      brouard  4867: 
                   4868: 
1.54      brouard  4869:   /*--------------- Prevalence limit  (stable prevalence) --------------*/
1.53      brouard  4870:   
                   4871:   strcpy(filerespl,"pl");
                   4872:   strcat(filerespl,fileres);
                   4873:   if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54      brouard  4874:     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
                   4875:     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53      brouard  4876:   }
1.54      brouard  4877:   printf("Computing stable prevalence: result on file '%s' \n", filerespl);
                   4878:   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
                   4879:   fprintf(ficrespl,"#Stable prevalence \n");
1.53      brouard  4880:   fprintf(ficrespl,"#Age ");
                   4881:   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
                   4882:   fprintf(ficrespl,"\n");
                   4883:   
                   4884:   prlim=matrix(1,nlstate,1,nlstate);
1.59      brouard  4885: 
1.53      brouard  4886:   agebase=ageminpar;
                   4887:   agelim=agemaxpar;
                   4888:   ftolpl=1.e-10;
                   4889:   i1=cptcoveff;
                   4890:   if (cptcovn < 1){i1=1;}
                   4891: 
1.59      brouard  4892:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4893:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59      brouard  4894:       k=k+1;
                   4895:       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
                   4896:       fprintf(ficrespl,"\n#******");
                   4897:       printf("\n#******");
                   4898:       fprintf(ficlog,"\n#******");
                   4899:       for(j=1;j<=cptcoveff;j++) {
                   4900:        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4901:        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4902:        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4903:       }
                   4904:       fprintf(ficrespl,"******\n");
                   4905:       printf("******\n");
                   4906:       fprintf(ficlog,"******\n");
1.53      brouard  4907:        
1.59      brouard  4908:       for (age=agebase; age<=agelim; age++){
                   4909:        prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69      brouard  4910:        fprintf(ficrespl,"%.0f ",age );
                   4911:         for(j=1;j<=cptcoveff;j++)
                   4912:          fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59      brouard  4913:        for(i=1; i<=nlstate;i++)
1.53      brouard  4914:          fprintf(ficrespl," %.5f", prlim[i][i]);
1.59      brouard  4915:        fprintf(ficrespl,"\n");
1.53      brouard  4916:       }
                   4917:     }
1.59      brouard  4918:   }
1.53      brouard  4919:   fclose(ficrespl);
                   4920: 
                   4921:   /*------------- h Pij x at various ages ------------*/
                   4922:   
                   4923:   strcpy(filerespij,"pij");  strcat(filerespij,fileres);
                   4924:   if((ficrespij=fopen(filerespij,"w"))==NULL) {
                   4925:     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
                   4926:     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
                   4927:   }
                   4928:   printf("Computing pij: result on file '%s' \n", filerespij);
                   4929:   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
                   4930:   
                   4931:   stepsize=(int) (stepm+YEARM-1)/YEARM;
                   4932:   /*if (stepm<=24) stepsize=2;*/
                   4933: 
                   4934:   agelim=AGESUP;
                   4935:   hstepm=stepsize*YEARM; /* Every year of age */
                   4936:   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   4937: 
                   4938:   /* hstepm=1;   aff par mois*/
                   4939: 
1.70      brouard  4940:   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59      brouard  4941:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  4942:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   4943:       k=k+1;
1.59      brouard  4944:       fprintf(ficrespij,"\n#****** ");
                   4945:       for(j=1;j<=cptcoveff;j++) 
                   4946:        fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   4947:       fprintf(ficrespij,"******\n");
1.53      brouard  4948:        
1.59      brouard  4949:       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
                   4950:        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                   4951:        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                   4952: 
                   4953:        /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   4954: 
                   4955:        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4956:        oldm=oldms;savm=savms;
                   4957:        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
1.70      brouard  4958:        fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59      brouard  4959:        for(i=1; i<=nlstate;i++)
                   4960:          for(j=1; j<=nlstate+ndeath;j++)
                   4961:            fprintf(ficrespij," %1d-%1d",i,j);
                   4962:        fprintf(ficrespij,"\n");
                   4963:        for (h=0; h<=nhstepm; h++){
1.70      brouard  4964:          fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53      brouard  4965:          for(i=1; i<=nlstate;i++)
                   4966:            for(j=1; j<=nlstate+ndeath;j++)
1.59      brouard  4967:              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53      brouard  4968:          fprintf(ficrespij,"\n");
                   4969:        }
1.59      brouard  4970:        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   4971:        fprintf(ficrespij,"\n");
                   4972:       }
1.53      brouard  4973:     }
                   4974:   }
                   4975: 
1.74      brouard  4976:   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53      brouard  4977: 
                   4978:   fclose(ficrespij);
                   4979: 
1.84      brouard  4980:   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.96      brouard  4981:   for(i=1;i<=AGESUP;i++)
                   4982:     for(j=1;j<=NCOVMAX;j++)
                   4983:       for(k=1;k<=NCOVMAX;k++)
                   4984:        probs[i][j][k]=0.;
1.53      brouard  4985: 
                   4986:   /*---------- Forecasting ------------------*/
1.69      brouard  4987:   /*if((stepm == 1) && (strcmp(model,".")==0)){*/
                   4988:   if(prevfcast==1){
1.74      brouard  4989:     /*    if(stepm ==1){*/
1.70      brouard  4990:       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74      brouard  4991:       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
                   4992: /*      }  */
                   4993: /*      else{ */
                   4994: /*        erreur=108; */
                   4995: /*        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); */
                   4996: /*        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); */
                   4997: /*      } */
1.69      brouard  4998:   }
1.53      brouard  4999:   
                   5000: 
                   5001:   /*---------- Health expectancies and variances ------------*/
                   5002: 
                   5003:   strcpy(filerest,"t");
                   5004:   strcat(filerest,fileres);
                   5005:   if((ficrest=fopen(filerest,"w"))==NULL) {
                   5006:     printf("Problem with total LE resultfile: %s\n", filerest);goto end;
                   5007:     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
                   5008:   }
                   5009:   printf("Computing Total LEs with variances: file '%s' \n", filerest); 
                   5010:   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
                   5011: 
                   5012: 
                   5013:   strcpy(filerese,"e");
                   5014:   strcat(filerese,fileres);
                   5015:   if((ficreseij=fopen(filerese,"w"))==NULL) {
                   5016:     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   5017:     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
                   5018:   }
                   5019:   printf("Computing Health Expectancies: result on file '%s' \n", filerese);
                   5020:   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68      lievre   5021: 
1.53      brouard  5022:   strcpy(fileresv,"v");
                   5023:   strcat(fileresv,fileres);
                   5024:   if((ficresvij=fopen(fileresv,"w"))==NULL) {
                   5025:     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
                   5026:     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
                   5027:   }
                   5028:   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
                   5029:   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58      lievre   5030: 
1.74      brouard  5031:   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84      brouard  5032:   prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74      brouard  5033:   /*  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",\
                   5034: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
                   5035:   */
1.58      lievre   5036: 
1.54      brouard  5037:   if (mobilav!=0) {
1.53      brouard  5038:     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54      brouard  5039:     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                   5040:       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                   5041:       printf(" Error in movingaverage mobilav=%d\n",mobilav);
                   5042:     }
1.53      brouard  5043:   }
                   5044: 
1.59      brouard  5045:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  5046:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   5047:       k=k+1; 
                   5048:       fprintf(ficrest,"\n#****** ");
                   5049:       for(j=1;j<=cptcoveff;j++) 
                   5050:        fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5051:       fprintf(ficrest,"******\n");
                   5052: 
                   5053:       fprintf(ficreseij,"\n#****** ");
                   5054:       for(j=1;j<=cptcoveff;j++) 
                   5055:        fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5056:       fprintf(ficreseij,"******\n");
                   5057: 
                   5058:       fprintf(ficresvij,"\n#****** ");
                   5059:       for(j=1;j<=cptcoveff;j++) 
                   5060:        fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5061:       fprintf(ficresvij,"******\n");
                   5062: 
                   5063:       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   5064:       oldm=oldms;savm=savms;
                   5065:       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
                   5066:  
                   5067:       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
                   5068:       oldm=oldms;savm=savms;
                   5069:       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
                   5070:       if(popbased==1){
                   5071:        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  5072:       }
1.53      brouard  5073: 
                   5074:  
                   5075:       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
                   5076:       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                   5077:       fprintf(ficrest,"\n");
                   5078: 
                   5079:       epj=vector(1,nlstate+1);
                   5080:       for(age=bage; age <=fage ;age++){
                   5081:        prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
                   5082:        if (popbased==1) {
1.54      brouard  5083:          if(mobilav ==0){
1.53      brouard  5084:            for(i=1; i<=nlstate;i++)
                   5085:              prlim[i][i]=probs[(int)age][i][k];
1.54      brouard  5086:          }else{ /* mobilav */ 
1.53      brouard  5087:            for(i=1; i<=nlstate;i++)
                   5088:              prlim[i][i]=mobaverage[(int)age][i][k];
                   5089:          }
                   5090:        }
                   5091:        
                   5092:        fprintf(ficrest," %4.0f",age);
                   5093:        for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                   5094:          for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   5095:            epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   5096:            /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                   5097:          }
                   5098:          epj[nlstate+1] +=epj[j];
                   5099:        }
                   5100: 
                   5101:        for(i=1, vepp=0.;i <=nlstate;i++)
                   5102:          for(j=1;j <=nlstate;j++)
                   5103:            vepp += vareij[i][j][(int)age];
                   5104:        fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                   5105:        for(j=1;j <=nlstate;j++){
                   5106:          fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                   5107:        }
                   5108:        fprintf(ficrest,"\n");
                   5109:       }
1.59      brouard  5110:       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   5111:       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
                   5112:       free_vector(epj,1,nlstate+1);
1.53      brouard  5113:     }
                   5114:   }
1.59      brouard  5115:   free_vector(weight,1,n);
                   5116:   free_imatrix(Tvard,1,15,1,2);
                   5117:   free_imatrix(s,1,maxwav+1,1,n);
                   5118:   free_matrix(anint,1,maxwav,1,n); 
                   5119:   free_matrix(mint,1,maxwav,1,n);
                   5120:   free_ivector(cod,1,n);
                   5121:   free_ivector(tab,1,NCOVMAX);
1.53      brouard  5122:   fclose(ficreseij);
                   5123:   fclose(ficresvij);
                   5124:   fclose(ficrest);
                   5125:   fclose(ficpar);
                   5126:   
1.54      brouard  5127:   /*------- Variance of stable prevalence------*/   
1.53      brouard  5128: 
                   5129:   strcpy(fileresvpl,"vpl");
                   5130:   strcat(fileresvpl,fileres);
                   5131:   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54      brouard  5132:     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
1.53      brouard  5133:     exit(0);
                   5134:   }
1.54      brouard  5135:   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53      brouard  5136: 
1.59      brouard  5137:   for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53      brouard  5138:     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
                   5139:       k=k+1;
                   5140:       fprintf(ficresvpl,"\n#****** ");
                   5141:       for(j=1;j<=cptcoveff;j++) 
                   5142:        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                   5143:       fprintf(ficresvpl,"******\n");
                   5144:       
                   5145:       varpl=matrix(1,nlstate,(int) bage, (int) fage);
                   5146:       oldm=oldms;savm=savms;
1.59      brouard  5147:       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
                   5148:       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53      brouard  5149:     }
1.59      brouard  5150:   }
1.53      brouard  5151: 
                   5152:   fclose(ficresvpl);
                   5153: 
                   5154:   /*---------- End : free ----------------*/
                   5155:   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
                   5156:   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   5157:   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
                   5158:   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65      lievre   5159:   
                   5160:   free_matrix(covar,0,NCOVMAX,1,n);
1.53      brouard  5161:   free_matrix(matcov,1,npar,1,npar);
1.74      brouard  5162:   /*free_vector(delti,1,npar);*/
                   5163:   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
1.53      brouard  5164:   free_matrix(agev,1,maxwav,1,imx);
                   5165:   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54      brouard  5166:   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74      brouard  5167:   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
                   5168: 
1.59      brouard  5169:   free_ivector(ncodemax,1,8);
                   5170:   free_ivector(Tvar,1,15);
                   5171:   free_ivector(Tprod,1,15);
                   5172:   free_ivector(Tvaraff,1,15);
                   5173:   free_ivector(Tage,1,15);
                   5174:   free_ivector(Tcode,1,100);
1.53      brouard  5175: 
1.88      brouard  5176:   fflush(fichtm);
                   5177:   fflush(ficgp);
1.53      brouard  5178:   
                   5179: 
1.91      brouard  5180:   if((nberr >0) || (nbwarn>0)){
1.95      brouard  5181:     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91      brouard  5182:     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53      brouard  5183:   }else{
1.91      brouard  5184:     printf("End of Imach\n");
                   5185:     fprintf(ficlog,"End of Imach\n");
1.53      brouard  5186:   }
                   5187:   printf("See log file on %s\n",filelog);
                   5188:   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
1.85      brouard  5189:   (void) gettimeofday(&end_time,&tzp);
                   5190:   tm = *localtime(&end_time.tv_sec);
                   5191:   tmg = *gmtime(&end_time.tv_sec);
1.88      brouard  5192:   strcpy(strtend,asctime(&tm));
1.94      brouard  5193:   printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
                   5194:   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
1.91      brouard  5195:   printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85      brouard  5196: 
1.91      brouard  5197:   printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
                   5198:   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
                   5199:   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85      brouard  5200:   /*  printf("Total time was %d uSec.\n", total_usecs);*/
1.87      brouard  5201: /*   if(fileappend(fichtm,optionfilehtm)){ */
1.88      brouard  5202:   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
1.87      brouard  5203:   fclose(fichtm);
1.91      brouard  5204:   fclose(fichtmcov);
1.88      brouard  5205:   fclose(ficgp);
1.91      brouard  5206:   fclose(ficlog);
1.53      brouard  5207:   /*------ End -----------*/
                   5208: 
1.88      brouard  5209:   chdir(path);
1.59      brouard  5210:   strcpy(plotcmd,GNUPLOTPROGRAM);
                   5211:   strcat(plotcmd," ");
                   5212:   strcat(plotcmd,optionfilegnuplot);
1.75      brouard  5213:   printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.91      brouard  5214:   if((outcmd=system(plotcmd)) != 0){
                   5215:     printf(" Problem with gnuplot\n");
                   5216:   }
1.75      brouard  5217:   printf(" Wait...");
1.53      brouard  5218:   while (z[0] != 'q') {
                   5219:     /* chdir(path); */
1.91      brouard  5220:     printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53      brouard  5221:     scanf("%s",z);
1.91      brouard  5222: /*     if (z[0] == 'c') system("./imach"); */
                   5223:     if (z[0] == 'e') system(optionfilehtm);
1.53      brouard  5224:     else if (z[0] == 'g') system(plotcmd);
                   5225:     else if (z[0] == 'q') exit(0);
                   5226:   }
1.91      brouard  5227:   end:
                   5228:   while (z[0] != 'q') {
                   5229:     printf("\nType  q for exiting: ");
                   5230:     scanf("%s",z);
                   5231:   }
1.53      brouard  5232: }
1.88      brouard  5233: 
1.53      brouard  5234: 
                   5235: 

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