Annotation of imach/src/imach.c, revision 1.107
1.107 ! brouard 1: /* $Id: imach.c,v 1.106 2006/01/19 13:24:36 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.107 ! brouard 4: Revision 1.106 2006/01/19 13:24:36 brouard
! 5: Some cleaning and links added in html output
! 6:
1.106 brouard 7: Revision 1.105 2006/01/05 20:23:19 lievre
8: *** empty log message ***
9:
1.105 lievre 10: Revision 1.104 2005/09/30 16:11:43 lievre
11: (Module): sump fixed, loop imx fixed, and simplifications.
12: (Module): If the status is missing at the last wave but we know
13: that the person is alive, then we can code his/her status as -2
14: (instead of missing=-1 in earlier versions) and his/her
15: contributions to the likelihood is 1 - Prob of dying from last
16: health status (= 1-p13= p11+p12 in the easiest case of somebody in
17: the healthy state at last known wave). Version is 0.98
18:
1.104 lievre 19: Revision 1.103 2005/09/30 15:54:49 lievre
20: (Module): sump fixed, loop imx fixed, and simplifications.
21:
1.103 lievre 22: Revision 1.102 2004/09/15 17:31:30 brouard
23: Add the possibility to read data file including tab characters.
24:
1.102 brouard 25: Revision 1.101 2004/09/15 10:38:38 brouard
26: Fix on curr_time
27:
1.101 brouard 28: Revision 1.100 2004/07/12 18:29:06 brouard
29: Add version for Mac OS X. Just define UNIX in Makefile
30:
1.100 brouard 31: Revision 1.99 2004/06/05 08:57:40 brouard
32: *** empty log message ***
33:
1.99 brouard 34: Revision 1.98 2004/05/16 15:05:56 brouard
35: New version 0.97 . First attempt to estimate force of mortality
36: directly from the data i.e. without the need of knowing the health
37: state at each age, but using a Gompertz model: log u =a + b*age .
38: This is the basic analysis of mortality and should be done before any
39: other analysis, in order to test if the mortality estimated from the
40: cross-longitudinal survey is different from the mortality estimated
41: from other sources like vital statistic data.
42:
43: The same imach parameter file can be used but the option for mle should be -3.
44:
45: Agnès, who wrote this part of the code, tried to keep most of the
46: former routines in order to include the new code within the former code.
47:
48: The output is very simple: only an estimate of the intercept and of
49: the slope with 95% confident intervals.
50:
51: Current limitations:
52: A) Even if you enter covariates, i.e. with the
53: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
54: B) There is no computation of Life Expectancy nor Life Table.
55:
1.98 brouard 56: Revision 1.97 2004/02/20 13:25:42 lievre
57: Version 0.96d. Population forecasting command line is (temporarily)
58: suppressed.
59:
1.97 lievre 60: Revision 1.96 2003/07/15 15:38:55 brouard
61: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
62: rewritten within the same printf. Workaround: many printfs.
63:
1.96 brouard 64: Revision 1.95 2003/07/08 07:54:34 brouard
65: * imach.c (Repository):
66: (Repository): Using imachwizard code to output a more meaningful covariance
67: matrix (cov(a12,c31) instead of numbers.
68:
1.95 brouard 69: Revision 1.94 2003/06/27 13:00:02 brouard
70: Just cleaning
71:
1.94 brouard 72: Revision 1.93 2003/06/25 16:33:55 brouard
73: (Module): On windows (cygwin) function asctime_r doesn't
74: exist so I changed back to asctime which exists.
75: (Module): Version 0.96b
76:
1.93 brouard 77: Revision 1.92 2003/06/25 16:30:45 brouard
78: (Module): On windows (cygwin) function asctime_r doesn't
79: exist so I changed back to asctime which exists.
80:
1.92 brouard 81: Revision 1.91 2003/06/25 15:30:29 brouard
82: * imach.c (Repository): Duplicated warning errors corrected.
83: (Repository): Elapsed time after each iteration is now output. It
84: helps to forecast when convergence will be reached. Elapsed time
85: is stamped in powell. We created a new html file for the graphs
86: concerning matrix of covariance. It has extension -cov.htm.
87:
1.91 brouard 88: Revision 1.90 2003/06/24 12:34:15 brouard
89: (Module): Some bugs corrected for windows. Also, when
90: mle=-1 a template is output in file "or"mypar.txt with the design
91: of the covariance matrix to be input.
92:
1.90 brouard 93: Revision 1.89 2003/06/24 12:30:52 brouard
94: (Module): Some bugs corrected for windows. Also, when
95: mle=-1 a template is output in file "or"mypar.txt with the design
96: of the covariance matrix to be input.
97:
1.89 brouard 98: Revision 1.88 2003/06/23 17:54:56 brouard
99: * 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.
100:
1.88 brouard 101: Revision 1.87 2003/06/18 12:26:01 brouard
102: Version 0.96
103:
1.87 brouard 104: Revision 1.86 2003/06/17 20:04:08 brouard
105: (Module): Change position of html and gnuplot routines and added
106: routine fileappend.
107:
1.86 brouard 108: Revision 1.85 2003/06/17 13:12:43 brouard
109: * imach.c (Repository): Check when date of death was earlier that
110: current date of interview. It may happen when the death was just
111: prior to the death. In this case, dh was negative and likelihood
112: was wrong (infinity). We still send an "Error" but patch by
113: assuming that the date of death was just one stepm after the
114: interview.
115: (Repository): Because some people have very long ID (first column)
116: we changed int to long in num[] and we added a new lvector for
117: memory allocation. But we also truncated to 8 characters (left
118: truncation)
119: (Repository): No more line truncation errors.
120:
1.85 brouard 121: Revision 1.84 2003/06/13 21:44:43 brouard
122: * imach.c (Repository): Replace "freqsummary" at a correct
123: place. It differs from routine "prevalence" which may be called
124: many times. Probs is memory consuming and must be used with
125: parcimony.
1.86 brouard 126: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 127:
1.84 brouard 128: Revision 1.83 2003/06/10 13:39:11 lievre
129: *** empty log message ***
130:
1.83 lievre 131: Revision 1.82 2003/06/05 15:57:20 brouard
132: Add log in imach.c and fullversion number is now printed.
133:
1.82 brouard 134: */
135: /*
1.53 brouard 136: Interpolated Markov Chain
137:
138: Short summary of the programme:
139:
140: This program computes Healthy Life Expectancies from
141: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
142: first survey ("cross") where individuals from different ages are
143: interviewed on their health status or degree of disability (in the
144: case of a health survey which is our main interest) -2- at least a
145: second wave of interviews ("longitudinal") which measure each change
146: (if any) in individual health status. Health expectancies are
147: computed from the time spent in each health state according to a
148: model. More health states you consider, more time is necessary to reach the
149: Maximum Likelihood of the parameters involved in the model. The
150: simplest model is the multinomial logistic model where pij is the
151: probability to be observed in state j at the second wave
152: conditional to be observed in state i at the first wave. Therefore
153: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
154: 'age' is age and 'sex' is a covariate. If you want to have a more
155: complex model than "constant and age", you should modify the program
156: where the markup *Covariates have to be included here again* invites
157: you to do it. More covariates you add, slower the
158: convergence.
159:
160: The advantage of this computer programme, compared to a simple
161: multinomial logistic model, is clear when the delay between waves is not
162: identical for each individual. Also, if a individual missed an
163: intermediate interview, the information is lost, but taken into
164: account using an interpolation or extrapolation.
165:
166: hPijx is the probability to be observed in state i at age x+h
167: conditional to the observed state i at age x. The delay 'h' can be
168: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 169: states. This elementary transition (by month, quarter,
170: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 171: matrix is simply the matrix product of nh*stepm elementary matrices
172: and the contribution of each individual to the likelihood is simply
173: hPijx.
174:
175: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 176: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 177:
178: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
179: Institut national d'études démographiques, Paris.
180: This software have been partly granted by Euro-REVES, a concerted action
181: from the European Union.
182: It is copyrighted identically to a GNU software product, ie programme and
183: software can be distributed freely for non commercial use. Latest version
184: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 185:
186: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
187: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
188:
1.53 brouard 189: **********************************************************************/
1.74 brouard 190: /*
191: main
192: read parameterfile
193: read datafile
194: concatwav
1.84 brouard 195: freqsummary
1.74 brouard 196: if (mle >= 1)
197: mlikeli
198: print results files
199: if mle==1
200: computes hessian
201: read end of parameter file: agemin, agemax, bage, fage, estepm
202: begin-prev-date,...
203: open gnuplot file
204: open html file
205: stable prevalence
206: for age prevalim()
207: h Pij x
208: variance of p varprob
209: forecasting if prevfcast==1 prevforecast call prevalence()
210: health expectancies
211: Variance-covariance of DFLE
212: prevalence()
213: movingaverage()
214: varevsij()
215: if popbased==1 varevsij(,popbased)
216: total life expectancies
217: Variance of stable prevalence
218: end
219: */
220:
221:
222:
1.53 brouard 223:
224: #include <math.h>
225: #include <stdio.h>
226: #include <stdlib.h>
1.106 brouard 227: #include <string.h>
1.53 brouard 228: #include <unistd.h>
229:
1.107 ! brouard 230: #include <sys/types.h>
! 231: #include <sys/stat.h>
! 232: #include <errno.h>
! 233: extern int errno;
! 234:
1.99 brouard 235: /* #include <sys/time.h> */
1.86 brouard 236: #include <time.h>
237: #include "timeval.h"
238:
1.95 brouard 239: /* #include <libintl.h> */
240: /* #define _(String) gettext (String) */
241:
1.53 brouard 242: #define MAXLINE 256
243: #define GNUPLOTPROGRAM "gnuplot"
244: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 245: #define FILENAMELENGTH 132
1.53 brouard 246: /*#define DEBUG*/
1.85 brouard 247: /*#define windows*/
1.53 brouard 248: #define GLOCK_ERROR_NOPATH -1 /* empty path */
249: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
250:
251: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
252: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
253:
254: #define NINTERVMAX 8
255: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
256: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
257: #define NCOVMAX 8 /* Maximum number of covariates */
258: #define MAXN 20000
259: #define YEARM 12. /* Number of months per year */
260: #define AGESUP 130
261: #define AGEBASE 40
1.98 brouard 262: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
1.100 brouard 263: #ifdef UNIX
1.85 brouard 264: #define DIRSEPARATOR '/'
1.107 ! brouard 265: #define CHARSEPARATOR "/"
1.85 brouard 266: #define ODIRSEPARATOR '\\'
267: #else
1.53 brouard 268: #define DIRSEPARATOR '\\'
1.107 ! brouard 269: #define CHARSEPARATOR "\\"
1.53 brouard 270: #define ODIRSEPARATOR '/'
271: #endif
272:
1.107 ! brouard 273: /* $Id: imach.c,v 1.106 2006/01/19 13:24:36 brouard Exp $ */
1.81 brouard 274: /* $State: Exp $ */
1.80 brouard 275:
1.106 brouard 276: char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
1.107 ! brouard 277: char fullversion[]="$Revision: 1.106 $ $Date: 2006/01/19 13:24:36 $";
1.91 brouard 278: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.53 brouard 279: int nvar;
280: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
281: int npar=NPARMAX;
282: int nlstate=2; /* Number of live states */
283: int ndeath=1; /* Number of dead states */
284: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
285: int popbased=0;
286:
287: int *wav; /* Number of waves for this individuual 0 is possible */
288: int maxwav; /* Maxim number of waves */
289: int jmin, jmax; /* min, max spacing between 2 waves */
1.87 brouard 290: int gipmx, gsw; /* Global variables on the number of contributions
291: to the likelihood and the sum of weights (done by funcone)*/
1.53 brouard 292: int mle, weightopt;
293: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
294: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 295: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
296: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 297: double jmean; /* Mean space between 2 waves */
298: double **oldm, **newm, **savm; /* Working pointers to matrices */
299: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
300: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 301: FILE *ficlog, *ficrespow;
1.85 brouard 302: int globpr; /* Global variable for printing or not */
303: double fretone; /* Only one call to likelihood */
304: long ipmx; /* Number of contributions */
305: double sw; /* Sum of weights */
1.98 brouard 306: char filerespow[FILENAMELENGTH];
1.85 brouard 307: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
308: FILE *ficresilk;
1.53 brouard 309: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
310: FILE *ficresprobmorprev;
1.91 brouard 311: FILE *fichtm, *fichtmcov; /* Html File */
1.53 brouard 312: FILE *ficreseij;
313: char filerese[FILENAMELENGTH];
314: FILE *ficresvij;
315: char fileresv[FILENAMELENGTH];
316: FILE *ficresvpl;
317: char fileresvpl[FILENAMELENGTH];
318: char title[MAXLINE];
319: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
320: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
1.96 brouard 321: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1.88 brouard 322: char command[FILENAMELENGTH];
323: int outcmd=0;
1.53 brouard 324:
325: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.94 brouard 326:
1.53 brouard 327: char filelog[FILENAMELENGTH]; /* Log file */
328: char filerest[FILENAMELENGTH];
329: char fileregp[FILENAMELENGTH];
330: char popfile[FILENAMELENGTH];
331:
1.91 brouard 332: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
333:
334: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
335: struct timezone tzp;
336: extern int gettimeofday();
337: struct tm tmg, tm, tmf, *gmtime(), *localtime();
338: long time_value;
339: extern long time();
340: char strcurr[80], strfor[80];
1.53 brouard 341:
342: #define NR_END 1
343: #define FREE_ARG char*
344: #define FTOL 1.0e-10
345:
346: #define NRANSI
347: #define ITMAX 200
348:
349: #define TOL 2.0e-4
350:
351: #define CGOLD 0.3819660
352: #define ZEPS 1.0e-10
353: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
354:
355: #define GOLD 1.618034
356: #define GLIMIT 100.0
357: #define TINY 1.0e-20
358:
359: static double maxarg1,maxarg2;
360: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
361: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
362:
363: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
364: #define rint(a) floor(a+0.5)
365:
366: static double sqrarg;
367: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
368: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1.98 brouard 369: int agegomp= AGEGOMP;
1.53 brouard 370:
371: int imx;
1.98 brouard 372: int stepm=1;
1.53 brouard 373: /* Stepm, step in month: minimum step interpolation*/
374:
375: int estepm;
376: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
377:
378: int m,nb;
1.85 brouard 379: long *num;
1.98 brouard 380: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
1.53 brouard 381: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 382: double **pmmij, ***probs;
1.98 brouard 383: double *ageexmed,*agecens;
1.53 brouard 384: double dateintmean=0;
385:
386: double *weight;
387: int **s; /* Status */
388: double *agedc, **covar, idx;
389: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.105 lievre 390: double *lsurv, *lpop, *tpop;
1.53 brouard 391:
392: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
393: double ftolhess; /* Tolerance for computing hessian */
394:
395: /**************** split *************************/
396: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
397: {
1.107 ! brouard 398: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1.99 brouard 399: the name of the file (name), its extension only (ext) and its first part of the name (finame)
400: */
1.59 brouard 401: char *ss; /* pointer */
402: int l1, l2; /* length counters */
1.53 brouard 403:
1.59 brouard 404: l1 = strlen(path ); /* length of path */
405: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
406: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1.107 ! brouard 407: if ( ss == NULL ) { /* no directory, so determine current directory */
! 408: strcpy( name, path ); /* we got the fullname name because no directory */
1.59 brouard 409: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
410: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 411: /* get current working directory */
412: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 413: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
414: return( GLOCK_ERROR_GETCWD );
415: }
1.107 ! brouard 416: /* got dirc from getcwd*/
! 417: printf(" DIRC = %s \n",dirc);
1.59 brouard 418: } else { /* strip direcotry from path */
419: ss++; /* after this, the filename */
420: l2 = strlen( ss ); /* length of filename */
421: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
422: strcpy( name, ss ); /* save file name */
423: strncpy( dirc, path, l1 - l2 ); /* now the directory */
424: dirc[l1-l2] = 0; /* add zero */
1.107 ! brouard 425: printf(" DIRC2 = %s \n",dirc);
1.59 brouard 426: }
1.107 ! brouard 427: /* We add a separator at the end of dirc if not exists */
1.59 brouard 428: l1 = strlen( dirc ); /* length of directory */
1.107 ! brouard 429: if( dirc[l1-1] != DIRSEPARATOR ){
! 430: dirc[l1] = DIRSEPARATOR;
! 431: dirc[l1+1] = 0;
! 432: printf(" DIRC3 = %s \n",dirc);
! 433: }
1.59 brouard 434: ss = strrchr( name, '.' ); /* find last / */
1.99 brouard 435: if (ss >0){
436: ss++;
437: strcpy(ext,ss); /* save extension */
438: l1= strlen( name);
439: l2= strlen(ss)+1;
440: strncpy( finame, name, l1-l2);
441: finame[l1-l2]= 0;
442: }
1.107 ! brouard 443:
1.59 brouard 444: return( 0 ); /* we're done */
1.53 brouard 445: }
446:
447:
448: /******************************************/
449:
1.89 brouard 450: void replace_back_to_slash(char *s, char*t)
1.53 brouard 451: {
452: int i;
1.89 brouard 453: int lg=0;
1.53 brouard 454: i=0;
455: lg=strlen(t);
456: for(i=0; i<= lg; i++) {
457: (s[i] = t[i]);
458: if (t[i]== '\\') s[i]='/';
459: }
460: }
461:
462: int nbocc(char *s, char occ)
463: {
464: int i,j=0;
465: int lg=20;
466: i=0;
467: lg=strlen(s);
468: for(i=0; i<= lg; i++) {
469: if (s[i] == occ ) j++;
470: }
471: return j;
472: }
473:
474: void cutv(char *u,char *v, char*t, char occ)
475: {
1.102 brouard 476: /* cuts string t into u and v where u ends before first occurence of char 'occ'
477: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
1.53 brouard 478: gives u="abcedf" and v="ghi2j" */
479: int i,lg,j,p=0;
480: i=0;
481: for(j=0; j<=strlen(t)-1; j++) {
482: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
483: }
484:
485: lg=strlen(t);
486: for(j=0; j<p; j++) {
487: (u[j] = t[j]);
488: }
489: u[p]='\0';
490:
491: for(j=0; j<= lg; j++) {
492: if (j>=(p+1))(v[j-p-1] = t[j]);
493: }
494: }
495:
496: /********************** nrerror ********************/
497:
498: void nrerror(char error_text[])
499: {
500: fprintf(stderr,"ERREUR ...\n");
501: fprintf(stderr,"%s\n",error_text);
1.59 brouard 502: exit(EXIT_FAILURE);
1.53 brouard 503: }
504: /*********************** vector *******************/
505: double *vector(int nl, int nh)
506: {
507: double *v;
508: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
509: if (!v) nrerror("allocation failure in vector");
510: return v-nl+NR_END;
511: }
512:
513: /************************ free vector ******************/
514: void free_vector(double*v, int nl, int nh)
515: {
516: free((FREE_ARG)(v+nl-NR_END));
517: }
518:
519: /************************ivector *******************************/
1.85 brouard 520: int *ivector(long nl,long nh)
1.76 brouard 521: {
1.85 brouard 522: int *v;
523: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
524: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 525: return v-nl+NR_END;
526: }
527:
528: /******************free ivector **************************/
1.85 brouard 529: void free_ivector(int *v, long nl, long nh)
1.76 brouard 530: {
531: free((FREE_ARG)(v+nl-NR_END));
532: }
533:
1.85 brouard 534: /************************lvector *******************************/
535: long *lvector(long nl,long nh)
1.53 brouard 536: {
1.85 brouard 537: long *v;
538: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 539: if (!v) nrerror("allocation failure in ivector");
540: return v-nl+NR_END;
541: }
542:
1.85 brouard 543: /******************free lvector **************************/
544: void free_lvector(long *v, long nl, long nh)
1.53 brouard 545: {
546: free((FREE_ARG)(v+nl-NR_END));
547: }
548:
549: /******************* imatrix *******************************/
550: int **imatrix(long nrl, long nrh, long ncl, long nch)
551: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
552: {
553: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
554: int **m;
555:
556: /* allocate pointers to rows */
557: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
558: if (!m) nrerror("allocation failure 1 in matrix()");
559: m += NR_END;
560: m -= nrl;
561:
562:
563: /* allocate rows and set pointers to them */
564: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
565: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
566: m[nrl] += NR_END;
567: m[nrl] -= ncl;
568:
569: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
570:
571: /* return pointer to array of pointers to rows */
572: return m;
573: }
574:
575: /****************** free_imatrix *************************/
576: void free_imatrix(m,nrl,nrh,ncl,nch)
577: int **m;
578: long nch,ncl,nrh,nrl;
579: /* free an int matrix allocated by imatrix() */
580: {
581: free((FREE_ARG) (m[nrl]+ncl-NR_END));
582: free((FREE_ARG) (m+nrl-NR_END));
583: }
584:
585: /******************* matrix *******************************/
586: double **matrix(long nrl, long nrh, long ncl, long nch)
587: {
588: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
589: double **m;
590:
591: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
592: if (!m) nrerror("allocation failure 1 in matrix()");
593: m += NR_END;
594: m -= nrl;
595:
596: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
597: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
598: m[nrl] += NR_END;
599: m[nrl] -= ncl;
600:
601: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
602: return m;
1.85 brouard 603: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 604: */
1.53 brouard 605: }
606:
607: /*************************free matrix ************************/
608: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
609: {
610: free((FREE_ARG)(m[nrl]+ncl-NR_END));
611: free((FREE_ARG)(m+nrl-NR_END));
612: }
613:
614: /******************* ma3x *******************************/
615: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
616: {
617: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
618: double ***m;
619:
620: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
621: if (!m) nrerror("allocation failure 1 in matrix()");
622: m += NR_END;
623: m -= nrl;
624:
625: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
626: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
627: m[nrl] += NR_END;
628: m[nrl] -= ncl;
629:
630: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
631:
632: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
633: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
634: m[nrl][ncl] += NR_END;
635: m[nrl][ncl] -= nll;
636: for (j=ncl+1; j<=nch; j++)
637: m[nrl][j]=m[nrl][j-1]+nlay;
638:
639: for (i=nrl+1; i<=nrh; i++) {
640: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
641: for (j=ncl+1; j<=nch; j++)
642: m[i][j]=m[i][j-1]+nlay;
643: }
1.74 brouard 644: return m;
645: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
646: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
647: */
1.53 brouard 648: }
649:
650: /*************************free ma3x ************************/
651: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
652: {
653: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
654: free((FREE_ARG)(m[nrl]+ncl-NR_END));
655: free((FREE_ARG)(m+nrl-NR_END));
656: }
657:
1.94 brouard 658: /*************** function subdirf ***********/
659: char *subdirf(char fileres[])
660: {
661: /* Caution optionfilefiname is hidden */
662: strcpy(tmpout,optionfilefiname);
663: strcat(tmpout,"/"); /* Add to the right */
664: strcat(tmpout,fileres);
665: return tmpout;
666: }
667:
668: /*************** function subdirf2 ***********/
669: char *subdirf2(char fileres[], char *preop)
670: {
671:
672: /* Caution optionfilefiname is hidden */
673: strcpy(tmpout,optionfilefiname);
674: strcat(tmpout,"/");
675: strcat(tmpout,preop);
676: strcat(tmpout,fileres);
677: return tmpout;
678: }
679:
680: /*************** function subdirf3 ***********/
681: char *subdirf3(char fileres[], char *preop, char *preop2)
682: {
683:
684: /* Caution optionfilefiname is hidden */
685: strcpy(tmpout,optionfilefiname);
686: strcat(tmpout,"/");
687: strcat(tmpout,preop);
688: strcat(tmpout,preop2);
689: strcat(tmpout,fileres);
690: return tmpout;
691: }
692:
1.53 brouard 693: /***************** f1dim *************************/
694: extern int ncom;
695: extern double *pcom,*xicom;
696: extern double (*nrfunc)(double []);
697:
698: double f1dim(double x)
699: {
700: int j;
701: double f;
702: double *xt;
703:
704: xt=vector(1,ncom);
705: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
706: f=(*nrfunc)(xt);
707: free_vector(xt,1,ncom);
708: return f;
709: }
710:
711: /*****************brent *************************/
712: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
713: {
714: int iter;
715: double a,b,d,etemp;
716: double fu,fv,fw,fx;
717: double ftemp;
718: double p,q,r,tol1,tol2,u,v,w,x,xm;
719: double e=0.0;
720:
721: a=(ax < cx ? ax : cx);
722: b=(ax > cx ? ax : cx);
723: x=w=v=bx;
724: fw=fv=fx=(*f)(x);
725: for (iter=1;iter<=ITMAX;iter++) {
726: xm=0.5*(a+b);
727: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
728: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
729: printf(".");fflush(stdout);
730: fprintf(ficlog,".");fflush(ficlog);
731: #ifdef DEBUG
732: 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);
733: 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);
734: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
735: #endif
736: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
737: *xmin=x;
738: return fx;
739: }
740: ftemp=fu;
741: if (fabs(e) > tol1) {
742: r=(x-w)*(fx-fv);
743: q=(x-v)*(fx-fw);
744: p=(x-v)*q-(x-w)*r;
745: q=2.0*(q-r);
746: if (q > 0.0) p = -p;
747: q=fabs(q);
748: etemp=e;
749: e=d;
750: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
751: d=CGOLD*(e=(x >= xm ? a-x : b-x));
752: else {
753: d=p/q;
754: u=x+d;
755: if (u-a < tol2 || b-u < tol2)
756: d=SIGN(tol1,xm-x);
757: }
758: } else {
759: d=CGOLD*(e=(x >= xm ? a-x : b-x));
760: }
761: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
762: fu=(*f)(u);
763: if (fu <= fx) {
764: if (u >= x) a=x; else b=x;
765: SHFT(v,w,x,u)
766: SHFT(fv,fw,fx,fu)
767: } else {
768: if (u < x) a=u; else b=u;
769: if (fu <= fw || w == x) {
770: v=w;
771: w=u;
772: fv=fw;
773: fw=fu;
774: } else if (fu <= fv || v == x || v == w) {
775: v=u;
776: fv=fu;
777: }
778: }
779: }
780: nrerror("Too many iterations in brent");
781: *xmin=x;
782: return fx;
783: }
784:
785: /****************** mnbrak ***********************/
786:
787: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
788: double (*func)(double))
789: {
790: double ulim,u,r,q, dum;
791: double fu;
792:
793: *fa=(*func)(*ax);
794: *fb=(*func)(*bx);
795: if (*fb > *fa) {
796: SHFT(dum,*ax,*bx,dum)
797: SHFT(dum,*fb,*fa,dum)
798: }
799: *cx=(*bx)+GOLD*(*bx-*ax);
800: *fc=(*func)(*cx);
801: while (*fb > *fc) {
802: r=(*bx-*ax)*(*fb-*fc);
803: q=(*bx-*cx)*(*fb-*fa);
804: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
805: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
806: ulim=(*bx)+GLIMIT*(*cx-*bx);
807: if ((*bx-u)*(u-*cx) > 0.0) {
808: fu=(*func)(u);
809: } else if ((*cx-u)*(u-ulim) > 0.0) {
810: fu=(*func)(u);
811: if (fu < *fc) {
812: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
813: SHFT(*fb,*fc,fu,(*func)(u))
814: }
815: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
816: u=ulim;
817: fu=(*func)(u);
818: } else {
819: u=(*cx)+GOLD*(*cx-*bx);
820: fu=(*func)(u);
821: }
822: SHFT(*ax,*bx,*cx,u)
823: SHFT(*fa,*fb,*fc,fu)
824: }
825: }
826:
827: /*************** linmin ************************/
828:
829: int ncom;
830: double *pcom,*xicom;
831: double (*nrfunc)(double []);
832:
833: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
834: {
835: double brent(double ax, double bx, double cx,
836: double (*f)(double), double tol, double *xmin);
837: double f1dim(double x);
838: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
839: double *fc, double (*func)(double));
840: int j;
841: double xx,xmin,bx,ax;
842: double fx,fb,fa;
843:
844: ncom=n;
845: pcom=vector(1,n);
846: xicom=vector(1,n);
847: nrfunc=func;
848: for (j=1;j<=n;j++) {
849: pcom[j]=p[j];
850: xicom[j]=xi[j];
851: }
852: ax=0.0;
853: xx=1.0;
854: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
855: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
856: #ifdef DEBUG
857: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
858: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
859: #endif
860: for (j=1;j<=n;j++) {
861: xi[j] *= xmin;
862: p[j] += xi[j];
863: }
864: free_vector(xicom,1,n);
865: free_vector(pcom,1,n);
866: }
867:
1.91 brouard 868: char *asc_diff_time(long time_sec, char ascdiff[])
869: {
870: long sec_left, days, hours, minutes;
871: days = (time_sec) / (60*60*24);
872: sec_left = (time_sec) % (60*60*24);
873: hours = (sec_left) / (60*60) ;
874: sec_left = (sec_left) %(60*60);
875: minutes = (sec_left) /60;
876: sec_left = (sec_left) % (60);
877: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
878: return ascdiff;
879: }
880:
1.53 brouard 881: /*************** powell ************************/
882: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
883: double (*func)(double []))
884: {
885: void linmin(double p[], double xi[], int n, double *fret,
886: double (*func)(double []));
887: int i,ibig,j;
888: double del,t,*pt,*ptt,*xit;
889: double fp,fptt;
890: double *xits;
1.91 brouard 891: int niterf, itmp;
892:
1.53 brouard 893: pt=vector(1,n);
894: ptt=vector(1,n);
895: xit=vector(1,n);
896: xits=vector(1,n);
897: *fret=(*func)(p);
898: for (j=1;j<=n;j++) pt[j]=p[j];
899: for (*iter=1;;++(*iter)) {
900: fp=(*fret);
901: ibig=0;
902: del=0.0;
1.91 brouard 903: last_time=curr_time;
904: (void) gettimeofday(&curr_time,&tzp);
905: 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);
1.98 brouard 906: /* 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);
1.91 brouard 907: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
1.98 brouard 908: */
909: for (i=1;i<=n;i++) {
1.53 brouard 910: printf(" %d %.12f",i, p[i]);
1.76 brouard 911: fprintf(ficlog," %d %.12lf",i, p[i]);
912: fprintf(ficrespow," %.12lf", p[i]);
913: }
1.53 brouard 914: printf("\n");
915: fprintf(ficlog,"\n");
1.91 brouard 916: fprintf(ficrespow,"\n");fflush(ficrespow);
917: if(*iter <=3){
918: tm = *localtime(&curr_time.tv_sec);
1.101 brouard 919: strcpy(strcurr,asctime(&tm));
1.92 brouard 920: /* asctime_r(&tm,strcurr); */
1.101 brouard 921: forecast_time=curr_time;
1.91 brouard 922: itmp = strlen(strcurr);
1.101 brouard 923: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.91 brouard 924: strcurr[itmp-1]='\0';
925: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
926: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
927: for(niterf=10;niterf<=30;niterf+=10){
928: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
929: tmf = *localtime(&forecast_time.tv_sec);
1.92 brouard 930: /* asctime_r(&tmf,strfor); */
931: strcpy(strfor,asctime(&tmf));
1.91 brouard 932: itmp = strlen(strfor);
933: if(strfor[itmp-1]=='\n')
934: strfor[itmp-1]='\0';
1.101 brouard 935: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
936: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
1.91 brouard 937: }
938: }
1.53 brouard 939: for (i=1;i<=n;i++) {
940: for (j=1;j<=n;j++) xit[j]=xi[j][i];
941: fptt=(*fret);
942: #ifdef DEBUG
943: printf("fret=%lf \n",*fret);
944: fprintf(ficlog,"fret=%lf \n",*fret);
945: #endif
946: printf("%d",i);fflush(stdout);
947: fprintf(ficlog,"%d",i);fflush(ficlog);
948: linmin(p,xit,n,fret,func);
949: if (fabs(fptt-(*fret)) > del) {
950: del=fabs(fptt-(*fret));
951: ibig=i;
952: }
953: #ifdef DEBUG
954: printf("%d %.12e",i,(*fret));
955: fprintf(ficlog,"%d %.12e",i,(*fret));
956: for (j=1;j<=n;j++) {
957: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
958: printf(" x(%d)=%.12e",j,xit[j]);
959: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
960: }
961: for(j=1;j<=n;j++) {
962: printf(" p=%.12e",p[j]);
963: fprintf(ficlog," p=%.12e",p[j]);
964: }
965: printf("\n");
966: fprintf(ficlog,"\n");
967: #endif
968: }
969: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
970: #ifdef DEBUG
971: int k[2],l;
972: k[0]=1;
973: k[1]=-1;
974: printf("Max: %.12e",(*func)(p));
975: fprintf(ficlog,"Max: %.12e",(*func)(p));
976: for (j=1;j<=n;j++) {
977: printf(" %.12e",p[j]);
978: fprintf(ficlog," %.12e",p[j]);
979: }
980: printf("\n");
981: fprintf(ficlog,"\n");
982: for(l=0;l<=1;l++) {
983: for (j=1;j<=n;j++) {
984: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
985: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
986: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
987: }
988: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
989: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
990: }
991: #endif
992:
993:
994: free_vector(xit,1,n);
995: free_vector(xits,1,n);
996: free_vector(ptt,1,n);
997: free_vector(pt,1,n);
998: return;
999: }
1000: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1001: for (j=1;j<=n;j++) {
1002: ptt[j]=2.0*p[j]-pt[j];
1003: xit[j]=p[j]-pt[j];
1004: pt[j]=p[j];
1005: }
1006: fptt=(*func)(ptt);
1007: if (fptt < fp) {
1008: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1009: if (t < 0.0) {
1010: linmin(p,xit,n,fret,func);
1011: for (j=1;j<=n;j++) {
1012: xi[j][ibig]=xi[j][n];
1013: xi[j][n]=xit[j];
1014: }
1015: #ifdef DEBUG
1016: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1017: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1018: for(j=1;j<=n;j++){
1019: printf(" %.12e",xit[j]);
1020: fprintf(ficlog," %.12e",xit[j]);
1021: }
1022: printf("\n");
1023: fprintf(ficlog,"\n");
1024: #endif
1.54 brouard 1025: }
1.53 brouard 1026: }
1027: }
1028: }
1029:
1.54 brouard 1030: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 1031:
1032: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1033: {
1034: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1035: matrix by transitions matrix until convergence is reached */
1036:
1037: int i, ii,j,k;
1038: double min, max, maxmin, maxmax,sumnew=0.;
1039: double **matprod2();
1040: double **out, cov[NCOVMAX], **pmij();
1041: double **newm;
1042: double agefin, delaymax=50 ; /* Max number of years to converge */
1043:
1044: for (ii=1;ii<=nlstate+ndeath;ii++)
1045: for (j=1;j<=nlstate+ndeath;j++){
1046: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1047: }
1048:
1049: cov[1]=1.;
1050:
1051: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1052: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1053: newm=savm;
1054: /* Covariates have to be included here again */
1055: cov[2]=agefin;
1056:
1057: for (k=1; k<=cptcovn;k++) {
1058: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1059: /* 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]]);*/
1060: }
1061: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1062: for (k=1; k<=cptcovprod;k++)
1063: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1064:
1065: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1066: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1067: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1068: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1069:
1070: savm=oldm;
1071: oldm=newm;
1072: maxmax=0.;
1073: for(j=1;j<=nlstate;j++){
1074: min=1.;
1075: max=0.;
1076: for(i=1; i<=nlstate; i++) {
1077: sumnew=0;
1078: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1079: prlim[i][j]= newm[i][j]/(1-sumnew);
1080: max=FMAX(max,prlim[i][j]);
1081: min=FMIN(min,prlim[i][j]);
1082: }
1083: maxmin=max-min;
1084: maxmax=FMAX(maxmax,maxmin);
1085: }
1086: if(maxmax < ftolpl){
1087: return prlim;
1088: }
1089: }
1090: }
1091:
1092: /*************** transition probabilities ***************/
1093:
1094: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1095: {
1096: double s1, s2;
1097: /*double t34;*/
1098: int i,j,j1, nc, ii, jj;
1099:
1100: for(i=1; i<= nlstate; i++){
1.99 brouard 1101: for(j=1; j<i;j++){
1102: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1103: /*s2 += param[i][j][nc]*cov[nc];*/
1104: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1105: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1106: }
1107: ps[i][j]=s2;
1108: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1109: }
1110: for(j=i+1; j<=nlstate+ndeath;j++){
1111: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1112: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1113: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1114: }
1115: ps[i][j]=s2;
1.53 brouard 1116: }
1117: }
1118: /*ps[3][2]=1;*/
1.99 brouard 1119:
1120: for(i=1; i<= nlstate; i++){
1121: s1=0;
1122: for(j=1; j<i; j++)
1123: s1+=exp(ps[i][j]);
1124: for(j=i+1; j<=nlstate+ndeath; j++)
1125: s1+=exp(ps[i][j]);
1126: ps[i][i]=1./(s1+1.);
1127: for(j=1; j<i; j++)
1128: ps[i][j]= exp(ps[i][j])*ps[i][i];
1129: for(j=i+1; j<=nlstate+ndeath; j++)
1130: ps[i][j]= exp(ps[i][j])*ps[i][i];
1131: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1132: } /* end i */
1133:
1134: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1135: for(jj=1; jj<= nlstate+ndeath; jj++){
1136: ps[ii][jj]=0;
1137: ps[ii][ii]=1;
1138: }
1.53 brouard 1139: }
1.99 brouard 1140:
1.53 brouard 1141:
1.99 brouard 1142: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1143: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1144: /* printf("ddd %lf ",ps[ii][jj]); */
1145: /* } */
1146: /* printf("\n "); */
1147: /* } */
1148: /* printf("\n ");printf("%lf ",cov[2]); */
1149: /*
1150: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1151: goto end;*/
1.53 brouard 1152: return ps;
1153: }
1154:
1155: /**************** Product of 2 matrices ******************/
1156:
1157: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1158: {
1159: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1160: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1161: /* in, b, out are matrice of pointers which should have been initialized
1162: before: only the contents of out is modified. The function returns
1163: a pointer to pointers identical to out */
1164: long i, j, k;
1165: for(i=nrl; i<= nrh; i++)
1166: for(k=ncolol; k<=ncoloh; k++)
1167: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1168: out[i][k] +=in[i][j]*b[j][k];
1169:
1170: return out;
1171: }
1172:
1173:
1174: /************* Higher Matrix Product ***************/
1175:
1176: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1177: {
1.66 brouard 1178: /* Computes the transition matrix starting at age 'age' over
1179: 'nhstepm*hstepm*stepm' months (i.e. until
1180: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1181: nhstepm*hstepm matrices.
1.53 brouard 1182: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 1183: (typically every 2 years instead of every month which is too big
1184: for the memory).
1.53 brouard 1185: Model is determined by parameters x and covariates have to be
1186: included manually here.
1187:
1188: */
1189:
1190: int i, j, d, h, k;
1191: double **out, cov[NCOVMAX];
1192: double **newm;
1193:
1194: /* Hstepm could be zero and should return the unit matrix */
1195: for (i=1;i<=nlstate+ndeath;i++)
1196: for (j=1;j<=nlstate+ndeath;j++){
1197: oldm[i][j]=(i==j ? 1.0 : 0.0);
1198: po[i][j][0]=(i==j ? 1.0 : 0.0);
1199: }
1200: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1201: for(h=1; h <=nhstepm; h++){
1202: for(d=1; d <=hstepm; d++){
1203: newm=savm;
1204: /* Covariates have to be included here again */
1205: cov[1]=1.;
1206: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1207: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1208: for (k=1; k<=cptcovage;k++)
1209: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1210: for (k=1; k<=cptcovprod;k++)
1211: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1212:
1213:
1214: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1215: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1216: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1217: pmij(pmmij,cov,ncovmodel,x,nlstate));
1218: savm=oldm;
1219: oldm=newm;
1220: }
1221: for(i=1; i<=nlstate+ndeath; i++)
1222: for(j=1;j<=nlstate+ndeath;j++) {
1223: po[i][j][h]=newm[i][j];
1224: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1225: */
1226: }
1227: } /* end h */
1228: return po;
1229: }
1230:
1231:
1232: /*************** log-likelihood *************/
1233: double func( double *x)
1234: {
1235: int i, ii, j, k, mi, d, kk;
1236: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1237: double **out;
1238: double sw; /* Sum of weights */
1239: double lli; /* Individual log likelihood */
1.59 brouard 1240: int s1, s2;
1.68 lievre 1241: double bbh, survp;
1.53 brouard 1242: long ipmx;
1243: /*extern weight */
1244: /* We are differentiating ll according to initial status */
1245: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1246: /*for(i=1;i<imx;i++)
1247: printf(" %d\n",s[4][i]);
1248: */
1249: cov[1]=1.;
1250:
1251: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1252:
1253: if(mle==1){
1254: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1255: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1256: for(mi=1; mi<= wav[i]-1; mi++){
1257: for (ii=1;ii<=nlstate+ndeath;ii++)
1258: for (j=1;j<=nlstate+ndeath;j++){
1259: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1260: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1261: }
1262: for(d=0; d<dh[mi][i]; d++){
1263: newm=savm;
1264: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1265: for (kk=1; kk<=cptcovage;kk++) {
1266: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1267: }
1268: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1269: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1270: savm=oldm;
1271: oldm=newm;
1272: } /* end mult */
1.53 brouard 1273:
1.61 brouard 1274: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1.101 brouard 1275: /* But now since version 0.9 we anticipate for bias at large stepm.
1.61 brouard 1276: * If stepm is larger than one month (smallest stepm) and if the exact delay
1277: * (in months) between two waves is not a multiple of stepm, we rounded to
1278: * the nearest (and in case of equal distance, to the lowest) interval but now
1279: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1.101 brouard 1280: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1.61 brouard 1281: * probability in order to take into account the bias as a fraction of the way
1.101 brouard 1282: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1.61 brouard 1283: * -stepm/2 to stepm/2 .
1284: * For stepm=1 the results are the same as for previous versions of Imach.
1285: * For stepm > 1 the results are less biased than in previous versions.
1286: */
1287: s1=s[mw[mi][i]][i];
1288: s2=s[mw[mi+1][i]][i];
1.64 lievre 1289: bbh=(double)bh[mi][i]/(double)stepm;
1.101 brouard 1290: /* bias bh is positive if real duration
1.64 lievre 1291: * is higher than the multiple of stepm and negative otherwise.
1292: */
1293: /* 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 1294: if( s2 > nlstate){
1.104 lievre 1295: /* i.e. if s2 is a death state and if the date of death is known
1296: then the contribution to the likelihood is the probability to
1297: die between last step unit time and current step unit time,
1298: which is also equal to probability to die before dh
1.101 brouard 1299: minus probability to die before dh-stepm .
1.71 brouard 1300: In version up to 0.92 likelihood was computed
1301: as if date of death was unknown. Death was treated as any other
1302: health state: the date of the interview describes the actual state
1303: and not the date of a change in health state. The former idea was
1304: to consider that at each interview the state was recorded
1305: (healthy, disable or death) and IMaCh was corrected; but when we
1306: introduced the exact date of death then we should have modified
1307: the contribution of an exact death to the likelihood. This new
1308: contribution is smaller and very dependent of the step unit
1309: stepm. It is no more the probability to die between last interview
1310: and month of death but the probability to survive from last
1311: interview up to one month before death multiplied by the
1312: probability to die within a month. Thanks to Chris
1313: Jackson for correcting this bug. Former versions increased
1314: mortality artificially. The bad side is that we add another loop
1315: which slows down the processing. The difference can be up to 10%
1316: lower mortality.
1317: */
1318: lli=log(out[s1][s2] - savm[s1][s2]);
1.104 lievre 1319:
1320:
1321: } else if (s2==-2) {
1322: for (j=1,survp=0. ; j<=nlstate; j++)
1323: survp += out[s1][j];
1324: lli= survp;
1325: }
1.105 lievre 1326:
1327: else if (s2==-4) {
1328: for (j=3,survp=0. ; j<=nlstate; j++)
1329: survp += out[s1][j];
1330: lli= survp;
1331: }
1332:
1333: else if (s2==-5) {
1334: for (j=1,survp=0. ; j<=2; j++)
1335: survp += out[s1][j];
1336: lli= survp;
1337: }
1.104 lievre 1338:
1339:
1340: else{
1.71 brouard 1341: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1342: /* 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 */
1343: }
1.64 lievre 1344: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1345: /*if(lli ==000.0)*/
1346: /*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 1347: ipmx +=1;
1.64 lievre 1348: sw += weight[i];
1349: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1350: } /* end of wave */
1351: } /* end of individual */
1352: } else if(mle==2){
1353: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1354: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1355: for(mi=1; mi<= wav[i]-1; mi++){
1356: for (ii=1;ii<=nlstate+ndeath;ii++)
1357: for (j=1;j<=nlstate+ndeath;j++){
1358: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1359: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1360: }
1361: for(d=0; d<=dh[mi][i]; d++){
1362: newm=savm;
1363: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1364: for (kk=1; kk<=cptcovage;kk++) {
1365: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1366: }
1367: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1368: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1369: savm=oldm;
1370: oldm=newm;
1371: } /* end mult */
1372:
1373: s1=s[mw[mi][i]][i];
1374: s2=s[mw[mi+1][i]][i];
1375: bbh=(double)bh[mi][i]/(double)stepm;
1.63 lievre 1376: 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 1377: ipmx +=1;
1378: sw += weight[i];
1379: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1380: } /* end of wave */
1381: } /* end of individual */
1382: } else if(mle==3){ /* exponential inter-extrapolation */
1383: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1384: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1385: for(mi=1; mi<= wav[i]-1; mi++){
1386: for (ii=1;ii<=nlstate+ndeath;ii++)
1387: for (j=1;j<=nlstate+ndeath;j++){
1388: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1389: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1390: }
1391: for(d=0; d<dh[mi][i]; d++){
1392: newm=savm;
1393: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1394: for (kk=1; kk<=cptcovage;kk++) {
1395: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1396: }
1397: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1398: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1399: savm=oldm;
1400: oldm=newm;
1401: } /* end mult */
1402:
1403: s1=s[mw[mi][i]][i];
1404: s2=s[mw[mi+1][i]][i];
1405: bbh=(double)bh[mi][i]/(double)stepm;
1406: 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 1407: ipmx +=1;
1408: sw += weight[i];
1409: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1410: } /* end of wave */
1411: } /* end of individual */
1.84 brouard 1412: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1413: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1414: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1415: for(mi=1; mi<= wav[i]-1; mi++){
1416: for (ii=1;ii<=nlstate+ndeath;ii++)
1417: for (j=1;j<=nlstate+ndeath;j++){
1418: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1419: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1420: }
1421: for(d=0; d<dh[mi][i]; d++){
1422: newm=savm;
1423: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1424: for (kk=1; kk<=cptcovage;kk++) {
1425: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1426: }
1427:
1428: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1429: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1430: savm=oldm;
1431: oldm=newm;
1432: } /* end mult */
1433:
1.84 brouard 1434: s1=s[mw[mi][i]][i];
1435: s2=s[mw[mi+1][i]][i];
1436: if( s2 > nlstate){
1437: lli=log(out[s1][s2] - savm[s1][s2]);
1438: }else{
1439: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1440: }
1441: ipmx +=1;
1442: sw += weight[i];
1443: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1444: /* 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 1445: } /* end of wave */
1446: } /* end of individual */
1447: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1448: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1449: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1450: for(mi=1; mi<= wav[i]-1; mi++){
1451: for (ii=1;ii<=nlstate+ndeath;ii++)
1452: for (j=1;j<=nlstate+ndeath;j++){
1453: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1454: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1455: }
1456: for(d=0; d<dh[mi][i]; d++){
1457: newm=savm;
1458: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1459: for (kk=1; kk<=cptcovage;kk++) {
1460: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1461: }
1462:
1463: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1464: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1465: savm=oldm;
1466: oldm=newm;
1467: } /* end mult */
1468:
1469: s1=s[mw[mi][i]][i];
1470: s2=s[mw[mi+1][i]][i];
1.61 brouard 1471: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1472: ipmx +=1;
1473: sw += weight[i];
1474: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1475: /*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 1476: } /* end of wave */
1477: } /* end of individual */
1478: } /* End of if */
1.53 brouard 1479: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1480: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1481: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1482: return -l;
1483: }
1484:
1485: /*************** log-likelihood *************/
1486: double funcone( double *x)
1487: {
1.87 brouard 1488: /* Same as likeli but slower because of a lot of printf and if */
1.85 brouard 1489: int i, ii, j, k, mi, d, kk;
1490: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1491: double **out;
1492: double lli; /* Individual log likelihood */
1.87 brouard 1493: double llt;
1.85 brouard 1494: int s1, s2;
1495: double bbh, survp;
1496: /*extern weight */
1497: /* We are differentiating ll according to initial status */
1498: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1499: /*for(i=1;i<imx;i++)
1500: printf(" %d\n",s[4][i]);
1501: */
1502: cov[1]=1.;
1503:
1504: for(k=1; k<=nlstate; k++) ll[k]=0.;
1505:
1506: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1507: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1508: for(mi=1; mi<= wav[i]-1; mi++){
1509: for (ii=1;ii<=nlstate+ndeath;ii++)
1510: for (j=1;j<=nlstate+ndeath;j++){
1511: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1512: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1513: }
1514: for(d=0; d<dh[mi][i]; d++){
1515: newm=savm;
1516: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1517: for (kk=1; kk<=cptcovage;kk++) {
1518: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1519: }
1520: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1521: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1522: savm=oldm;
1523: oldm=newm;
1524: } /* end mult */
1525:
1526: s1=s[mw[mi][i]][i];
1527: s2=s[mw[mi+1][i]][i];
1528: bbh=(double)bh[mi][i]/(double)stepm;
1529: /* bias is positive if real duration
1530: * is higher than the multiple of stepm and negative otherwise.
1531: */
1532: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1533: lli=log(out[s1][s2] - savm[s1][s2]);
1534: } else if (mle==1){
1535: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1536: } else if(mle==2){
1537: 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 */
1538: } else if(mle==3){ /* exponential inter-extrapolation */
1539: 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 */
1540: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1541: lli=log(out[s1][s2]); /* Original formula */
1542: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1543: lli=log(out[s1][s2]); /* Original formula */
1544: } /* End of if */
1545: ipmx +=1;
1546: sw += weight[i];
1547: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1548: /* 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]); */
1549: if(globpr){
1.88 brouard 1550: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1.86 brouard 1551: %10.6f %10.6f %10.6f ", \
1552: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1553: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.87 brouard 1554: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1555: llt +=ll[k]*gipmx/gsw;
1556: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1557: }
1558: fprintf(ficresilk," %10.6f\n", -llt);
1.85 brouard 1559: }
1560: } /* end of wave */
1561: } /* end of individual */
1562: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1563: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1564: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.87 brouard 1565: if(globpr==0){ /* First time we count the contributions and weights */
1566: gipmx=ipmx;
1567: gsw=sw;
1568: }
1.53 brouard 1569: return -l;
1570: }
1571:
1572:
1.94 brouard 1573: /*************** function likelione ***********/
1.87 brouard 1574: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1.85 brouard 1575: {
1.87 brouard 1576: /* This routine should help understanding what is done with
1577: the selection of individuals/waves and
1.85 brouard 1578: to check the exact contribution to the likelihood.
1579: Plotting could be done.
1580: */
1581: int k;
1.87 brouard 1582:
1.88 brouard 1583: if(*globpri !=0){ /* Just counts and sums, no printings */
1.85 brouard 1584: strcpy(fileresilk,"ilk");
1585: strcat(fileresilk,fileres);
1586: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1587: printf("Problem with resultfile: %s\n", fileresilk);
1588: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1589: }
1.87 brouard 1590: 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 1591: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1.85 brouard 1592: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1593: for(k=1; k<=nlstate; k++)
1.87 brouard 1594: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1595: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1.85 brouard 1596: }
1597:
1598: *fretone=(*funcone)(p);
1.87 brouard 1599: if(*globpri !=0){
1.85 brouard 1600: fclose(ficresilk);
1.88 brouard 1601: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.87 brouard 1602: fflush(fichtm);
1603: }
1.85 brouard 1604: return;
1605: }
1606:
1.88 brouard 1607:
1.53 brouard 1608: /*********** Maximum Likelihood Estimation ***************/
1609:
1610: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1611: {
1612: int i,j, iter;
1.74 brouard 1613: double **xi;
1.53 brouard 1614: double fret;
1.85 brouard 1615: double fretone; /* Only one call to likelihood */
1.98 brouard 1616: /* char filerespow[FILENAMELENGTH];*/
1.53 brouard 1617: xi=matrix(1,npar,1,npar);
1618: for (i=1;i<=npar;i++)
1619: for (j=1;j<=npar;j++)
1620: xi[i][j]=(i==j ? 1.0 : 0.0);
1621: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1622: strcpy(filerespow,"pow");
1623: strcat(filerespow,fileres);
1624: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1625: printf("Problem with resultfile: %s\n", filerespow);
1626: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1627: }
1628: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1629: for (i=1;i<=nlstate;i++)
1630: for(j=1;j<=nlstate+ndeath;j++)
1631: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1632: fprintf(ficrespow,"\n");
1.85 brouard 1633:
1.53 brouard 1634: powell(p,xi,npar,ftol,&iter,&fret,func);
1635:
1.76 brouard 1636: fclose(ficrespow);
1637: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1638: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1639: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1640:
1641: }
1642:
1643: /**** Computes Hessian and covariance matrix ***/
1644: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1645: {
1646: double **a,**y,*x,pd;
1647: double **hess;
1648: int i, j,jk;
1649: int *indx;
1650:
1.98 brouard 1651: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1652: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1.53 brouard 1653: void lubksb(double **a, int npar, int *indx, double b[]) ;
1654: void ludcmp(double **a, int npar, int *indx, double *d) ;
1.98 brouard 1655: double gompertz(double p[]);
1.53 brouard 1656: hess=matrix(1,npar,1,npar);
1657:
1658: printf("\nCalculation of the hessian matrix. Wait...\n");
1659: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1660: for (i=1;i<=npar;i++){
1661: printf("%d",i);fflush(stdout);
1662: fprintf(ficlog,"%d",i);fflush(ficlog);
1.98 brouard 1663:
1664: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1665:
1666: /* printf(" %f ",p[i]);
1667: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1.53 brouard 1668: }
1669:
1670: for (i=1;i<=npar;i++) {
1671: for (j=1;j<=npar;j++) {
1672: if (j>i) {
1673: printf(".%d%d",i,j);fflush(stdout);
1674: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1.98 brouard 1675: hess[i][j]=hessij(p,delti,i,j,func,npar);
1676:
1.53 brouard 1677: hess[j][i]=hess[i][j];
1678: /*printf(" %lf ",hess[i][j]);*/
1679: }
1680: }
1681: }
1682: printf("\n");
1683: fprintf(ficlog,"\n");
1684:
1685: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1686: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1687:
1688: a=matrix(1,npar,1,npar);
1689: y=matrix(1,npar,1,npar);
1690: x=vector(1,npar);
1691: indx=ivector(1,npar);
1692: for (i=1;i<=npar;i++)
1693: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1694: ludcmp(a,npar,indx,&pd);
1695:
1696: for (j=1;j<=npar;j++) {
1697: for (i=1;i<=npar;i++) x[i]=0;
1698: x[j]=1;
1699: lubksb(a,npar,indx,x);
1700: for (i=1;i<=npar;i++){
1701: matcov[i][j]=x[i];
1702: }
1703: }
1704:
1705: printf("\n#Hessian matrix#\n");
1706: fprintf(ficlog,"\n#Hessian matrix#\n");
1707: for (i=1;i<=npar;i++) {
1708: for (j=1;j<=npar;j++) {
1709: printf("%.3e ",hess[i][j]);
1710: fprintf(ficlog,"%.3e ",hess[i][j]);
1711: }
1712: printf("\n");
1713: fprintf(ficlog,"\n");
1714: }
1715:
1716: /* Recompute Inverse */
1717: for (i=1;i<=npar;i++)
1718: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1719: ludcmp(a,npar,indx,&pd);
1720:
1721: /* printf("\n#Hessian matrix recomputed#\n");
1722:
1723: for (j=1;j<=npar;j++) {
1724: for (i=1;i<=npar;i++) x[i]=0;
1725: x[j]=1;
1726: lubksb(a,npar,indx,x);
1727: for (i=1;i<=npar;i++){
1728: y[i][j]=x[i];
1729: printf("%.3e ",y[i][j]);
1730: fprintf(ficlog,"%.3e ",y[i][j]);
1731: }
1732: printf("\n");
1733: fprintf(ficlog,"\n");
1734: }
1735: */
1736:
1737: free_matrix(a,1,npar,1,npar);
1738: free_matrix(y,1,npar,1,npar);
1739: free_vector(x,1,npar);
1740: free_ivector(indx,1,npar);
1741: free_matrix(hess,1,npar,1,npar);
1742:
1743:
1744: }
1745:
1746: /*************** hessian matrix ****************/
1.98 brouard 1747: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.53 brouard 1748: {
1749: int i;
1750: int l=1, lmax=20;
1751: double k1,k2;
1752: double p2[NPARMAX+1];
1753: double res;
1.98 brouard 1754: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1.53 brouard 1755: double fx;
1756: int k=0,kmax=10;
1757: double l1;
1758:
1759: fx=func(x);
1760: for (i=1;i<=npar;i++) p2[i]=x[i];
1761: for(l=0 ; l <=lmax; l++){
1762: l1=pow(10,l);
1763: delts=delt;
1764: for(k=1 ; k <kmax; k=k+1){
1765: delt = delta*(l1*k);
1766: p2[theta]=x[theta] +delt;
1767: k1=func(p2)-fx;
1768: p2[theta]=x[theta]-delt;
1769: k2=func(p2)-fx;
1770: /*res= (k1-2.0*fx+k2)/delt/delt; */
1771: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1772:
1773: #ifdef DEBUG
1774: 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);
1775: 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);
1776: #endif
1777: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1778: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1779: k=kmax;
1780: }
1781: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1782: k=kmax; l=lmax*10.;
1783: }
1784: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1785: delts=delt;
1786: }
1787: }
1788: }
1789: delti[theta]=delts;
1790: return res;
1791:
1792: }
1793:
1.98 brouard 1794: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.53 brouard 1795: {
1796: int i;
1797: int l=1, l1, lmax=20;
1798: double k1,k2,k3,k4,res,fx;
1799: double p2[NPARMAX+1];
1800: int k;
1801:
1802: fx=func(x);
1803: for (k=1; k<=2; k++) {
1804: for (i=1;i<=npar;i++) p2[i]=x[i];
1805: p2[thetai]=x[thetai]+delti[thetai]/k;
1806: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1807: k1=func(p2)-fx;
1808:
1809: p2[thetai]=x[thetai]+delti[thetai]/k;
1810: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1811: k2=func(p2)-fx;
1812:
1813: p2[thetai]=x[thetai]-delti[thetai]/k;
1814: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1815: k3=func(p2)-fx;
1816:
1817: p2[thetai]=x[thetai]-delti[thetai]/k;
1818: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1819: k4=func(p2)-fx;
1820: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1821: #ifdef DEBUG
1822: 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);
1823: 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);
1824: #endif
1825: }
1826: return res;
1827: }
1828:
1829: /************** Inverse of matrix **************/
1830: void ludcmp(double **a, int n, int *indx, double *d)
1831: {
1832: int i,imax,j,k;
1833: double big,dum,sum,temp;
1834: double *vv;
1835:
1836: vv=vector(1,n);
1837: *d=1.0;
1838: for (i=1;i<=n;i++) {
1839: big=0.0;
1840: for (j=1;j<=n;j++)
1841: if ((temp=fabs(a[i][j])) > big) big=temp;
1842: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1843: vv[i]=1.0/big;
1844: }
1845: for (j=1;j<=n;j++) {
1846: for (i=1;i<j;i++) {
1847: sum=a[i][j];
1848: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1849: a[i][j]=sum;
1850: }
1851: big=0.0;
1852: for (i=j;i<=n;i++) {
1853: sum=a[i][j];
1854: for (k=1;k<j;k++)
1855: sum -= a[i][k]*a[k][j];
1856: a[i][j]=sum;
1857: if ( (dum=vv[i]*fabs(sum)) >= big) {
1858: big=dum;
1859: imax=i;
1860: }
1861: }
1862: if (j != imax) {
1863: for (k=1;k<=n;k++) {
1864: dum=a[imax][k];
1865: a[imax][k]=a[j][k];
1866: a[j][k]=dum;
1867: }
1868: *d = -(*d);
1869: vv[imax]=vv[j];
1870: }
1871: indx[j]=imax;
1872: if (a[j][j] == 0.0) a[j][j]=TINY;
1873: if (j != n) {
1874: dum=1.0/(a[j][j]);
1875: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1876: }
1877: }
1878: free_vector(vv,1,n); /* Doesn't work */
1879: ;
1880: }
1881:
1882: void lubksb(double **a, int n, int *indx, double b[])
1883: {
1884: int i,ii=0,ip,j;
1885: double sum;
1886:
1887: for (i=1;i<=n;i++) {
1888: ip=indx[i];
1889: sum=b[ip];
1890: b[ip]=b[i];
1891: if (ii)
1892: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1893: else if (sum) ii=i;
1894: b[i]=sum;
1895: }
1896: for (i=n;i>=1;i--) {
1897: sum=b[i];
1898: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1899: b[i]=sum/a[i][i];
1900: }
1901: }
1902:
1903: /************ Frequencies ********************/
1.105 lievre 1904: 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, char strstart[])
1.53 brouard 1905: { /* Some frequencies */
1906:
1907: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1908: int first;
1909: double ***freq; /* Frequencies */
1.73 lievre 1910: double *pp, **prop;
1911: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1912: FILE *ficresp;
1913: char fileresp[FILENAMELENGTH];
1914:
1915: pp=vector(1,nlstate);
1.74 brouard 1916: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1917: strcpy(fileresp,"p");
1918: strcat(fileresp,fileres);
1919: if((ficresp=fopen(fileresp,"w"))==NULL) {
1920: printf("Problem with prevalence resultfile: %s\n", fileresp);
1921: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1922: exit(0);
1923: }
1.105 lievre 1924: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1925: j1=0;
1926:
1927: j=cptcoveff;
1928: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1929:
1930: first=1;
1931:
1932: for(k1=1; k1<=j;k1++){
1933: for(i1=1; i1<=ncodemax[k1];i1++){
1934: j1++;
1935: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1936: scanf("%d", i);*/
1.105 lievre 1937: for (i=-5; i<=nlstate+ndeath; i++)
1938: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.74 brouard 1939: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1940: freq[i][jk][m]=0;
1.73 lievre 1941:
1942: for (i=1; i<=nlstate; i++)
1.74 brouard 1943: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1944: prop[i][m]=0;
1.53 brouard 1945:
1946: dateintsum=0;
1947: k2cpt=0;
1948: for (i=1; i<=imx; i++) {
1949: bool=1;
1950: if (cptcovn>0) {
1951: for (z1=1; z1<=cptcoveff; z1++)
1952: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1953: bool=0;
1954: }
1.58 lievre 1955: if (bool==1){
1.53 brouard 1956: for(m=firstpass; m<=lastpass; m++){
1957: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1958: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1959: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1960: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1961: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1962: if (m<lastpass) {
1963: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1964: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1965: }
1966:
1.74 brouard 1967: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1968: dateintsum=dateintsum+k2;
1969: k2cpt++;
1970: }
1.84 brouard 1971: /*}*/
1.53 brouard 1972: }
1973: }
1974: }
1975:
1.84 brouard 1976: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.105 lievre 1977: fprintf(ficresp, "#Local time at start: %s", strstart);
1.53 brouard 1978: if (cptcovn>0) {
1979: fprintf(ficresp, "\n#********** Variable ");
1980: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1981: fprintf(ficresp, "**********\n#");
1982: }
1983: for(i=1; i<=nlstate;i++)
1984: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1985: fprintf(ficresp, "\n");
1986:
1.74 brouard 1987: for(i=iagemin; i <= iagemax+3; i++){
1988: if(i==iagemax+3){
1.53 brouard 1989: fprintf(ficlog,"Total");
1990: }else{
1991: if(first==1){
1992: first=0;
1993: printf("See log file for details...\n");
1994: }
1995: fprintf(ficlog,"Age %d", i);
1996: }
1997: for(jk=1; jk <=nlstate ; jk++){
1998: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1999: pp[jk] += freq[jk][m][i];
2000: }
2001: for(jk=1; jk <=nlstate ; jk++){
2002: for(m=-1, pos=0; m <=0 ; m++)
2003: pos += freq[jk][m][i];
2004: if(pp[jk]>=1.e-10){
2005: if(first==1){
2006: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2007: }
2008: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2009: }else{
2010: if(first==1)
2011: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2012: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2013: }
2014: }
2015:
2016: for(jk=1; jk <=nlstate ; jk++){
2017: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2018: pp[jk] += freq[jk][m][i];
1.73 lievre 2019: }
2020: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2021: pos += pp[jk];
2022: posprop += prop[jk][i];
1.53 brouard 2023: }
2024: for(jk=1; jk <=nlstate ; jk++){
2025: if(pos>=1.e-5){
2026: if(first==1)
2027: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2028: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2029: }else{
2030: if(first==1)
2031: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2032: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2033: }
1.74 brouard 2034: if( i <= iagemax){
1.53 brouard 2035: if(pos>=1.e-5){
1.73 lievre 2036: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 2037: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 2038: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2039: }
2040: else
1.73 lievre 2041: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 2042: }
2043: }
2044:
1.69 brouard 2045: for(jk=-1; jk <=nlstate+ndeath; jk++)
2046: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 2047: if(freq[jk][m][i] !=0 ) {
2048: if(first==1)
2049: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2050: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2051: }
1.74 brouard 2052: if(i <= iagemax)
1.53 brouard 2053: fprintf(ficresp,"\n");
2054: if(first==1)
2055: printf("Others in log...\n");
2056: fprintf(ficlog,"\n");
2057: }
2058: }
2059: }
2060: dateintmean=dateintsum/k2cpt;
2061:
2062: fclose(ficresp);
1.105 lievre 2063: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 2064: free_vector(pp,1,nlstate);
1.74 brouard 2065: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 2066: /* End of Freq */
2067: }
2068:
2069: /************ Prevalence ********************/
1.84 brouard 2070: 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 2071: {
2072: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2073: in each health status at the date of interview (if between dateprev1 and dateprev2).
2074: We still use firstpass and lastpass as another selection.
2075: */
1.53 brouard 2076:
2077: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2078: double ***freq; /* Frequencies */
1.73 lievre 2079: double *pp, **prop;
2080: double pos,posprop;
1.69 brouard 2081: double y2; /* in fractional years */
1.74 brouard 2082: int iagemin, iagemax;
1.53 brouard 2083:
1.74 brouard 2084: iagemin= (int) agemin;
2085: iagemax= (int) agemax;
2086: /*pp=vector(1,nlstate);*/
2087: prop=matrix(1,nlstate,iagemin,iagemax+3);
2088: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 2089: j1=0;
2090:
2091: j=cptcoveff;
2092: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2093:
2094: for(k1=1; k1<=j;k1++){
2095: for(i1=1; i1<=ncodemax[k1];i1++){
2096: j1++;
2097:
1.73 lievre 2098: for (i=1; i<=nlstate; i++)
1.74 brouard 2099: for(m=iagemin; m <= iagemax+3; m++)
2100: prop[i][m]=0.0;
1.53 brouard 2101:
1.69 brouard 2102: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 2103: bool=1;
2104: if (cptcovn>0) {
2105: for (z1=1; z1<=cptcoveff; z1++)
2106: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2107: bool=0;
2108: }
2109: if (bool==1) {
1.69 brouard 2110: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2111: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2112: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 2113: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2114: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2115: 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);
2116: if (s[m][i]>0 && s[m][i]<=nlstate) {
2117: /*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]]);*/
2118: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2119: prop[s[m][i]][iagemax+3] += weight[i];
2120: }
1.53 brouard 2121: }
1.69 brouard 2122: } /* end selection of waves */
1.53 brouard 2123: }
2124: }
1.74 brouard 2125: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 2126:
1.74 brouard 2127: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2128: posprop += prop[jk][i];
2129: }
2130:
2131: for(jk=1; jk <=nlstate ; jk++){
2132: if( i <= iagemax){
2133: if(posprop>=1.e-5){
2134: probs[i][jk][j1]= prop[jk][i]/posprop;
2135: }
2136: }
2137: }/* end jk */
2138: }/* end i */
1.53 brouard 2139: } /* end i1 */
2140: } /* end k1 */
2141:
1.74 brouard 2142: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2143: /*free_vector(pp,1,nlstate);*/
2144: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2145: } /* End of prevalence */
1.53 brouard 2146:
2147: /************* Waves Concatenation ***************/
2148:
1.59 brouard 2149: 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 2150: {
2151: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2152: Death is a valid wave (if date is known).
2153: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 2154: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 2155: and mw[mi+1][i]. dh depends on stepm.
2156: */
2157:
2158: int i, mi, m;
2159: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2160: double sum=0., jmean=0.;*/
2161: int first;
2162: int j, k=0,jk, ju, jl;
2163: double sum=0.;
2164: first=0;
2165: jmin=1e+5;
2166: jmax=-1;
2167: jmean=0.;
2168: for(i=1; i<=imx; i++){
2169: mi=0;
2170: m=firstpass;
2171: while(s[m][i] <= nlstate){
1.105 lievre 2172: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
1.53 brouard 2173: mw[++mi][i]=m;
2174: if(m >=lastpass)
2175: break;
2176: else
2177: m++;
2178: }/* end while */
2179: if (s[m][i] > nlstate){
2180: mi++; /* Death is another wave */
2181: /* if(mi==0) never been interviewed correctly before death */
2182: /* Only death is a correct wave */
2183: mw[mi][i]=m;
2184: }
2185:
2186: wav[i]=mi;
2187: if(mi==0){
1.91 brouard 2188: nbwarn++;
1.53 brouard 2189: if(first==0){
1.85 brouard 2190: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 2191: first=1;
2192: }
2193: if(first==1){
1.85 brouard 2194: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 2195: }
2196: } /* end mi==0 */
1.77 brouard 2197: } /* End individuals */
1.53 brouard 2198:
2199: for(i=1; i<=imx; i++){
2200: for(mi=1; mi<wav[i];mi++){
2201: if (stepm <=0)
2202: dh[mi][i]=1;
2203: else{
1.77 brouard 2204: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 2205: if (agedc[i] < 2*AGESUP) {
1.85 brouard 2206: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2207: if(j==0) j=1; /* Survives at least one month after exam */
2208: else if(j<0){
1.91 brouard 2209: nberr++;
1.85 brouard 2210: 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 2211: j=1; /* Temporary Dangerous patch */
1.105 lievre 2212: 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. You MUST fix the contradiction between dates.\n",stepm);
1.91 brouard 2213: 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]);
1.105 lievre 2214: 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. You MUST fix the contradiction between dates.\n",stepm);
1.85 brouard 2215: }
2216: k=k+1;
2217: if (j >= jmax) jmax=j;
2218: if (j <= jmin) jmin=j;
2219: sum=sum+j;
2220: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2221: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2222: }
2223: }
2224: else{
2225: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.104 lievre 2226: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
2227:
1.53 brouard 2228: k=k+1;
2229: if (j >= jmax) jmax=j;
2230: else if (j <= jmin)jmin=j;
2231: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2232: /*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 2233: if(j<0){
1.91 brouard 2234: nberr++;
1.85 brouard 2235: 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]);
2236: 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]);
2237: }
1.53 brouard 2238: sum=sum+j;
2239: }
2240: jk= j/stepm;
2241: jl= j -jk*stepm;
2242: ju= j -(jk+1)*stepm;
1.85 brouard 2243: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2244: if(jl==0){
2245: dh[mi][i]=jk;
2246: bh[mi][i]=0;
2247: }else{ /* We want a negative bias in order to only have interpolation ie
2248: * at the price of an extra matrix product in likelihood */
2249: dh[mi][i]=jk+1;
2250: bh[mi][i]=ju;
2251: }
2252: }else{
2253: if(jl <= -ju){
2254: dh[mi][i]=jk;
2255: bh[mi][i]=jl; /* bias is positive if real duration
2256: * is higher than the multiple of stepm and negative otherwise.
2257: */
2258: }
2259: else{
2260: dh[mi][i]=jk+1;
2261: bh[mi][i]=ju;
2262: }
2263: if(dh[mi][i]==0){
2264: dh[mi][i]=1; /* At least one step */
2265: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2266: /* 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 2267: }
1.85 brouard 2268: } /* end if mle */
2269: }
1.64 lievre 2270: } /* end wave */
1.53 brouard 2271: }
2272: jmean=sum/k;
2273: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2274: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2275: }
2276:
2277: /*********** Tricode ****************************/
2278: void tricode(int *Tvar, int **nbcode, int imx)
2279: {
1.58 lievre 2280:
2281: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2282: int cptcode=0;
2283: cptcoveff=0;
2284:
1.58 lievre 2285: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2286: for (k=1; k<=7; k++) ncodemax[k]=0;
2287:
2288: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2289: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2290: modality*/
2291: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2292: Ndum[ij]++; /*store the modality */
1.53 brouard 2293: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2294: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2295: Tvar[j]. If V=sex and male is 0 and
2296: female is 1, then cptcode=1.*/
1.53 brouard 2297: }
2298:
2299: for (i=0; i<=cptcode; i++) {
1.58 lievre 2300: 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 2301: }
1.58 lievre 2302:
1.53 brouard 2303: ij=1;
2304: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2305: for (k=0; k<= maxncov; k++) {
1.53 brouard 2306: if (Ndum[k] != 0) {
2307: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2308: /* 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 2309:
2310: ij++;
2311: }
2312: if (ij > ncodemax[j]) break;
2313: }
2314: }
2315: }
2316:
1.58 lievre 2317: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2318:
1.58 lievre 2319: for (i=1; i<=ncovmodel-2; i++) {
1.104 lievre 2320: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 2321: ij=Tvar[i];
1.58 lievre 2322: Ndum[ij]++;
1.53 brouard 2323: }
2324:
2325: ij=1;
1.58 lievre 2326: for (i=1; i<= maxncov; i++) {
1.53 brouard 2327: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2328: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2329: ij++;
2330: }
2331: }
2332:
1.58 lievre 2333: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2334: }
2335:
2336: /*********** Health Expectancies ****************/
2337:
1.105 lievre 2338: 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,char strstart[] )
1.53 brouard 2339:
2340: {
2341: /* Health expectancies */
2342: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2343: double age, agelim, hf;
2344: double ***p3mat,***varhe;
2345: double **dnewm,**doldm;
2346: double *xp;
2347: double **gp, **gm;
2348: double ***gradg, ***trgradg;
2349: int theta;
2350:
1.74 brouard 2351: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2352: xp=vector(1,npar);
1.74 brouard 2353: dnewm=matrix(1,nlstate*nlstate,1,npar);
2354: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2355:
1.105 lievre 2356: fprintf(ficreseij,"# Local time at start: %s", strstart);
1.53 brouard 2357: fprintf(ficreseij,"# Health expectancies\n");
2358: fprintf(ficreseij,"# Age");
2359: for(i=1; i<=nlstate;i++)
2360: for(j=1; j<=nlstate;j++)
2361: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2362: fprintf(ficreseij,"\n");
2363:
2364: if(estepm < stepm){
2365: printf ("Problem %d lower than %d\n",estepm, stepm);
2366: }
2367: else hstepm=estepm;
2368: /* We compute the life expectancy from trapezoids spaced every estepm months
2369: * This is mainly to measure the difference between two models: for example
2370: * if stepm=24 months pijx are given only every 2 years and by summing them
2371: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2372: * progression in between and thus overestimating or underestimating according
1.53 brouard 2373: * to the curvature of the survival function. If, for the same date, we
2374: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2375: * to compare the new estimate of Life expectancy with the same linear
2376: * hypothesis. A more precise result, taking into account a more precise
2377: * curvature will be obtained if estepm is as small as stepm. */
2378:
2379: /* For example we decided to compute the life expectancy with the smallest unit */
2380: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2381: nhstepm is the number of hstepm from age to agelim
2382: nstepm is the number of stepm from age to agelin.
2383: Look at hpijx to understand the reason of that which relies in memory size
2384: and note for a fixed period like estepm months */
2385: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2386: survival function given by stepm (the optimization length). Unfortunately it
2387: means that if the survival funtion is printed only each two years of age and if
2388: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2389: results. So we changed our mind and took the option of the best precision.
2390: */
2391: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2392:
2393: agelim=AGESUP;
2394: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2395: /* nhstepm age range expressed in number of stepm */
2396: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2397: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2398: /* if (stepm >= YEARM) hstepm=1;*/
2399: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2400: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2401: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2402: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2403: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2404:
2405: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2406: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2407: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2408:
2409:
2410: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2411:
1.95 brouard 2412: /* Computing Variances of health expectancies */
1.53 brouard 2413:
2414: for(theta=1; theta <=npar; theta++){
2415: for(i=1; i<=npar; i++){
2416: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2417: }
2418: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2419:
2420: cptj=0;
2421: for(j=1; j<= nlstate; j++){
2422: for(i=1; i<=nlstate; i++){
2423: cptj=cptj+1;
2424: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2425: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2426: }
2427: }
2428: }
2429:
2430:
2431: for(i=1; i<=npar; i++)
2432: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2433: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2434:
2435: cptj=0;
2436: for(j=1; j<= nlstate; j++){
2437: for(i=1;i<=nlstate;i++){
2438: cptj=cptj+1;
2439: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2440:
1.53 brouard 2441: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2442: }
2443: }
2444: }
1.74 brouard 2445: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2446: for(h=0; h<=nhstepm-1; h++){
2447: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2448: }
2449: }
2450:
2451: /* End theta */
2452:
1.74 brouard 2453: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2454:
2455: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2456: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2457: for(theta=1; theta <=npar; theta++)
2458: trgradg[h][j][theta]=gradg[h][theta][j];
2459:
2460:
1.74 brouard 2461: for(i=1;i<=nlstate*nlstate;i++)
2462: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2463: varhe[i][j][(int)age] =0.;
2464:
2465: printf("%d|",(int)age);fflush(stdout);
2466: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2467: for(h=0;h<=nhstepm-1;h++){
2468: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2469: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2470: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2471: for(i=1;i<=nlstate*nlstate;i++)
2472: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2473: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2474: }
2475: }
2476: /* Computing expectancies */
2477: for(i=1; i<=nlstate;i++)
2478: for(j=1; j<=nlstate;j++)
2479: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2480: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2481:
2482: /* 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]);*/
2483:
2484: }
2485:
2486: fprintf(ficreseij,"%3.0f",age );
2487: cptj=0;
2488: for(i=1; i<=nlstate;i++)
2489: for(j=1; j<=nlstate;j++){
2490: cptj++;
2491: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2492: }
2493: fprintf(ficreseij,"\n");
2494:
1.74 brouard 2495: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2496: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2497: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2498: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2499: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2500: }
2501: printf("\n");
2502: fprintf(ficlog,"\n");
2503:
2504: free_vector(xp,1,npar);
1.74 brouard 2505: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2506: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2507: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2508: }
2509:
2510: /************ Variance ******************/
1.105 lievre 2511: 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, char strstart[])
1.53 brouard 2512: {
2513: /* Variance of health expectancies */
2514: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2515: /* double **newm;*/
2516: double **dnewm,**doldm;
2517: double **dnewmp,**doldmp;
2518: int i, j, nhstepm, hstepm, h, nstepm ;
2519: int k, cptcode;
2520: double *xp;
2521: double **gp, **gm; /* for var eij */
2522: double ***gradg, ***trgradg; /*for var eij */
2523: double **gradgp, **trgradgp; /* for var p point j */
2524: double *gpp, *gmp; /* for var p point j */
2525: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2526: double ***p3mat;
2527: double age,agelim, hf;
2528: double ***mobaverage;
2529: int theta;
2530: char digit[4];
1.55 lievre 2531: char digitp[25];
1.53 brouard 2532:
2533: char fileresprobmorprev[FILENAMELENGTH];
2534:
1.55 lievre 2535: if(popbased==1){
1.58 lievre 2536: if(mobilav!=0)
1.55 lievre 2537: strcpy(digitp,"-populbased-mobilav-");
2538: else strcpy(digitp,"-populbased-nomobil-");
2539: }
2540: else
1.53 brouard 2541: strcpy(digitp,"-stablbased-");
1.56 lievre 2542:
1.54 brouard 2543: if (mobilav!=0) {
1.53 brouard 2544: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2545: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2546: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2547: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2548: }
1.53 brouard 2549: }
2550:
2551: strcpy(fileresprobmorprev,"prmorprev");
2552: sprintf(digit,"%-d",ij);
2553: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2554: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2555: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2556: strcat(fileresprobmorprev,fileres);
2557: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2558: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2559: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2560: }
2561: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2562:
1.53 brouard 2563: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.105 lievre 2564: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
1.66 brouard 2565: 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 2566: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2567: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2568: fprintf(ficresprobmorprev," p.%-d SE",j);
2569: for(i=1; i<=nlstate;i++)
2570: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2571: }
2572: fprintf(ficresprobmorprev,"\n");
1.88 brouard 2573: fprintf(ficgp,"\n# Routine varevsij");
1.106 brouard 2574: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.87 brouard 2575: 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");
2576: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2577: /* } */
1.53 brouard 2578: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.105 lievre 2579: fprintf(ficresvij, "#Local time at start: %s", strstart);
1.53 brouard 2580: 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");
2581: fprintf(ficresvij,"# Age");
2582: for(i=1; i<=nlstate;i++)
2583: for(j=1; j<=nlstate;j++)
2584: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2585: fprintf(ficresvij,"\n");
2586:
2587: xp=vector(1,npar);
2588: dnewm=matrix(1,nlstate,1,npar);
2589: doldm=matrix(1,nlstate,1,nlstate);
2590: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2591: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2592:
2593: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2594: gpp=vector(nlstate+1,nlstate+ndeath);
2595: gmp=vector(nlstate+1,nlstate+ndeath);
2596: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2597:
2598: if(estepm < stepm){
2599: printf ("Problem %d lower than %d\n",estepm, stepm);
2600: }
2601: else hstepm=estepm;
2602: /* For example we decided to compute the life expectancy with the smallest unit */
2603: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2604: nhstepm is the number of hstepm from age to agelim
2605: nstepm is the number of stepm from age to agelin.
2606: Look at hpijx to understand the reason of that which relies in memory size
2607: and note for a fixed period like k years */
2608: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2609: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2610: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2611: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2612: results. So we changed our mind and took the option of the best precision.
2613: */
2614: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2615: agelim = AGESUP;
2616: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2617: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2618: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2619: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2620: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2621: gp=matrix(0,nhstepm,1,nlstate);
2622: gm=matrix(0,nhstepm,1,nlstate);
2623:
2624:
2625: for(theta=1; theta <=npar; theta++){
1.66 brouard 2626: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2627: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2628: }
2629: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2630: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2631:
2632: if (popbased==1) {
1.54 brouard 2633: if(mobilav ==0){
1.53 brouard 2634: for(i=1; i<=nlstate;i++)
2635: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2636: }else{ /* mobilav */
1.53 brouard 2637: for(i=1; i<=nlstate;i++)
2638: prlim[i][i]=mobaverage[(int)age][i][ij];
2639: }
2640: }
2641:
2642: for(j=1; j<= nlstate; j++){
2643: for(h=0; h<=nhstepm; h++){
2644: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2645: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2646: }
2647: }
1.66 brouard 2648: /* This for computing probability of death (h=1 means
2649: computed over hstepm matrices product = hstepm*stepm months)
2650: as a weighted average of prlim.
2651: */
1.69 brouard 2652: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2653: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2654: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2655: }
1.66 brouard 2656: /* end probability of death */
1.53 brouard 2657:
1.66 brouard 2658: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2659: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2660: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2661: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2662:
2663: if (popbased==1) {
1.54 brouard 2664: if(mobilav ==0){
1.53 brouard 2665: for(i=1; i<=nlstate;i++)
2666: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2667: }else{ /* mobilav */
1.53 brouard 2668: for(i=1; i<=nlstate;i++)
2669: prlim[i][i]=mobaverage[(int)age][i][ij];
2670: }
2671: }
2672:
2673: for(j=1; j<= nlstate; j++){
2674: for(h=0; h<=nhstepm; h++){
2675: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2676: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2677: }
2678: }
1.66 brouard 2679: /* This for computing probability of death (h=1 means
2680: computed over hstepm matrices product = hstepm*stepm months)
2681: as a weighted average of prlim.
2682: */
1.69 brouard 2683: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2684: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2685: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2686: }
1.66 brouard 2687: /* end probability of death */
1.53 brouard 2688:
2689: for(j=1; j<= nlstate; j++) /* vareij */
2690: for(h=0; h<=nhstepm; h++){
2691: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2692: }
1.68 lievre 2693:
1.53 brouard 2694: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2695: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2696: }
2697:
2698: } /* End theta */
2699:
2700: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2701:
2702: for(h=0; h<=nhstepm; h++) /* veij */
2703: for(j=1; j<=nlstate;j++)
2704: for(theta=1; theta <=npar; theta++)
2705: trgradg[h][j][theta]=gradg[h][theta][j];
2706:
2707: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2708: for(theta=1; theta <=npar; theta++)
1.53 brouard 2709: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2710:
1.53 brouard 2711:
2712: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2713: for(i=1;i<=nlstate;i++)
2714: for(j=1;j<=nlstate;j++)
2715: vareij[i][j][(int)age] =0.;
2716:
2717: for(h=0;h<=nhstepm;h++){
2718: for(k=0;k<=nhstepm;k++){
2719: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2720: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2721: for(i=1;i<=nlstate;i++)
2722: for(j=1;j<=nlstate;j++)
2723: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2724: }
2725: }
1.70 brouard 2726:
1.53 brouard 2727: /* pptj */
2728: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2729: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2730: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2731: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2732: varppt[j][i]=doldmp[j][i];
2733: /* end ppptj */
1.66 brouard 2734: /* x centered again */
1.53 brouard 2735: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2736: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2737:
2738: if (popbased==1) {
1.54 brouard 2739: if(mobilav ==0){
1.53 brouard 2740: for(i=1; i<=nlstate;i++)
2741: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2742: }else{ /* mobilav */
1.53 brouard 2743: for(i=1; i<=nlstate;i++)
2744: prlim[i][i]=mobaverage[(int)age][i][ij];
2745: }
2746: }
1.70 brouard 2747:
1.66 brouard 2748: /* This for computing probability of death (h=1 means
2749: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2750: as a weighted average of prlim.
2751: */
1.68 lievre 2752: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2753: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2754: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2755: }
1.66 brouard 2756: /* end probability of death */
1.53 brouard 2757:
2758: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2759: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2760: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2761: for(i=1; i<=nlstate;i++){
2762: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2763: }
2764: }
2765: fprintf(ficresprobmorprev,"\n");
2766:
2767: fprintf(ficresvij,"%.0f ",age );
2768: for(i=1; i<=nlstate;i++)
2769: for(j=1; j<=nlstate;j++){
2770: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2771: }
2772: fprintf(ficresvij,"\n");
2773: free_matrix(gp,0,nhstepm,1,nlstate);
2774: free_matrix(gm,0,nhstepm,1,nlstate);
2775: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2776: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2777: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2778: } /* End age */
2779: free_vector(gpp,nlstate+1,nlstate+ndeath);
2780: free_vector(gmp,nlstate+1,nlstate+ndeath);
2781: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2782: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2783: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2784: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2785: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2786: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2787: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2788: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.88 brouard 2789: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2790: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2791: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2792: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2793: 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 2794: /* 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);
2795: */
1.88 brouard 2796: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
1.89 brouard 2797: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
1.53 brouard 2798:
2799: free_vector(xp,1,npar);
2800: free_matrix(doldm,1,nlstate,1,nlstate);
2801: free_matrix(dnewm,1,nlstate,1,npar);
2802: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2803: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2804: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2805: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2806: fclose(ficresprobmorprev);
1.88 brouard 2807: fflush(ficgp);
2808: fflush(fichtm);
1.84 brouard 2809: } /* end varevsij */
1.53 brouard 2810:
2811: /************ Variance of prevlim ******************/
1.105 lievre 2812: 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, char strstart[])
1.53 brouard 2813: {
2814: /* Variance of prevalence limit */
1.59 brouard 2815: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2816: double **newm;
2817: double **dnewm,**doldm;
2818: int i, j, nhstepm, hstepm;
2819: int k, cptcode;
2820: double *xp;
2821: double *gp, *gm;
2822: double **gradg, **trgradg;
2823: double age,agelim;
2824: int theta;
1.105 lievre 2825: fprintf(ficresvpl, "#Local time at start: %s", strstart);
1.54 brouard 2826: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2827: fprintf(ficresvpl,"# Age");
2828: for(i=1; i<=nlstate;i++)
2829: fprintf(ficresvpl," %1d-%1d",i,i);
2830: fprintf(ficresvpl,"\n");
2831:
2832: xp=vector(1,npar);
2833: dnewm=matrix(1,nlstate,1,npar);
2834: doldm=matrix(1,nlstate,1,nlstate);
2835:
2836: hstepm=1*YEARM; /* Every year of age */
2837: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2838: agelim = AGESUP;
2839: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2840: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2841: if (stepm >= YEARM) hstepm=1;
2842: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2843: gradg=matrix(1,npar,1,nlstate);
2844: gp=vector(1,nlstate);
2845: gm=vector(1,nlstate);
2846:
2847: for(theta=1; theta <=npar; theta++){
2848: for(i=1; i<=npar; i++){ /* Computes gradient */
2849: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2850: }
2851: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2852: for(i=1;i<=nlstate;i++)
2853: gp[i] = prlim[i][i];
2854:
2855: for(i=1; i<=npar; i++) /* Computes gradient */
2856: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2857: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2858: for(i=1;i<=nlstate;i++)
2859: gm[i] = prlim[i][i];
2860:
2861: for(i=1;i<=nlstate;i++)
2862: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2863: } /* End theta */
2864:
2865: trgradg =matrix(1,nlstate,1,npar);
2866:
2867: for(j=1; j<=nlstate;j++)
2868: for(theta=1; theta <=npar; theta++)
2869: trgradg[j][theta]=gradg[theta][j];
2870:
2871: for(i=1;i<=nlstate;i++)
2872: varpl[i][(int)age] =0.;
2873: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2874: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2875: for(i=1;i<=nlstate;i++)
2876: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2877:
2878: fprintf(ficresvpl,"%.0f ",age );
2879: for(i=1; i<=nlstate;i++)
2880: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2881: fprintf(ficresvpl,"\n");
2882: free_vector(gp,1,nlstate);
2883: free_vector(gm,1,nlstate);
2884: free_matrix(gradg,1,npar,1,nlstate);
2885: free_matrix(trgradg,1,nlstate,1,npar);
2886: } /* End age */
2887:
2888: free_vector(xp,1,npar);
2889: free_matrix(doldm,1,nlstate,1,npar);
2890: free_matrix(dnewm,1,nlstate,1,nlstate);
2891:
2892: }
2893:
2894: /************ Variance of one-step probabilities ******************/
1.105 lievre 2895: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.53 brouard 2896: {
2897: int i, j=0, i1, k1, l1, t, tj;
2898: int k2, l2, j1, z1;
2899: int k=0,l, cptcode;
2900: int first=1, first1;
2901: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2902: double **dnewm,**doldm;
2903: double *xp;
2904: double *gp, *gm;
2905: double **gradg, **trgradg;
2906: double **mu;
2907: double age,agelim, cov[NCOVMAX];
2908: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2909: int theta;
2910: char fileresprob[FILENAMELENGTH];
2911: char fileresprobcov[FILENAMELENGTH];
2912: char fileresprobcor[FILENAMELENGTH];
2913:
2914: double ***varpij;
2915:
2916: strcpy(fileresprob,"prob");
2917: strcat(fileresprob,fileres);
2918: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2919: printf("Problem with resultfile: %s\n", fileresprob);
2920: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2921: }
2922: strcpy(fileresprobcov,"probcov");
2923: strcat(fileresprobcov,fileres);
2924: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2925: printf("Problem with resultfile: %s\n", fileresprobcov);
2926: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2927: }
2928: strcpy(fileresprobcor,"probcor");
2929: strcat(fileresprobcor,fileres);
2930: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2931: printf("Problem with resultfile: %s\n", fileresprobcor);
2932: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2933: }
2934: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2935: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2936: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2937: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2938: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2939: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
1.105 lievre 2940: fprintf(ficresprob, "#Local time at start: %s", strstart);
1.53 brouard 2941: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2942: fprintf(ficresprob,"# Age");
1.105 lievre 2943: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
1.53 brouard 2944: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2945: fprintf(ficresprobcov,"# Age");
1.105 lievre 2946: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
1.53 brouard 2947: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2948: fprintf(ficresprobcov,"# Age");
2949:
2950:
2951: for(i=1; i<=nlstate;i++)
2952: for(j=1; j<=(nlstate+ndeath);j++){
2953: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2954: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2955: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2956: }
1.69 brouard 2957: /* fprintf(ficresprob,"\n");
1.53 brouard 2958: fprintf(ficresprobcov,"\n");
2959: fprintf(ficresprobcor,"\n");
1.69 brouard 2960: */
2961: xp=vector(1,npar);
1.53 brouard 2962: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2963: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2964: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2965: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2966: first=1;
1.88 brouard 2967: fprintf(ficgp,"\n# Routine varprob");
2968: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2969: fprintf(fichtm,"\n");
2970:
1.95 brouard 2971: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2972: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
1.91 brouard 2973: file %s<br>\n",optionfilehtmcov);
2974: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2975: and drawn. It helps understanding how is the covariance between two incidences.\
2976: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2977: 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. \
2978: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2979: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2980: standard deviations wide on each axis. <br>\
2981: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2982: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2983: 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 2984:
2985: cov[1]=1;
2986: tj=cptcoveff;
2987: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2988: j1=0;
2989: for(t=1; t<=tj;t++){
2990: for(i1=1; i1<=ncodemax[t];i1++){
2991: j1++;
2992: if (cptcovn>0) {
2993: fprintf(ficresprob, "\n#********** Variable ");
2994: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2995: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2996: fprintf(ficresprobcov, "\n#********** Variable ");
2997: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2998: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2999:
3000: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 3001: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3002: fprintf(ficgp, "**********\n#\n");
1.53 brouard 3003:
3004:
1.96 brouard 3005: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.53 brouard 3006: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.96 brouard 3007: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.53 brouard 3008:
3009: fprintf(ficresprobcor, "\n#********** Variable ");
3010: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 3011: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 3012: }
3013:
3014: for (age=bage; age<=fage; age ++){
3015: cov[2]=age;
3016: for (k=1; k<=cptcovn;k++) {
3017: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3018: }
3019: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3020: for (k=1; k<=cptcovprod;k++)
3021: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3022:
3023: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3024: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3025: gp=vector(1,(nlstate)*(nlstate+ndeath));
3026: gm=vector(1,(nlstate)*(nlstate+ndeath));
3027:
3028: for(theta=1; theta <=npar; theta++){
3029: for(i=1; i<=npar; i++)
1.74 brouard 3030: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 3031:
3032: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3033:
3034: k=0;
3035: for(i=1; i<= (nlstate); i++){
3036: for(j=1; j<=(nlstate+ndeath);j++){
3037: k=k+1;
3038: gp[k]=pmmij[i][j];
3039: }
3040: }
3041:
3042: for(i=1; i<=npar; i++)
1.74 brouard 3043: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 3044:
3045: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3046: k=0;
3047: for(i=1; i<=(nlstate); i++){
3048: for(j=1; j<=(nlstate+ndeath);j++){
3049: k=k+1;
3050: gm[k]=pmmij[i][j];
3051: }
3052: }
3053:
3054: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 3055: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 3056: }
3057:
3058: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3059: for(theta=1; theta <=npar; theta++)
3060: trgradg[j][theta]=gradg[theta][j];
3061:
3062: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3063: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 3064: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3065: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3066: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3067: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3068:
1.53 brouard 3069: pmij(pmmij,cov,ncovmodel,x,nlstate);
3070:
3071: k=0;
3072: for(i=1; i<=(nlstate); i++){
3073: for(j=1; j<=(nlstate+ndeath);j++){
3074: k=k+1;
3075: mu[k][(int) age]=pmmij[i][j];
3076: }
3077: }
3078: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3079: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3080: varpij[i][j][(int)age] = doldm[i][j];
3081:
3082: /*printf("\n%d ",(int)age);
1.59 brouard 3083: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3084: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3085: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3086: }*/
1.53 brouard 3087:
3088: fprintf(ficresprob,"\n%d ",(int)age);
3089: fprintf(ficresprobcov,"\n%d ",(int)age);
3090: fprintf(ficresprobcor,"\n%d ",(int)age);
3091:
3092: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3093: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3094: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3095: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3096: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3097: }
3098: i=0;
3099: for (k=1; k<=(nlstate);k++){
3100: for (l=1; l<=(nlstate+ndeath);l++){
3101: i=i++;
3102: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3103: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3104: for (j=1; j<=i;j++){
3105: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3106: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3107: }
3108: }
3109: }/* end of loop for state */
3110: } /* end of loop for age */
3111:
3112: /* Confidence intervalle of pij */
3113: /*
1.59 brouard 3114: fprintf(ficgp,"\nset noparametric;unset label");
3115: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3116: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3117: 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);
3118: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3119: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3120: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 3121: */
3122:
3123: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3124: first1=1;
3125: for (k2=1; k2<=(nlstate);k2++){
3126: for (l2=1; l2<=(nlstate+ndeath);l2++){
3127: if(l2==k2) continue;
3128: j=(k2-1)*(nlstate+ndeath)+l2;
3129: for (k1=1; k1<=(nlstate);k1++){
3130: for (l1=1; l1<=(nlstate+ndeath);l1++){
3131: if(l1==k1) continue;
3132: i=(k1-1)*(nlstate+ndeath)+l1;
3133: if(i<=j) continue;
3134: for (age=bage; age<=fage; age ++){
3135: if ((int)age %5==0){
3136: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3137: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3138: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3139: mu1=mu[i][(int) age]/stepm*YEARM ;
3140: mu2=mu[j][(int) age]/stepm*YEARM;
3141: c12=cv12/sqrt(v1*v2);
3142: /* Computing eigen value of matrix of covariance */
3143: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3144: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3145: /* Eigen vectors */
3146: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3147: /*v21=sqrt(1.-v11*v11); *//* error */
3148: v21=(lc1-v1)/cv12*v11;
3149: v12=-v21;
3150: v22=v11;
3151: tnalp=v21/v11;
3152: if(first1==1){
3153: first1=0;
3154: 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);
3155: }
3156: 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);
3157: /*printf(fignu*/
3158: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3159: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3160: if(first==1){
3161: first=0;
3162: fprintf(ficgp,"\nset parametric;unset label");
3163: 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);
3164: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
1.91 brouard 3165: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.88 brouard 3166: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3167: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3168: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3169: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.91 brouard 3170: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3171: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.88 brouard 3172: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3173: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3174: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3175: 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",\
3176: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3177: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3178: }else{
3179: first=0;
1.91 brouard 3180: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
1.53 brouard 3181: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3182: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3183: 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",\
3184: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3185: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3186: }/* if first */
3187: } /* age mod 5 */
3188: } /* end loop age */
1.88 brouard 3189: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
1.53 brouard 3190: first=1;
3191: } /*l12 */
3192: } /* k12 */
3193: } /*l1 */
3194: }/* k1 */
3195: } /* loop covariates */
3196: }
1.59 brouard 3197: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3198: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 3199: free_vector(xp,1,npar);
3200: fclose(ficresprob);
3201: fclose(ficresprobcov);
3202: fclose(ficresprobcor);
1.91 brouard 3203: fflush(ficgp);
3204: fflush(fichtmcov);
1.53 brouard 3205: }
3206:
3207:
3208: /******************* Printing html file ***********/
3209: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3210: int lastpass, int stepm, int weightopt, char model[],\
3211: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3212: int popforecast, int estepm ,\
3213: double jprev1, double mprev1,double anprev1, \
3214: double jprev2, double mprev2,double anprev2){
3215: int jj1, k1, i1, cpt;
3216:
1.107 ! brouard 3217: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
! 3218: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
1.106 brouard 3219: </ul>");
1.107 ! brouard 3220: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
1.96 brouard 3221: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3222: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3223: fprintf(fichtm,"\
3224: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3225: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3226: fprintf(fichtm,"\
3227: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3228: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3229: fprintf(fichtm,"\
1.85 brouard 3230: - Life expectancies by age and initial health status (estepm=%2d months): \
1.96 brouard 3231: <a href=\"%s\">%s</a> <br>\n</li>",
1.88 brouard 3232: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
1.53 brouard 3233:
3234: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3235:
3236: m=cptcoveff;
3237: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3238:
3239: jj1=0;
3240: for(k1=1; k1<=m;k1++){
3241: for(i1=1; i1<=ncodemax[k1];i1++){
3242: jj1++;
3243: if (cptcovn > 0) {
3244: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3245: for (cpt=1; cpt<=cptcoveff;cpt++)
3246: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3247: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3248: }
3249: /* Pij */
1.88 brouard 3250: 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> \
3251: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3252: /* Quasi-incidences */
1.85 brouard 3253: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.88 brouard 3254: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3255: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.53 brouard 3256: /* Stable prevalence in each health state */
3257: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3258: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.88 brouard 3259: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.53 brouard 3260: }
3261: for(cpt=1; cpt<=nlstate;cpt++) {
1.88 brouard 3262: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
1.89 brouard 3263: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.53 brouard 3264: }
3265: } /* end i1 */
3266: }/* End k1 */
3267: fprintf(fichtm,"</ul>");
3268:
3269:
1.96 brouard 3270: fprintf(fichtm,"\
1.107 ! brouard 3271: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.96 brouard 3272: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3273:
3274: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3275: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3276: fprintf(fichtm,"\
3277: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3278: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3279:
3280: fprintf(fichtm,"\
3281: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3282: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3283: fprintf(fichtm,"\
3284: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3285: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3286: fprintf(fichtm,"\
3287: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3288: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3289: fprintf(fichtm,"\
1.88 brouard 3290: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3291: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
1.53 brouard 3292:
1.76 brouard 3293: /* if(popforecast==1) fprintf(fichtm,"\n */
3294: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3295: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3296: /* <br>",fileres,fileres,fileres,fileres); */
3297: /* else */
3298: /* 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 3299: fflush(fichtm);
3300: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.53 brouard 3301:
3302: m=cptcoveff;
3303: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3304:
3305: jj1=0;
3306: for(k1=1; k1<=m;k1++){
3307: for(i1=1; i1<=ncodemax[k1];i1++){
3308: jj1++;
3309: if (cptcovn > 0) {
3310: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3311: for (cpt=1; cpt<=cptcoveff;cpt++)
3312: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3313: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3314: }
3315: for(cpt=1; cpt<=nlstate;cpt++) {
1.95 brouard 3316: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3317: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
1.90 brouard 3318: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.53 brouard 3319: }
1.96 brouard 3320: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3321: health expectancies in states (1) and (2): %s%d.png<br>\
3322: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.53 brouard 3323: } /* end i1 */
3324: }/* End k1 */
3325: fprintf(fichtm,"</ul>");
1.87 brouard 3326: fflush(fichtm);
1.53 brouard 3327: }
3328:
3329: /******************* Gnuplot file **************/
1.89 brouard 3330: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.53 brouard 3331:
1.88 brouard 3332: char dirfileres[132],optfileres[132];
1.53 brouard 3333: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3334: int ng;
1.88 brouard 3335: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3336: /* printf("Problem with file %s",optionfilegnuplot); */
3337: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3338: /* } */
1.53 brouard 3339:
1.54 brouard 3340: /*#ifdef windows */
1.89 brouard 3341: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3342: /*#endif */
1.88 brouard 3343: m=pow(2,cptcoveff);
3344:
3345: strcpy(dirfileres,optionfilefiname);
3346: strcpy(optfileres,"vpl");
1.53 brouard 3347: /* 1eme*/
3348: for (cpt=1; cpt<= nlstate ; cpt ++) {
3349: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3350: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3351: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3352: fprintf(ficgp,"set xlabel \"Age\" \n\
3353: set ylabel \"Probability\" \n\
3354: set ter png small\n\
3355: set size 0.65,0.65\n\
3356: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3357:
3358: for (i=1; i<= nlstate ; i ++) {
3359: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3360: else fprintf(ficgp," \%%*lf (\%%*lf)");
3361: }
1.88 brouard 3362: 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 3363: for (i=1; i<= nlstate ; i ++) {
3364: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3365: else fprintf(ficgp," \%%*lf (\%%*lf)");
3366: }
1.88 brouard 3367: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.53 brouard 3368: for (i=1; i<= nlstate ; i ++) {
3369: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3370: else fprintf(ficgp," \%%*lf (\%%*lf)");
3371: }
1.88 brouard 3372: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.53 brouard 3373: }
3374: }
3375: /*2 eme*/
3376:
3377: for (k1=1; k1<= m ; k1 ++) {
1.88 brouard 3378: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.53 brouard 3379: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3380:
3381: for (i=1; i<= nlstate+1 ; i ++) {
3382: k=2*i;
1.88 brouard 3383: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3384: for (j=1; j<= nlstate+1 ; j ++) {
3385: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3386: else fprintf(ficgp," \%%*lf (\%%*lf)");
3387: }
3388: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3389: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.88 brouard 3390: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3391: for (j=1; j<= nlstate+1 ; j ++) {
3392: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3393: else fprintf(ficgp," \%%*lf (\%%*lf)");
3394: }
3395: fprintf(ficgp,"\" t\"\" w l 0,");
1.88 brouard 3396: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.53 brouard 3397: for (j=1; j<= nlstate+1 ; j ++) {
3398: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3399: else fprintf(ficgp," \%%*lf (\%%*lf)");
3400: }
3401: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3402: else fprintf(ficgp,"\" t\"\" w l 0,");
3403: }
3404: }
3405:
3406: /*3eme*/
3407:
3408: for (k1=1; k1<= m ; k1 ++) {
3409: for (cpt=1; cpt<= nlstate ; cpt ++) {
3410: k=2+nlstate*(2*cpt-2);
1.88 brouard 3411: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3412: fprintf(ficgp,"set ter png small\n\
3413: set size 0.65,0.65\n\
3414: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
1.53 brouard 3415: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3416: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3417: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3418: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3419: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3420: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3421:
3422: */
3423: for (i=1; i< nlstate ; i ++) {
1.88 brouard 3424: 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 3425:
3426: }
3427: }
3428: }
3429:
1.76 brouard 3430: /* CV preval stable (period) */
1.53 brouard 3431: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3432: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3433: k=3;
1.88 brouard 3434: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3435: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3436: set ter png small\nset size 0.65,0.65\n\
1.89 brouard 3437: unset log y\n\
1.88 brouard 3438: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
1.53 brouard 3439:
1.83 lievre 3440: for (i=1; i< nlstate ; i ++)
1.53 brouard 3441: fprintf(ficgp,"+$%d",k+i+1);
3442: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3443:
3444: l=3+(nlstate+ndeath)*cpt;
1.88 brouard 3445: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
1.53 brouard 3446: for (i=1; i< nlstate ; i ++) {
3447: l=3+(nlstate+ndeath)*cpt;
3448: fprintf(ficgp,"+$%d",l+i+1);
3449: }
3450: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3451: }
3452: }
3453:
3454: /* proba elementaires */
3455: for(i=1,jk=1; i <=nlstate; i++){
3456: for(k=1; k <=(nlstate+ndeath); k++){
3457: if (k != i) {
3458: for(j=1; j <=ncovmodel; j++){
3459: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3460: jk++;
3461: fprintf(ficgp,"\n");
3462: }
3463: }
3464: }
3465: }
3466:
3467: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3468: for(jk=1; jk <=m; jk++) {
1.88 brouard 3469: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.53 brouard 3470: if (ng==2)
3471: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3472: else
3473: fprintf(ficgp,"\nset title \"Probability\"\n");
3474: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3475: i=1;
3476: for(k2=1; k2<=nlstate; k2++) {
3477: k3=i;
3478: for(k=1; k<=(nlstate+ndeath); k++) {
3479: if (k != k2){
3480: if(ng==2)
3481: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3482: else
3483: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3484: ij=1;
3485: for(j=3; j <=ncovmodel; j++) {
3486: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3487: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3488: ij++;
3489: }
3490: else
3491: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3492: }
3493: fprintf(ficgp,")/(1");
3494:
3495: for(k1=1; k1 <=nlstate; k1++){
3496: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3497: ij=1;
3498: for(j=3; j <=ncovmodel; j++){
3499: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3500: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3501: ij++;
3502: }
3503: else
3504: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3505: }
3506: fprintf(ficgp,")");
3507: }
3508: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3509: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3510: i=i+ncovmodel;
3511: }
3512: } /* end k */
3513: } /* end k2 */
3514: } /* end jk */
3515: } /* end ng */
1.88 brouard 3516: fflush(ficgp);
1.53 brouard 3517: } /* end gnuplot */
3518:
3519:
3520: /*************** Moving average **************/
1.54 brouard 3521: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3522:
3523: int i, cpt, cptcod;
1.58 lievre 3524: int modcovmax =1;
1.54 brouard 3525: int mobilavrange, mob;
1.53 brouard 3526: double age;
1.58 lievre 3527:
3528: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3529: a covariate has 2 modalities */
3530: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3531:
1.54 brouard 3532: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3533: if(mobilav==1) mobilavrange=5; /* default */
3534: else mobilavrange=mobilav;
3535: for (age=bage; age<=fage; age++)
3536: for (i=1; i<=nlstate;i++)
1.58 lievre 3537: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3538: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3539: /* We keep the original values on the extreme ages bage, fage and for
3540: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3541: we use a 5 terms etc. until the borders are no more concerned.
3542: */
3543: for (mob=3;mob <=mobilavrange;mob=mob+2){
3544: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3545: for (i=1; i<=nlstate;i++){
1.58 lievre 3546: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3547: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3548: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3549: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3550: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3551: }
3552: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3553: }
1.53 brouard 3554: }
1.54 brouard 3555: }/* end age */
3556: }/* end mob */
3557: }else return -1;
3558: return 0;
3559: }/* End movingaverage */
1.53 brouard 3560:
3561:
3562: /************** Forecasting ******************/
1.70 brouard 3563: 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 3564: /* proj1, year, month, day of starting projection
3565: agemin, agemax range of age
3566: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3567: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3568: */
1.73 lievre 3569: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3570: int *popage;
1.70 brouard 3571: double agec; /* generic age */
3572: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3573: double *popeffectif,*popcount;
3574: double ***p3mat;
1.55 lievre 3575: double ***mobaverage;
1.53 brouard 3576: char fileresf[FILENAMELENGTH];
3577:
1.69 brouard 3578: agelim=AGESUP;
1.84 brouard 3579: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3580:
3581: strcpy(fileresf,"f");
3582: strcat(fileresf,fileres);
3583: if((ficresf=fopen(fileresf,"w"))==NULL) {
3584: printf("Problem with forecast resultfile: %s\n", fileresf);
3585: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3586: }
3587: printf("Computing forecasting: result on file '%s' \n", fileresf);
3588: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3589:
3590: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3591:
1.54 brouard 3592: if (mobilav!=0) {
1.53 brouard 3593: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3594: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3595: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3596: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3597: }
1.53 brouard 3598: }
3599:
3600: stepsize=(int) (stepm+YEARM-1)/YEARM;
3601: if (stepm<=12) stepsize=1;
1.74 brouard 3602: if(estepm < stepm){
3603: printf ("Problem %d lower than %d\n",estepm, stepm);
3604: }
3605: else hstepm=estepm;
3606:
1.53 brouard 3607: hstepm=hstepm/stepm;
1.69 brouard 3608: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3609: fractional in yp1 */
1.53 brouard 3610: anprojmean=yp;
3611: yp2=modf((yp1*12),&yp);
3612: mprojmean=yp;
3613: yp1=modf((yp2*30.5),&yp);
3614: jprojmean=yp;
3615: if(jprojmean==0) jprojmean=1;
3616: if(mprojmean==0) jprojmean=1;
1.73 lievre 3617:
3618: i1=cptcoveff;
3619: if (cptcovn < 1){i1=1;}
1.53 brouard 3620:
1.70 brouard 3621: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3622:
1.70 brouard 3623: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3624:
1.75 brouard 3625: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3626: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3627: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3628: k=k+1;
3629: fprintf(ficresf,"\n#******");
3630: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3631: 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 3632: }
3633: fprintf(ficresf,"******\n");
1.70 brouard 3634: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3635: for(j=1; j<=nlstate+ndeath;j++){
3636: for(i=1; i<=nlstate;i++)
3637: fprintf(ficresf," p%d%d",i,j);
3638: fprintf(ficresf," p.%d",j);
3639: }
1.74 brouard 3640: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3641: fprintf(ficresf,"\n");
1.70 brouard 3642: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3643:
1.71 brouard 3644: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3645: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3646: nhstepm = nhstepm/hstepm;
3647: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3648: oldm=oldms;savm=savms;
1.70 brouard 3649: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3650:
3651: for (h=0; h<=nhstepm; h++){
1.75 brouard 3652: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3653: fprintf(ficresf,"\n");
3654: for(j=1;j<=cptcoveff;j++)
3655: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3656: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3657: }
3658: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3659: ppij=0.;
1.71 brouard 3660: for(i=1; i<=nlstate;i++) {
1.53 brouard 3661: if (mobilav==1)
1.71 brouard 3662: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3663: else {
1.71 brouard 3664: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3665: }
1.75 brouard 3666: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3667: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3668: }
3669: } /* end i */
3670: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3671: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3672: }
1.75 brouard 3673: }/* end j */
3674: } /* end h */
1.53 brouard 3675: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3676: } /* end agec */
3677: } /* end yearp */
3678: } /* end cptcod */
3679: } /* end cptcov */
1.53 brouard 3680:
1.54 brouard 3681: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3682:
3683: fclose(ficresf);
3684: }
1.70 brouard 3685:
3686: /************** Forecasting *****not tested NB*************/
1.53 brouard 3687: 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){
3688:
3689: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3690: int *popage;
1.69 brouard 3691: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3692: double *popeffectif,*popcount;
3693: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3694: double ***mobaverage;
1.53 brouard 3695: char filerespop[FILENAMELENGTH];
3696:
3697: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3698: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3699: agelim=AGESUP;
1.69 brouard 3700: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3701:
1.84 brouard 3702: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3703:
3704:
3705: strcpy(filerespop,"pop");
3706: strcat(filerespop,fileres);
3707: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3708: printf("Problem with forecast resultfile: %s\n", filerespop);
3709: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3710: }
3711: printf("Computing forecasting: result on file '%s' \n", filerespop);
3712: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3713:
3714: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3715:
1.54 brouard 3716: if (mobilav!=0) {
1.53 brouard 3717: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3718: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3719: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3720: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3721: }
1.53 brouard 3722: }
3723:
3724: stepsize=(int) (stepm+YEARM-1)/YEARM;
3725: if (stepm<=12) stepsize=1;
3726:
3727: agelim=AGESUP;
3728:
3729: hstepm=1;
3730: hstepm=hstepm/stepm;
3731:
3732: if (popforecast==1) {
3733: if((ficpop=fopen(popfile,"r"))==NULL) {
3734: printf("Problem with population file : %s\n",popfile);exit(0);
3735: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3736: }
3737: popage=ivector(0,AGESUP);
3738: popeffectif=vector(0,AGESUP);
3739: popcount=vector(0,AGESUP);
3740:
3741: i=1;
3742: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3743:
3744: imx=i;
3745: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3746: }
3747:
1.69 brouard 3748: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3749: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3750: k=k+1;
3751: fprintf(ficrespop,"\n#******");
3752: for(j=1;j<=cptcoveff;j++) {
3753: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3754: }
3755: fprintf(ficrespop,"******\n");
3756: fprintf(ficrespop,"# Age");
3757: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3758: if (popforecast==1) fprintf(ficrespop," [Population]");
3759:
3760: for (cpt=0; cpt<=0;cpt++) {
3761: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3762:
1.69 brouard 3763: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3764: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3765: nhstepm = nhstepm/hstepm;
3766:
3767: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3768: oldm=oldms;savm=savms;
3769: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3770:
3771: for (h=0; h<=nhstepm; h++){
1.69 brouard 3772: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3773: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3774: }
3775: for(j=1; j<=nlstate+ndeath;j++) {
3776: kk1=0.;kk2=0;
3777: for(i=1; i<=nlstate;i++) {
3778: if (mobilav==1)
3779: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3780: else {
3781: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3782: }
3783: }
1.69 brouard 3784: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3785: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3786: /*fprintf(ficrespop," %.3f", kk1);
3787: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3788: }
3789: }
3790: for(i=1; i<=nlstate;i++){
3791: kk1=0.;
3792: for(j=1; j<=nlstate;j++){
3793: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3794: }
1.69 brouard 3795: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3796: }
3797:
1.69 brouard 3798: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3799: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3800: }
3801: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3802: }
3803: }
3804:
3805: /******/
3806:
3807: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3808: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3809: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3810: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3811: nhstepm = nhstepm/hstepm;
3812:
3813: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3814: oldm=oldms;savm=savms;
3815: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3816: for (h=0; h<=nhstepm; h++){
1.69 brouard 3817: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3818: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3819: }
3820: for(j=1; j<=nlstate+ndeath;j++) {
3821: kk1=0.;kk2=0;
3822: for(i=1; i<=nlstate;i++) {
3823: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3824: }
1.69 brouard 3825: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3826: }
3827: }
3828: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3829: }
3830: }
3831: }
3832: }
3833:
1.54 brouard 3834: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3835:
3836: if (popforecast==1) {
3837: free_ivector(popage,0,AGESUP);
3838: free_vector(popeffectif,0,AGESUP);
3839: free_vector(popcount,0,AGESUP);
3840: }
3841: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3842: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3843: fclose(ficrespop);
1.84 brouard 3844: } /* End of popforecast */
1.53 brouard 3845:
1.87 brouard 3846: int fileappend(FILE *fichier, char *optionfich)
1.86 brouard 3847: {
1.87 brouard 3848: if((fichier=fopen(optionfich,"a"))==NULL) {
3849: printf("Problem with file: %s\n", optionfich);
3850: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3851: return (0);
1.86 brouard 3852: }
1.87 brouard 3853: fflush(fichier);
3854: return (1);
1.86 brouard 3855: }
1.94 brouard 3856:
3857:
3858: /**************** function prwizard **********************/
1.88 brouard 3859: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3860: {
3861:
1.94 brouard 3862: /* Wizard to print covariance matrix template */
3863:
1.88 brouard 3864: char ca[32], cb[32], cc[32];
3865: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3866: int numlinepar;
3867:
3868: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3869: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3870: for(i=1; i <=nlstate; i++){
3871: jj=0;
3872: for(j=1; j <=nlstate+ndeath; j++){
3873: if(j==i) continue;
3874: jj++;
3875: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3876: printf("%1d%1d",i,j);
3877: fprintf(ficparo,"%1d%1d",i,j);
3878: for(k=1; k<=ncovmodel;k++){
3879: /* printf(" %lf",param[i][j][k]); */
3880: /* fprintf(ficparo," %lf",param[i][j][k]); */
3881: printf(" 0.");
3882: fprintf(ficparo," 0.");
3883: }
3884: printf("\n");
3885: fprintf(ficparo,"\n");
3886: }
3887: }
3888: printf("# Scales (for hessian or gradient estimation)\n");
3889: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3890: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3891: for(i=1; i <=nlstate; i++){
3892: jj=0;
3893: for(j=1; j <=nlstate+ndeath; j++){
3894: if(j==i) continue;
3895: jj++;
3896: fprintf(ficparo,"%1d%1d",i,j);
3897: printf("%1d%1d",i,j);
3898: fflush(stdout);
3899: for(k=1; k<=ncovmodel;k++){
3900: /* printf(" %le",delti3[i][j][k]); */
3901: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3902: printf(" 0.");
3903: fprintf(ficparo," 0.");
3904: }
3905: numlinepar++;
3906: printf("\n");
3907: fprintf(ficparo,"\n");
3908: }
3909: }
3910: printf("# Covariance matrix\n");
3911: /* # 121 Var(a12)\n\ */
3912: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3913: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3914: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3915: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3916: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3917: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3918: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3919: fflush(stdout);
3920: fprintf(ficparo,"# Covariance matrix\n");
3921: /* # 121 Var(a12)\n\ */
3922: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3923: /* # ...\n\ */
3924: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3925:
3926: for(itimes=1;itimes<=2;itimes++){
3927: jj=0;
3928: for(i=1; i <=nlstate; i++){
3929: for(j=1; j <=nlstate+ndeath; j++){
3930: if(j==i) continue;
3931: for(k=1; k<=ncovmodel;k++){
3932: jj++;
3933: ca[0]= k+'a'-1;ca[1]='\0';
3934: if(itimes==1){
3935: printf("#%1d%1d%d",i,j,k);
3936: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3937: }else{
3938: printf("%1d%1d%d",i,j,k);
3939: fprintf(ficparo,"%1d%1d%d",i,j,k);
3940: /* printf(" %.5le",matcov[i][j]); */
3941: }
3942: ll=0;
3943: for(li=1;li <=nlstate; li++){
3944: for(lj=1;lj <=nlstate+ndeath; lj++){
3945: if(lj==li) continue;
3946: for(lk=1;lk<=ncovmodel;lk++){
3947: ll++;
3948: if(ll<=jj){
3949: cb[0]= lk +'a'-1;cb[1]='\0';
3950: if(ll<jj){
3951: if(itimes==1){
3952: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3953: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3954: }else{
3955: printf(" 0.");
3956: fprintf(ficparo," 0.");
3957: }
3958: }else{
3959: if(itimes==1){
3960: printf(" Var(%s%1d%1d)",ca,i,j);
3961: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3962: }else{
3963: printf(" 0.");
3964: fprintf(ficparo," 0.");
3965: }
3966: }
3967: }
3968: } /* end lk */
3969: } /* end lj */
3970: } /* end li */
3971: printf("\n");
3972: fprintf(ficparo,"\n");
3973: numlinepar++;
3974: } /* end k*/
3975: } /*end j */
3976: } /* end i */
1.95 brouard 3977: } /* end itimes */
1.88 brouard 3978:
3979: } /* end of prwizard */
1.98 brouard 3980: /******************* Gompertz Likelihood ******************************/
3981: double gompertz(double x[])
3982: {
3983: double A,B,L=0.0,sump=0.,num=0.;
3984: int i,n=0; /* n is the size of the sample */
3985: for (i=0;i<=imx-1 ; i++) {
3986: sump=sump+weight[i];
1.103 lievre 3987: /* sump=sump+1;*/
1.98 brouard 3988: num=num+1;
3989: }
3990:
3991:
1.103 lievre 3992: /* for (i=0; i<=imx; i++)
1.98 brouard 3993: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
3994:
1.103 lievre 3995: for (i=1;i<=imx ; i++)
1.98 brouard 3996: {
3997: if (cens[i]==1 & wav[i]>1)
1.103 lievre 3998: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
1.98 brouard 3999:
4000: if (cens[i]==0 & wav[i]>1)
1.103 lievre 4001: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4002: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
1.98 brouard 4003:
4004: if (wav[i]>1 & agecens[i]>15) {
4005: L=L+A*weight[i];
4006: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
4007: }
4008: }
4009:
4010: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4011:
4012: return -2*L*num/sump;
4013: }
4014:
4015: /******************* Printing html file ***********/
4016: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4017: int lastpass, int stepm, int weightopt, char model[],\
1.105 lievre 4018: int imx, double p[],double **matcov,double agemortsup){
4019: int i,k;
1.98 brouard 4020:
4021: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4022: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4023: for (i=1;i<=2;i++)
4024: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4025: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4026: fprintf(fichtm,"</ul>");
1.105 lievre 4027:
4028: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4029:
1.106 brouard 4030: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
1.105 lievre 4031:
4032: for (k=agegomp;k<(agemortsup-2);k++)
4033: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4034:
4035:
1.98 brouard 4036: fflush(fichtm);
4037: }
4038:
4039: /******************* Gnuplot file **************/
4040: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4041:
4042: char dirfileres[132],optfileres[132];
4043: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4044: int ng;
4045:
4046:
4047: /*#ifdef windows */
4048: fprintf(ficgp,"cd \"%s\" \n",pathc);
4049: /*#endif */
4050:
4051:
4052: strcpy(dirfileres,optionfilefiname);
4053: strcpy(optfileres,"vpl");
4054: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4055: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4056: fprintf(ficgp, "set ter png small\n set log y\n");
4057: fprintf(ficgp, "set size 0.65,0.65\n");
4058: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4059:
4060: }
4061:
4062:
1.88 brouard 4063:
1.91 brouard 4064:
1.53 brouard 4065: /***********************************************/
4066: /**************** Main Program *****************/
4067: /***********************************************/
4068:
4069: int main(int argc, char *argv[])
4070: {
1.61 brouard 4071: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 4072: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.95 brouard 4073: int jj, ll, li, lj, lk, imk;
1.85 brouard 4074: int numlinepar=0; /* Current linenumber of parameter file */
1.95 brouard 4075: int itimes;
1.98 brouard 4076: int NDIM=2;
1.95 brouard 4077:
4078: char ca[32], cb[32], cc[32];
1.87 brouard 4079: /* FILE *fichtm; *//* Html File */
4080: /* FILE *ficgp;*/ /*Gnuplot File */
1.107 ! brouard 4081: struct stat info;
1.53 brouard 4082: double agedeb, agefin,hf;
4083: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4084:
4085: double fret;
4086: double **xi,tmp,delta;
4087:
4088: double dum; /* Dummy variable */
4089: double ***p3mat;
4090: double ***mobaverage;
4091: int *indx;
4092: char line[MAXLINE], linepar[MAXLINE];
1.88 brouard 4093: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
1.99 brouard 4094: char pathr[MAXLINE], pathimach[MAXLINE];
1.53 brouard 4095: int firstobs=1, lastobs=10;
4096: int sdeb, sfin; /* Status at beginning and end */
4097: int c, h , cpt,l;
4098: int ju,jl, mi;
4099: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 4100: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 4101: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 4102: int mobilav=0,popforecast=0;
4103: int hstepm, nhstepm;
1.105 lievre 4104: int agemortsup;
4105: float sumlpop=0.;
1.74 brouard 4106: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4107: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 4108:
4109: double bage, fage, age, agelim, agebase;
4110: double ftolpl=FTOL;
4111: double **prlim;
4112: double *severity;
4113: double ***param; /* Matrix of parameters */
4114: double *p;
4115: double **matcov; /* Matrix of covariance */
4116: double ***delti3; /* Scale */
4117: double *delti; /* Scale */
4118: double ***eij, ***vareij;
4119: double **varpl; /* Variances of prevalence limits by age */
4120: double *epj, vepp;
4121: double kk1, kk2;
1.74 brouard 4122: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.98 brouard 4123: double **ximort;
1.53 brouard 4124: char *alph[]={"a","a","b","c","d","e"}, str[4];
1.98 brouard 4125: int *dcwave;
1.53 brouard 4126:
4127: char z[1]="c", occ;
1.86 brouard 4128:
1.53 brouard 4129: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.88 brouard 4130: char strstart[80], *strt, strtend[80];
1.85 brouard 4131: char *stratrunc;
4132: int lstra;
4133:
4134: long total_usecs;
1.53 brouard 4135:
1.95 brouard 4136: /* setlocale (LC_ALL, ""); */
4137: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4138: /* textdomain (PACKAGE); */
4139: /* setlocale (LC_CTYPE, ""); */
4140: /* setlocale (LC_MESSAGES, ""); */
4141:
1.85 brouard 4142: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4143: (void) gettimeofday(&start_time,&tzp);
1.91 brouard 4144: curr_time=start_time;
1.85 brouard 4145: tm = *localtime(&start_time.tv_sec);
4146: tmg = *gmtime(&start_time.tv_sec);
1.88 brouard 4147: strcpy(strstart,asctime(&tm));
1.86 brouard 4148:
1.88 brouard 4149: /* printf("Localtime (at start)=%s",strstart); */
1.85 brouard 4150: /* tp.tv_sec = tp.tv_sec +86400; */
4151: /* tm = *localtime(&start_time.tv_sec); */
4152: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4153: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4154: /* tmg.tm_hour=tmg.tm_hour + 1; */
4155: /* tp.tv_sec = mktime(&tmg); */
4156: /* strt=asctime(&tmg); */
1.88 brouard 4157: /* printf("Time(after) =%s",strstart); */
1.85 brouard 4158: /* (void) time (&time_value);
4159: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4160: * tm = *localtime(&time_value);
1.88 brouard 4161: * strstart=asctime(&tm);
4162: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
1.85 brouard 4163: */
4164:
1.91 brouard 4165: nberr=0; /* Number of errors and warnings */
4166: nbwarn=0;
1.53 brouard 4167: getcwd(pathcd, size);
4168:
1.81 brouard 4169: printf("\n%s\n%s",version,fullversion);
1.53 brouard 4170: if(argc <=1){
4171: printf("\nEnter the parameter file name: ");
4172: scanf("%s",pathtot);
4173: }
4174: else{
4175: strcpy(pathtot,argv[1]);
4176: }
1.88 brouard 4177: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 4178: /*cygwin_split_path(pathtot,path,optionfile);
4179: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4180: /* cutv(path,optionfile,pathtot,'\\');*/
4181:
1.107 ! brouard 4182: /* Split argv[0], imach program to get pathimach */
! 4183: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
1.99 brouard 4184: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.107 ! brouard 4185: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
1.99 brouard 4186: /* strcpy(pathimach,argv[0]); */
1.107 ! brouard 4187: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
1.53 brouard 4188: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.107 ! brouard 4189: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 4190: chdir(path);
1.88 brouard 4191: strcpy(command,"mkdir ");
4192: strcat(command,optionfilefiname);
4193: if((outcmd=system(command)) != 0){
4194: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4195: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4196: /* fclose(ficlog); */
4197: /* exit(1); */
4198: }
4199: /* if((imk=mkdir(optionfilefiname))<0){ */
4200: /* perror("mkdir"); */
4201: /* } */
1.53 brouard 4202:
1.59 brouard 4203: /*-------- arguments in the command line --------*/
1.53 brouard 4204:
4205: /* Log file */
4206: strcat(filelog, optionfilefiname);
4207: strcat(filelog,".log"); /* */
4208: if((ficlog=fopen(filelog,"w"))==NULL) {
4209: printf("Problem with logfile %s\n",filelog);
4210: goto end;
4211: }
4212: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 4213: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.99 brouard 4214: fprintf(ficlog,"\nEnter the parameter file name: \n");
4215: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
1.88 brouard 4216: path=%s \n\
4217: optionfile=%s\n\
4218: optionfilext=%s\n\
1.99 brouard 4219: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 brouard 4220:
1.94 brouard 4221: printf("Local time (at start):%s",strstart);
4222: fprintf(ficlog,"Local time (at start): %s",strstart);
1.53 brouard 4223: fflush(ficlog);
1.91 brouard 4224: /* (void) gettimeofday(&curr_time,&tzp); */
4225: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
1.53 brouard 4226:
4227: /* */
4228: strcpy(fileres,"r");
4229: strcat(fileres, optionfilefiname);
4230: strcat(fileres,".txt"); /* Other files have txt extension */
4231:
4232: /*---------arguments file --------*/
4233:
4234: if((ficpar=fopen(optionfile,"r"))==NULL) {
4235: printf("Problem with optionfile %s\n",optionfile);
4236: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 4237: fflush(ficlog);
1.53 brouard 4238: goto end;
4239: }
4240:
1.88 brouard 4241:
4242:
1.53 brouard 4243: strcpy(filereso,"o");
4244: strcat(filereso,fileres);
1.88 brouard 4245: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
1.53 brouard 4246: printf("Problem with Output resultfile: %s\n", filereso);
4247: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 4248: fflush(ficlog);
1.53 brouard 4249: goto end;
4250: }
4251:
4252: /* Reads comments: lines beginning with '#' */
1.85 brouard 4253: numlinepar=0;
1.53 brouard 4254: while((c=getc(ficpar))=='#' && c!= EOF){
4255: ungetc(c,ficpar);
4256: fgets(line, MAXLINE, ficpar);
1.85 brouard 4257: numlinepar++;
1.53 brouard 4258: puts(line);
4259: fputs(line,ficparo);
1.85 brouard 4260: fputs(line,ficlog);
1.53 brouard 4261: }
4262: ungetc(c,ficpar);
4263:
4264: 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 4265: numlinepar++;
1.53 brouard 4266: 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);
4267: 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 4268: 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);
4269: fflush(ficlog);
1.59 brouard 4270: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4271: ungetc(c,ficpar);
4272: fgets(line, MAXLINE, ficpar);
1.85 brouard 4273: numlinepar++;
1.53 brouard 4274: puts(line);
4275: fputs(line,ficparo);
1.85 brouard 4276: fputs(line,ficlog);
1.53 brouard 4277: }
4278: ungetc(c,ficpar);
1.85 brouard 4279:
1.53 brouard 4280:
4281: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 4282: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 4283: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4284:
1.58 lievre 4285: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 4286: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.98 brouard 4287: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4288:
4289: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4290: delti=delti3[1][1];
4291: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
1.88 brouard 4292: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4293: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4294: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4295: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.98 brouard 4296: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.88 brouard 4297: fclose (ficparo);
4298: fclose (ficlog);
4299: exit(0);
4300: }
1.98 brouard 4301: else if(mle==-3) {
4302: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4303: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4304: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4305: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4306: matcov=matrix(1,npar,1,npar);
1.53 brouard 4307: }
1.98 brouard 4308: else{
4309: /* Read guess parameters */
4310: /* Reads comments: lines beginning with '#' */
4311: while((c=getc(ficpar))=='#' && c!= EOF){
4312: ungetc(c,ficpar);
4313: fgets(line, MAXLINE, ficpar);
1.85 brouard 4314: numlinepar++;
1.98 brouard 4315: puts(line);
4316: fputs(line,ficparo);
4317: fputs(line,ficlog);
1.53 brouard 4318: }
1.98 brouard 4319: ungetc(c,ficpar);
4320:
4321: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4322: for(i=1; i <=nlstate; i++){
4323: j=0;
4324: for(jj=1; jj <=nlstate+ndeath; jj++){
4325: if(jj==i) continue;
4326: j++;
4327: fscanf(ficpar,"%1d%1d",&i1,&j1);
4328: if ((i1 != i) && (j1 != j)){
4329: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4330: exit(1);
4331: }
4332: fprintf(ficparo,"%1d%1d",i1,j1);
4333: if(mle==1)
4334: printf("%1d%1d",i,j);
4335: fprintf(ficlog,"%1d%1d",i,j);
4336: for(k=1; k<=ncovmodel;k++){
4337: fscanf(ficpar," %lf",¶m[i][j][k]);
4338: if(mle==1){
4339: printf(" %lf",param[i][j][k]);
4340: fprintf(ficlog," %lf",param[i][j][k]);
4341: }
4342: else
4343: fprintf(ficlog," %lf",param[i][j][k]);
4344: fprintf(ficparo," %lf",param[i][j][k]);
4345: }
4346: fscanf(ficpar,"\n");
4347: numlinepar++;
4348: if(mle==1)
4349: printf("\n");
4350: fprintf(ficlog,"\n");
4351: fprintf(ficparo,"\n");
4352: }
4353: }
4354: fflush(ficlog);
1.85 brouard 4355:
1.53 brouard 4356:
1.98 brouard 4357: p=param[1][1];
4358:
4359: /* Reads comments: lines beginning with '#' */
4360: while((c=getc(ficpar))=='#' && c!= EOF){
4361: ungetc(c,ficpar);
4362: fgets(line, MAXLINE, ficpar);
4363: numlinepar++;
4364: puts(line);
4365: fputs(line,ficparo);
4366: fputs(line,ficlog);
4367: }
1.53 brouard 4368: ungetc(c,ficpar);
4369:
1.98 brouard 4370: for(i=1; i <=nlstate; i++){
4371: for(j=1; j <=nlstate+ndeath-1; j++){
4372: fscanf(ficpar,"%1d%1d",&i1,&j1);
4373: if ((i1-i)*(j1-j)!=0){
4374: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4375: exit(1);
4376: }
4377: printf("%1d%1d",i,j);
4378: fprintf(ficparo,"%1d%1d",i1,j1);
4379: fprintf(ficlog,"%1d%1d",i1,j1);
4380: for(k=1; k<=ncovmodel;k++){
4381: fscanf(ficpar,"%le",&delti3[i][j][k]);
4382: printf(" %le",delti3[i][j][k]);
4383: fprintf(ficparo," %le",delti3[i][j][k]);
4384: fprintf(ficlog," %le",delti3[i][j][k]);
4385: }
4386: fscanf(ficpar,"\n");
4387: numlinepar++;
4388: printf("\n");
4389: fprintf(ficparo,"\n");
4390: fprintf(ficlog,"\n");
1.85 brouard 4391: }
1.53 brouard 4392: }
1.98 brouard 4393: fflush(ficlog);
1.85 brouard 4394:
1.98 brouard 4395: delti=delti3[1][1];
1.74 brouard 4396:
4397:
1.98 brouard 4398: /* 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 4399:
1.98 brouard 4400: /* Reads comments: lines beginning with '#' */
4401: while((c=getc(ficpar))=='#' && c!= EOF){
4402: ungetc(c,ficpar);
4403: fgets(line, MAXLINE, ficpar);
4404: numlinepar++;
4405: puts(line);
4406: fputs(line,ficparo);
4407: fputs(line,ficlog);
4408: }
1.53 brouard 4409: ungetc(c,ficpar);
4410:
1.98 brouard 4411: matcov=matrix(1,npar,1,npar);
4412: for(i=1; i <=npar; i++){
4413: fscanf(ficpar,"%s",&str);
4414: if(mle==1)
4415: printf("%s",str);
4416: fprintf(ficlog,"%s",str);
4417: fprintf(ficparo,"%s",str);
4418: for(j=1; j <=i; j++){
4419: fscanf(ficpar," %le",&matcov[i][j]);
4420: if(mle==1){
4421: printf(" %.5le",matcov[i][j]);
4422: }
4423: fprintf(ficlog," %.5le",matcov[i][j]);
4424: fprintf(ficparo," %.5le",matcov[i][j]);
1.53 brouard 4425: }
1.98 brouard 4426: fscanf(ficpar,"\n");
4427: numlinepar++;
4428: if(mle==1)
4429: printf("\n");
4430: fprintf(ficlog,"\n");
4431: fprintf(ficparo,"\n");
1.53 brouard 4432: }
1.98 brouard 4433: for(i=1; i <=npar; i++)
4434: for(j=i+1;j<=npar;j++)
4435: matcov[i][j]=matcov[j][i];
4436:
1.53 brouard 4437: if(mle==1)
4438: printf("\n");
4439: fprintf(ficlog,"\n");
1.98 brouard 4440:
4441: fflush(ficlog);
4442:
4443: /*-------- Rewriting parameter file ----------*/
4444: strcpy(rfileres,"r"); /* "Rparameterfile */
4445: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4446: strcat(rfileres,"."); /* */
4447: strcat(rfileres,optionfilext); /* Other files have txt extension */
4448: if((ficres =fopen(rfileres,"w"))==NULL) {
4449: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4450: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4451: }
4452: fprintf(ficres,"#%s\n",version);
4453: } /* End of mle != -3 */
1.53 brouard 4454:
1.59 brouard 4455: /*-------- data file ----------*/
4456: if((fic=fopen(datafile,"r"))==NULL) {
4457: printf("Problem with datafile: %s\n", datafile);goto end;
4458: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4459: }
4460:
4461: n= lastobs;
4462: severity = vector(1,maxwav);
4463: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 4464: num=lvector(1,n);
1.59 brouard 4465: moisnais=vector(1,n);
4466: annais=vector(1,n);
4467: moisdc=vector(1,n);
4468: andc=vector(1,n);
4469: agedc=vector(1,n);
4470: cod=ivector(1,n);
4471: weight=vector(1,n);
4472: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4473: mint=matrix(1,maxwav,1,n);
4474: anint=matrix(1,maxwav,1,n);
4475: s=imatrix(1,maxwav+1,1,n);
4476: tab=ivector(1,NCOVMAX);
4477: ncodemax=ivector(1,8);
4478:
4479: i=1;
4480: while (fgets(line, MAXLINE, fic) != NULL) {
4481: if ((i >= firstobs) && (i <=lastobs)) {
1.102 brouard 4482: for(j=0; line[j] != '\n';j++){ /* Untabifies line */
4483: if(line[j] == '\t')
4484: line[j] = ' ';
4485: }
1.59 brouard 4486: for (j=maxwav;j>=1;j--){
4487: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4488: strcpy(line,stra);
4489: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4490: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4491: }
1.53 brouard 4492:
1.59 brouard 4493: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4494: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4495:
1.59 brouard 4496: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4497: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 4498:
1.59 brouard 4499: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4500: for (j=ncovcol;j>=1;j--){
4501: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4502: }
1.85 brouard 4503: lstra=strlen(stra);
4504: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4505: stratrunc = &(stra[lstra-9]);
4506: num[i]=atol(stratrunc);
4507: }
4508: else
4509: num[i]=atol(stra);
1.53 brouard 4510:
1.59 brouard 4511: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4512: 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 4513:
1.59 brouard 4514: i=i+1;
4515: }
4516: }
4517: /* printf("ii=%d", ij);
4518: scanf("%d",i);*/
1.53 brouard 4519: imx=i-1; /* Number of individuals */
4520:
4521: /* for (i=1; i<=imx; i++){
4522: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4523: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4524: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4525: }*/
4526: /* for (i=1; i<=imx; i++){
4527: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4528: 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 4529:
1.106 brouard 4530: /* for (i=1; i<=imx; i++) */
1.53 brouard 4531:
1.71 brouard 4532: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4533: else weight[i]=1;*/
4534:
1.106 brouard 4535: /* Calculation of the number of parameters from char model */
1.53 brouard 4536: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4537: Tprod=ivector(1,15);
4538: Tvaraff=ivector(1,15);
4539: Tvard=imatrix(1,15,1,2);
4540: Tage=ivector(1,15);
4541:
1.58 lievre 4542: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4543: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4544: j=nbocc(model,'+'); /* j=Number of '+' */
4545: j1=nbocc(model,'*'); /* j1=Number of '*' */
4546: cptcovn=j+1;
4547: cptcovprod=j1; /*Number of products */
1.53 brouard 4548:
4549: strcpy(modelsav,model);
4550: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4551: printf("Error. Non available option model=%s ",model);
4552: fprintf(ficlog,"Error. Non available option model=%s ",model);
4553: goto end;
4554: }
4555:
1.59 brouard 4556: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4557:
1.53 brouard 4558: for(i=(j+1); i>=1;i--){
4559: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4560: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4561: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4562: /*scanf("%d",i);*/
4563: if (strchr(strb,'*')) { /* Model includes a product */
4564: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4565: if (strcmp(strc,"age")==0) { /* Vn*age */
4566: cptcovprod--;
4567: cutv(strb,stre,strd,'V');
4568: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4569: cptcovage++;
4570: Tage[cptcovage]=i;
4571: /*printf("stre=%s ", stre);*/
4572: }
4573: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4574: cptcovprod--;
4575: cutv(strb,stre,strc,'V');
4576: Tvar[i]=atoi(stre);
4577: cptcovage++;
4578: Tage[cptcovage]=i;
4579: }
4580: else { /* Age is not in the model */
4581: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4582: Tvar[i]=ncovcol+k1;
4583: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4584: Tprod[k1]=i;
4585: Tvard[k1][1]=atoi(strc); /* m*/
4586: Tvard[k1][2]=atoi(stre); /* n */
4587: Tvar[cptcovn+k2]=Tvard[k1][1];
4588: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4589: for (k=1; k<=lastobs;k++)
4590: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4591: k1++;
4592: k2=k2+2;
4593: }
4594: }
4595: else { /* no more sum */
4596: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4597: /* scanf("%d",i);*/
4598: cutv(strd,strc,strb,'V');
4599: Tvar[i]=atoi(strc);
4600: }
4601: strcpy(modelsav,stra);
4602: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4603: scanf("%d",i);*/
4604: } /* end of loop + */
4605: } /* end model */
4606:
1.58 lievre 4607: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4608: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4609:
1.53 brouard 4610: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4611: printf("cptcovprod=%d ", cptcovprod);
4612: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4613:
4614: scanf("%d ",i);
4615: fclose(fic);*/
1.53 brouard 4616:
4617: /* if(mle==1){*/
1.59 brouard 4618: if (weightopt != 1) { /* Maximisation without weights*/
4619: for(i=1;i<=n;i++) weight[i]=1.0;
4620: }
1.53 brouard 4621: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4622: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4623:
1.59 brouard 4624: for (i=1; i<=imx; i++) {
4625: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4626: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4627: anint[m][i]=9999;
4628: s[m][i]=-1;
4629: }
1.76 brouard 4630: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.91 brouard 4631: nberr++;
1.85 brouard 4632: 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);
4633: 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 4634: s[m][i]=-1;
4635: }
4636: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.91 brouard 4637: nberr++;
1.85 brouard 4638: 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]);
4639: 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 4640: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4641: }
1.53 brouard 4642: }
1.59 brouard 4643: }
1.53 brouard 4644:
1.59 brouard 4645: for (i=1; i<=imx; i++) {
4646: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4647: for(m=firstpass; (m<= lastpass); m++){
1.105 lievre 4648: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
1.59 brouard 4649: if (s[m][i] >= nlstate+1) {
4650: if(agedc[i]>0)
1.76 brouard 4651: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4652: agev[m][i]=agedc[i];
1.59 brouard 4653: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4654: else {
1.76 brouard 4655: if ((int)andc[i]!=9999){
1.91 brouard 4656: nbwarn++;
1.85 brouard 4657: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4658: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4659: agev[m][i]=-1;
1.53 brouard 4660: }
4661: }
1.70 brouard 4662: }
1.69 brouard 4663: else if(s[m][i] !=9){ /* Standard case, age in fractional
4664: years but with the precision of a
4665: month */
1.59 brouard 4666: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4667: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4668: agev[m][i]=1;
4669: else if(agev[m][i] <agemin){
4670: agemin=agev[m][i];
4671: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4672: }
1.59 brouard 4673: else if(agev[m][i] >agemax){
4674: agemax=agev[m][i];
4675: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4676: }
1.59 brouard 4677: /*agev[m][i]=anint[m][i]-annais[i];*/
4678: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4679: }
1.59 brouard 4680: else { /* =9 */
1.53 brouard 4681: agev[m][i]=1;
1.59 brouard 4682: s[m][i]=-1;
4683: }
1.53 brouard 4684: }
1.59 brouard 4685: else /*= 0 Unknown */
4686: agev[m][i]=1;
4687: }
1.53 brouard 4688:
1.59 brouard 4689: }
4690: for (i=1; i<=imx; i++) {
1.71 brouard 4691: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4692: if (s[m][i] > (nlstate+ndeath)) {
1.91 brouard 4693: nberr++;
1.59 brouard 4694: 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);
4695: 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);
4696: goto end;
1.53 brouard 4697: }
4698: }
1.59 brouard 4699: }
1.53 brouard 4700:
1.71 brouard 4701: /*for (i=1; i<=imx; i++){
4702: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4703: 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 4704: }
4705:
4706: }*/
4707:
1.97 lievre 4708:
1.59 brouard 4709: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4710: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4711:
1.98 brouard 4712: agegomp=(int)agemin;
1.59 brouard 4713: free_vector(severity,1,maxwav);
4714: free_imatrix(outcome,1,maxwav+1,1,n);
4715: free_vector(moisnais,1,n);
4716: free_vector(annais,1,n);
4717: /* free_matrix(mint,1,maxwav,1,n);
4718: free_matrix(anint,1,maxwav,1,n);*/
4719: free_vector(moisdc,1,n);
4720: free_vector(andc,1,n);
1.53 brouard 4721:
4722:
1.59 brouard 4723: wav=ivector(1,imx);
4724: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4725: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4726: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4727:
1.59 brouard 4728: /* Concatenates waves */
4729: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4730:
1.59 brouard 4731: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4732:
1.59 brouard 4733: Tcode=ivector(1,100);
4734: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4735: ncodemax[1]=1;
4736: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4737:
1.59 brouard 4738: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4739: the estimations*/
4740: h=0;
4741: m=pow(2,cptcoveff);
1.53 brouard 4742:
1.59 brouard 4743: for(k=1;k<=cptcoveff; k++){
4744: for(i=1; i <=(m/pow(2,k));i++){
4745: for(j=1; j <= ncodemax[k]; j++){
4746: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4747: h++;
4748: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4749: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4750: }
4751: }
4752: }
4753: }
4754: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4755: codtab[1][2]=1;codtab[2][2]=2; */
4756: /* for(i=1; i <=m ;i++){
4757: for(k=1; k <=cptcovn; k++){
4758: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4759: }
4760: printf("\n");
1.53 brouard 4761: }
1.59 brouard 4762: scanf("%d",i);*/
1.53 brouard 4763:
1.86 brouard 4764: /*------------ gnuplot -------------*/
4765: strcpy(optionfilegnuplot,optionfilefiname);
1.98 brouard 4766: if(mle==-3)
4767: strcat(optionfilegnuplot,"-mort");
1.86 brouard 4768: strcat(optionfilegnuplot,".gp");
1.98 brouard 4769:
1.86 brouard 4770: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4771: printf("Problem with file %s",optionfilegnuplot);
4772: }
4773: else{
4774: fprintf(ficgp,"\n# %s\n", version);
4775: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4776: fprintf(ficgp,"set missing 'NaNq'\n");
4777: }
1.88 brouard 4778: /* fclose(ficgp);*/
1.86 brouard 4779: /*--------- index.htm --------*/
4780:
1.91 brouard 4781: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
1.98 brouard 4782: if(mle==-3)
4783: strcat(optionfilehtm,"-mort");
1.86 brouard 4784: strcat(optionfilehtm,".htm");
4785: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4786: printf("Problem with %s \n",optionfilehtm), exit(0);
4787: }
4788:
1.91 brouard 4789: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4790: strcat(optionfilehtmcov,"-cov.htm");
4791: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4792: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4793: }
4794: else{
4795: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4796: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4797: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4798: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4799: }
4800:
1.87 brouard 4801: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
1.86 brouard 4802: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4803: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4804: \n\
4805: <hr size=\"2\" color=\"#EC5E5E\">\
4806: <ul><li><h4>Parameter files</h4>\n\
4807: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4808: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
1.87 brouard 4809: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
1.86 brouard 4810: - Date and time at start: %s</ul>\n",\
1.91 brouard 4811: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4812: fileres,fileres,\
1.88 brouard 4813: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
1.87 brouard 4814: fflush(fichtm);
1.86 brouard 4815:
1.88 brouard 4816: strcpy(pathr,path);
4817: strcat(pathr,optionfilefiname);
4818: chdir(optionfilefiname); /* Move to directory named optionfile */
4819:
1.59 brouard 4820: /* Calculates basic frequencies. Computes observed prevalence at single age
4821: and prints on file fileres'p'. */
1.105 lievre 4822: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
1.53 brouard 4823:
1.88 brouard 4824: fprintf(fichtm,"\n");
4825: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
1.86 brouard 4826: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4827: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.88 brouard 4828: imx,agemin,agemax,jmin,jmax,jmean);
4829: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.60 brouard 4830: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4831: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4832: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4833: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4834:
4835:
1.59 brouard 4836: /* For Powell, parameters are in a vector p[] starting at p[1]
4837: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4838: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4839:
1.86 brouard 4840: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.98 brouard 4841: if (mle==-3){
4842: ximort=matrix(1,NDIM,1,NDIM);
4843: cens=ivector(1,n);
4844: ageexmed=vector(1,n);
4845: agecens=vector(1,n);
4846: dcwave=ivector(1,n);
4847:
4848: for (i=1; i<=imx; i++){
4849: dcwave[i]=-1;
4850: for (j=1; j<=lastpass; j++)
4851: if (s[j][i]>nlstate) {
4852: dcwave[i]=j;
4853: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4854: break;
4855: }
4856: }
4857:
4858: for (i=1; i<=imx; i++) {
4859: if (wav[i]>0){
4860: ageexmed[i]=agev[mw[1][i]][i];
4861: j=wav[i];agecens[i]=1.;
4862: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4863: cens[i]=1;
4864:
4865: if (ageexmed[i]<1) cens[i]=-1;
4866: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4867: }
4868: else cens[i]=-1;
4869: }
4870:
4871: for (i=1;i<=NDIM;i++) {
4872: for (j=1;j<=NDIM;j++)
4873: ximort[i][j]=(i == j ? 1.0 : 0.0);
4874: }
4875:
4876: p[1]=0.1; p[2]=0.1;
4877: /*printf("%lf %lf", p[1], p[2]);*/
4878:
4879:
4880: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4881: strcpy(filerespow,"pow-mort");
4882: strcat(filerespow,fileres);
4883: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4884: printf("Problem with resultfile: %s\n", filerespow);
4885: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1.59 brouard 4886: }
1.98 brouard 4887: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4888: /* for (i=1;i<=nlstate;i++)
4889: for(j=1;j<=nlstate+ndeath;j++)
4890: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4891: */
4892: fprintf(ficrespow,"\n");
4893:
4894: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4895: fclose(ficrespow);
1.53 brouard 4896:
1.98 brouard 4897: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
1.53 brouard 4898:
1.98 brouard 4899: for(i=1; i <=NDIM; i++)
4900: for(j=i+1;j<=NDIM;j++)
4901: matcov[i][j]=matcov[j][i];
4902:
4903: printf("\nCovariance matrix\n ");
4904: for(i=1; i <=NDIM; i++) {
4905: for(j=1;j<=NDIM;j++){
4906: printf("%f ",matcov[i][j]);
1.95 brouard 4907: }
1.98 brouard 4908: printf("\n ");
4909: }
4910:
4911: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4912: for (i=1;i<=NDIM;i++)
4913: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.105 lievre 4914:
4915: lsurv=vector(1,AGESUP);
4916: lpop=vector(1,AGESUP);
4917: tpop=vector(1,AGESUP);
4918: lsurv[agegomp]=100000;
4919:
4920: for (k=agegomp;k<=AGESUP;k++) {
4921: agemortsup=k;
4922: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
4923: }
4924:
4925: for (k=agegomp;k<agemortsup;k++)
4926: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
4927:
4928: for (k=agegomp;k<agemortsup;k++){
4929: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
4930: sumlpop=sumlpop+lpop[k];
4931: }
4932:
4933: tpop[agegomp]=sumlpop;
4934: for (k=agegomp;k<(agemortsup-3);k++){
4935: /* tpop[k+1]=2;*/
4936: tpop[k+1]=tpop[k]-lpop[k];
4937: }
4938:
4939:
4940: printf("\nAge lx qx dx Lx Tx e(x)\n");
4941: for (k=agegomp;k<(agemortsup-2);k++)
4942: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4943:
4944:
1.98 brouard 4945: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4946: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4947:
4948: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4949: stepm, weightopt,\
1.105 lievre 4950: model,imx,p,matcov,agemortsup);
4951:
4952: free_vector(lsurv,1,AGESUP);
4953: free_vector(lpop,1,AGESUP);
4954: free_vector(tpop,1,AGESUP);
1.98 brouard 4955: } /* Endof if mle==-3 */
4956:
4957: else{ /* For mle >=1 */
4958:
4959: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4960: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4961: for (k=1; k<=npar;k++)
4962: printf(" %d %8.5f",k,p[k]);
4963: printf("\n");
4964: globpr=1; /* to print the contributions */
4965: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4966: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4967: for (k=1; k<=npar;k++)
4968: printf(" %d %8.5f",k,p[k]);
4969: printf("\n");
4970: if(mle>=1){ /* Could be 1 or 2 */
4971: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4972: }
1.98 brouard 4973:
4974: /*--------- results files --------------*/
4975: 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);
4976:
4977:
4978: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4979: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4980: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4981: for(i=1,jk=1; i <=nlstate; i++){
4982: for(k=1; k <=(nlstate+ndeath); k++){
4983: if (k != i) {
4984: printf("%d%d ",i,k);
4985: fprintf(ficlog,"%d%d ",i,k);
4986: fprintf(ficres,"%1d%1d ",i,k);
4987: for(j=1; j <=ncovmodel; j++){
4988: printf("%f ",p[jk]);
4989: fprintf(ficlog,"%f ",p[jk]);
4990: fprintf(ficres,"%f ",p[jk]);
4991: jk++;
4992: }
4993: printf("\n");
4994: fprintf(ficlog,"\n");
4995: fprintf(ficres,"\n");
1.59 brouard 4996: }
4997: }
4998: }
1.98 brouard 4999: if(mle!=0){
5000: /* Computing hessian and covariance matrix */
5001: ftolhess=ftol; /* Usually correct */
5002: hesscov(matcov, p, npar, delti, ftolhess, func);
5003: }
5004: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5005: printf("# Scales (for hessian or gradient estimation)\n");
5006: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5007: for(i=1,jk=1; i <=nlstate; i++){
1.95 brouard 5008: for(j=1; j <=nlstate+ndeath; j++){
1.98 brouard 5009: if (j!=i) {
5010: fprintf(ficres,"%1d%1d",i,j);
5011: printf("%1d%1d",i,j);
5012: fprintf(ficlog,"%1d%1d",i,j);
5013: for(k=1; k<=ncovmodel;k++){
5014: printf(" %.5e",delti[jk]);
5015: fprintf(ficlog," %.5e",delti[jk]);
5016: fprintf(ficres," %.5e",delti[jk]);
5017: jk++;
1.95 brouard 5018: }
1.98 brouard 5019: printf("\n");
5020: fprintf(ficlog,"\n");
5021: fprintf(ficres,"\n");
5022: }
5023: }
5024: }
5025:
5026: 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");
5027: if(mle>=1)
5028: 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");
5029: 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");
5030: /* # 121 Var(a12)\n\ */
5031: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5032: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5033: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5034: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5035: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5036: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5037: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5038:
5039:
5040: /* Just to have a covariance matrix which will be more understandable
5041: even is we still don't want to manage dictionary of variables
5042: */
5043: for(itimes=1;itimes<=2;itimes++){
5044: jj=0;
5045: for(i=1; i <=nlstate; i++){
5046: for(j=1; j <=nlstate+ndeath; j++){
5047: if(j==i) continue;
5048: for(k=1; k<=ncovmodel;k++){
5049: jj++;
5050: ca[0]= k+'a'-1;ca[1]='\0';
5051: if(itimes==1){
5052: if(mle>=1)
5053: printf("#%1d%1d%d",i,j,k);
5054: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5055: fprintf(ficres,"#%1d%1d%d",i,j,k);
5056: }else{
5057: if(mle>=1)
5058: printf("%1d%1d%d",i,j,k);
5059: fprintf(ficlog,"%1d%1d%d",i,j,k);
5060: fprintf(ficres,"%1d%1d%d",i,j,k);
5061: }
5062: ll=0;
5063: for(li=1;li <=nlstate; li++){
5064: for(lj=1;lj <=nlstate+ndeath; lj++){
5065: if(lj==li) continue;
5066: for(lk=1;lk<=ncovmodel;lk++){
5067: ll++;
5068: if(ll<=jj){
5069: cb[0]= lk +'a'-1;cb[1]='\0';
5070: if(ll<jj){
5071: if(itimes==1){
5072: if(mle>=1)
5073: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5074: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5075: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5076: }else{
5077: if(mle>=1)
5078: printf(" %.5e",matcov[jj][ll]);
5079: fprintf(ficlog," %.5e",matcov[jj][ll]);
5080: fprintf(ficres," %.5e",matcov[jj][ll]);
5081: }
1.95 brouard 5082: }else{
1.98 brouard 5083: if(itimes==1){
5084: if(mle>=1)
5085: printf(" Var(%s%1d%1d)",ca,i,j);
5086: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5087: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5088: }else{
5089: if(mle>=1)
5090: printf(" %.5e",matcov[jj][ll]);
5091: fprintf(ficlog," %.5e",matcov[jj][ll]);
5092: fprintf(ficres," %.5e",matcov[jj][ll]);
5093: }
1.95 brouard 5094: }
5095: }
1.98 brouard 5096: } /* end lk */
5097: } /* end lj */
5098: } /* end li */
5099: if(mle>=1)
5100: printf("\n");
5101: fprintf(ficlog,"\n");
5102: fprintf(ficres,"\n");
5103: numlinepar++;
5104: } /* end k*/
5105: } /*end j */
5106: } /* end i */
5107: } /* end itimes */
5108:
5109: fflush(ficlog);
5110: fflush(ficres);
5111:
5112: while((c=getc(ficpar))=='#' && c!= EOF){
5113: ungetc(c,ficpar);
5114: fgets(line, MAXLINE, ficpar);
5115: puts(line);
5116: fputs(line,ficparo);
5117: }
1.59 brouard 5118: ungetc(c,ficpar);
1.98 brouard 5119:
5120: estepm=0;
5121: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5122: if (estepm==0 || estepm < stepm) estepm=stepm;
5123: if (fage <= 2) {
5124: bage = ageminpar;
5125: fage = agemaxpar;
5126: }
5127:
5128: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5129: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5130: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5131:
5132: while((c=getc(ficpar))=='#' && c!= EOF){
5133: ungetc(c,ficpar);
5134: fgets(line, MAXLINE, ficpar);
5135: puts(line);
5136: fputs(line,ficparo);
5137: }
1.59 brouard 5138: ungetc(c,ficpar);
1.98 brouard 5139:
5140: 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);
5141: 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);
5142: 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);
5143: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5144: 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);
5145:
5146: while((c=getc(ficpar))=='#' && c!= EOF){
5147: ungetc(c,ficpar);
5148: fgets(line, MAXLINE, ficpar);
5149: puts(line);
5150: fputs(line,ficparo);
5151: }
1.59 brouard 5152: ungetc(c,ficpar);
1.98 brouard 5153:
5154:
5155: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5156: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5157:
5158: fscanf(ficpar,"pop_based=%d\n",&popbased);
5159: fprintf(ficparo,"pop_based=%d\n",popbased);
5160: fprintf(ficres,"pop_based=%d\n",popbased);
5161:
5162: while((c=getc(ficpar))=='#' && c!= EOF){
5163: ungetc(c,ficpar);
5164: fgets(line, MAXLINE, ficpar);
5165: puts(line);
5166: fputs(line,ficparo);
5167: }
1.53 brouard 5168: ungetc(c,ficpar);
1.98 brouard 5169:
5170: 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);
5171: 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);
5172: 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);
5173: 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);
5174: 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);
5175: /* day and month of proj2 are not used but only year anproj2.*/
5176:
5177:
5178:
5179: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5180: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5181:
5182: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5183: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5184:
5185: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5186: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5187: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5188:
5189: /*------------ free_vector -------------*/
5190: /* chdir(path); */
1.53 brouard 5191:
1.98 brouard 5192: free_ivector(wav,1,imx);
5193: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5194: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5195: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5196: free_lvector(num,1,n);
5197: free_vector(agedc,1,n);
5198: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5199: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5200: fclose(ficparo);
5201: fclose(ficres);
5202:
5203:
5204: /*--------------- Prevalence limit (stable prevalence) --------------*/
5205:
5206: strcpy(filerespl,"pl");
5207: strcat(filerespl,fileres);
5208: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5209: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5210: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5211: }
5212: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5213: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
1.105 lievre 5214: fprintf(ficrespl, "#Local time at start: %s", strstart);
1.98 brouard 5215: fprintf(ficrespl,"#Stable prevalence \n");
5216: fprintf(ficrespl,"#Age ");
5217: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5218: fprintf(ficrespl,"\n");
5219:
5220: prlim=matrix(1,nlstate,1,nlstate);
5221:
5222: agebase=ageminpar;
5223: agelim=agemaxpar;
5224: ftolpl=1.e-10;
5225: i1=cptcoveff;
5226: if (cptcovn < 1){i1=1;}
5227:
5228: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5229: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5230: k=k+1;
5231: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5232: fprintf(ficrespl,"\n#******");
5233: printf("\n#******");
5234: fprintf(ficlog,"\n#******");
5235: for(j=1;j<=cptcoveff;j++) {
5236: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5237: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5238: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5239: }
5240: fprintf(ficrespl,"******\n");
5241: printf("******\n");
5242: fprintf(ficlog,"******\n");
1.53 brouard 5243:
1.98 brouard 5244: for (age=agebase; age<=agelim; age++){
5245: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5246: fprintf(ficrespl,"%.0f ",age );
5247: for(j=1;j<=cptcoveff;j++)
5248: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5249: for(i=1; i<=nlstate;i++)
5250: fprintf(ficrespl," %.5f", prlim[i][i]);
5251: fprintf(ficrespl,"\n");
5252: }
1.53 brouard 5253: }
5254: }
1.98 brouard 5255: fclose(ficrespl);
1.53 brouard 5256:
1.98 brouard 5257: /*------------- h Pij x at various ages ------------*/
1.53 brouard 5258:
1.98 brouard 5259: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5260: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5261: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5262: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5263: }
5264: printf("Computing pij: result on file '%s' \n", filerespij);
5265: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
1.53 brouard 5266:
1.98 brouard 5267: stepsize=(int) (stepm+YEARM-1)/YEARM;
5268: /*if (stepm<=24) stepsize=2;*/
1.53 brouard 5269:
1.98 brouard 5270: agelim=AGESUP;
5271: hstepm=stepsize*YEARM; /* Every year of age */
5272: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.53 brouard 5273:
1.98 brouard 5274: /* hstepm=1; aff par mois*/
1.105 lievre 5275: fprintf(ficrespij, "#Local time at start: %s", strstart);
1.98 brouard 5276: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5277: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5278: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5279: k=k+1;
5280: fprintf(ficrespij,"\n#****** ");
5281: for(j=1;j<=cptcoveff;j++)
5282: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5283: fprintf(ficrespij,"******\n");
1.53 brouard 5284:
1.98 brouard 5285: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5286: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5287: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
1.59 brouard 5288:
1.98 brouard 5289: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.59 brouard 5290:
1.98 brouard 5291: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5292: oldm=oldms;savm=savms;
5293: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5294: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.53 brouard 5295: for(i=1; i<=nlstate;i++)
5296: for(j=1; j<=nlstate+ndeath;j++)
1.98 brouard 5297: fprintf(ficrespij," %1d-%1d",i,j);
5298: fprintf(ficrespij,"\n");
5299: for (h=0; h<=nhstepm; h++){
5300: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5301: for(i=1; i<=nlstate;i++)
5302: for(j=1; j<=nlstate+ndeath;j++)
5303: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5304: fprintf(ficrespij,"\n");
5305: }
5306: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.53 brouard 5307: fprintf(ficrespij,"\n");
5308: }
1.59 brouard 5309: }
1.53 brouard 5310: }
5311:
1.105 lievre 5312: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.53 brouard 5313:
1.98 brouard 5314: fclose(ficrespij);
1.53 brouard 5315:
1.98 brouard 5316: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5317: for(i=1;i<=AGESUP;i++)
5318: for(j=1;j<=NCOVMAX;j++)
5319: for(k=1;k<=NCOVMAX;k++)
5320: probs[i][j][k]=0.;
5321:
5322: /*---------- Forecasting ------------------*/
5323: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5324: if(prevfcast==1){
5325: /* if(stepm ==1){*/
1.70 brouard 5326: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 5327: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
1.98 brouard 5328: /* } */
5329: /* else{ */
5330: /* erreur=108; */
5331: /* 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); */
5332: /* 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); */
5333: /* } */
5334: }
1.53 brouard 5335:
5336:
1.98 brouard 5337: /*---------- Health expectancies and variances ------------*/
1.53 brouard 5338:
1.98 brouard 5339: strcpy(filerest,"t");
5340: strcat(filerest,fileres);
5341: if((ficrest=fopen(filerest,"w"))==NULL) {
5342: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5343: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5344: }
5345: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5346: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
1.53 brouard 5347:
5348:
1.98 brouard 5349: strcpy(filerese,"e");
5350: strcat(filerese,fileres);
5351: if((ficreseij=fopen(filerese,"w"))==NULL) {
5352: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5353: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5354: }
5355: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5356: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 5357:
1.98 brouard 5358: strcpy(fileresv,"v");
5359: strcat(fileresv,fileres);
5360: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5361: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5362: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5363: }
5364: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5365: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 5366:
1.98 brouard 5367: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5368: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5369: /* 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",\
5370: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5371: */
1.58 lievre 5372:
1.98 brouard 5373: if (mobilav!=0) {
5374: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5375: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5376: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5377: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5378: }
1.54 brouard 5379: }
1.53 brouard 5380:
1.98 brouard 5381: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5382: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5383: k=k+1;
5384: fprintf(ficrest,"\n#****** ");
5385: for(j=1;j<=cptcoveff;j++)
5386: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5387: fprintf(ficrest,"******\n");
5388:
5389: fprintf(ficreseij,"\n#****** ");
5390: for(j=1;j<=cptcoveff;j++)
5391: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5392: fprintf(ficreseij,"******\n");
5393:
5394: fprintf(ficresvij,"\n#****** ");
5395: for(j=1;j<=cptcoveff;j++)
5396: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5397: fprintf(ficresvij,"******\n");
5398:
5399: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5400: oldm=oldms;savm=savms;
1.105 lievre 5401: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.53 brouard 5402:
1.98 brouard 5403: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5404: oldm=oldms;savm=savms;
1.105 lievre 5405: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
1.98 brouard 5406: if(popbased==1){
1.105 lievre 5407: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
1.98 brouard 5408: }
1.53 brouard 5409:
1.105 lievre 5410: fprintf(ficrest, "#Local time at start: %s", strstart);
1.98 brouard 5411: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5412: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5413: fprintf(ficrest,"\n");
5414:
5415: epj=vector(1,nlstate+1);
5416: for(age=bage; age <=fage ;age++){
5417: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5418: if (popbased==1) {
5419: if(mobilav ==0){
5420: for(i=1; i<=nlstate;i++)
5421: prlim[i][i]=probs[(int)age][i][k];
5422: }else{ /* mobilav */
5423: for(i=1; i<=nlstate;i++)
5424: prlim[i][i]=mobaverage[(int)age][i][k];
5425: }
1.53 brouard 5426: }
5427:
1.98 brouard 5428: fprintf(ficrest," %4.0f",age);
5429: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5430: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5431: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5432: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5433: }
5434: epj[nlstate+1] +=epj[j];
1.53 brouard 5435: }
5436:
1.98 brouard 5437: for(i=1, vepp=0.;i <=nlstate;i++)
5438: for(j=1;j <=nlstate;j++)
5439: vepp += vareij[i][j][(int)age];
5440: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5441: for(j=1;j <=nlstate;j++){
5442: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5443: }
5444: fprintf(ficrest,"\n");
1.53 brouard 5445: }
1.98 brouard 5446: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5447: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5448: free_vector(epj,1,nlstate+1);
5449: }
5450: }
5451: free_vector(weight,1,n);
5452: free_imatrix(Tvard,1,15,1,2);
5453: free_imatrix(s,1,maxwav+1,1,n);
5454: free_matrix(anint,1,maxwav,1,n);
5455: free_matrix(mint,1,maxwav,1,n);
5456: free_ivector(cod,1,n);
5457: free_ivector(tab,1,NCOVMAX);
5458: fclose(ficreseij);
5459: fclose(ficresvij);
5460: fclose(ficrest);
5461: fclose(ficpar);
5462:
5463: /*------- Variance of stable prevalence------*/
5464:
5465: strcpy(fileresvpl,"vpl");
5466: strcat(fileresvpl,fileres);
5467: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5468: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5469: exit(0);
5470: }
5471: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5472:
5473: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5474: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5475: k=k+1;
5476: fprintf(ficresvpl,"\n#****** ");
5477: for(j=1;j<=cptcoveff;j++)
5478: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5479: fprintf(ficresvpl,"******\n");
5480:
5481: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5482: oldm=oldms;savm=savms;
1.105 lievre 5483: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
1.98 brouard 5484: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 5485: }
1.98 brouard 5486: }
1.53 brouard 5487:
1.98 brouard 5488: fclose(ficresvpl);
1.53 brouard 5489:
1.98 brouard 5490: /*---------- End : free ----------------*/
5491: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5492: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5493:
5494: } /* mle==-3 arrives here for freeing */
5495: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5496: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5497: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5498: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5499:
5500: free_matrix(covar,0,NCOVMAX,1,n);
5501: free_matrix(matcov,1,npar,1,npar);
5502: /*free_vector(delti,1,npar);*/
5503: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5504: free_matrix(agev,1,maxwav,1,imx);
5505: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5506:
5507: free_ivector(ncodemax,1,8);
5508: free_ivector(Tvar,1,15);
5509: free_ivector(Tprod,1,15);
5510: free_ivector(Tvaraff,1,15);
5511: free_ivector(Tage,1,15);
5512: free_ivector(Tcode,1,100);
1.74 brouard 5513:
1.53 brouard 5514:
1.88 brouard 5515: fflush(fichtm);
5516: fflush(ficgp);
1.53 brouard 5517:
5518:
1.91 brouard 5519: if((nberr >0) || (nbwarn>0)){
1.95 brouard 5520: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
1.91 brouard 5521: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
1.53 brouard 5522: }else{
1.91 brouard 5523: printf("End of Imach\n");
5524: fprintf(ficlog,"End of Imach\n");
1.53 brouard 5525: }
5526: printf("See log file on %s\n",filelog);
5527: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 5528: (void) gettimeofday(&end_time,&tzp);
5529: tm = *localtime(&end_time.tv_sec);
5530: tmg = *gmtime(&end_time.tv_sec);
1.88 brouard 5531: strcpy(strtend,asctime(&tm));
1.105 lievre 5532: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
1.94 brouard 5533: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.91 brouard 5534: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.85 brouard 5535:
1.91 brouard 5536: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5537: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5538: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.85 brouard 5539: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.87 brouard 5540: /* if(fileappend(fichtm,optionfilehtm)){ */
1.88 brouard 5541: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
1.87 brouard 5542: fclose(fichtm);
1.91 brouard 5543: fclose(fichtmcov);
1.88 brouard 5544: fclose(ficgp);
1.91 brouard 5545: fclose(ficlog);
1.53 brouard 5546: /*------ End -----------*/
5547:
1.88 brouard 5548: chdir(path);
1.107 ! brouard 5549: #ifndef UNIX
1.99 brouard 5550: strcpy(plotcmd,"\"");
1.107 ! brouard 5551: #endif
1.99 brouard 5552: strcat(plotcmd,pathimach);
1.107 ! brouard 5553: /*strcat(plotcmd,CHARSEPARATOR);*/
1.99 brouard 5554: strcat(plotcmd,GNUPLOTPROGRAM);
1.107 ! brouard 5555: #ifndef UNIX
1.99 brouard 5556: strcat(plotcmd,"\"");
1.107 ! brouard 5557: #endif
! 5558: if(stat(plotcmd,&info)){
! 5559: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
! 5560: }
1.59 brouard 5561: strcat(plotcmd," ");
5562: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 5563: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.107 ! brouard 5564:
1.91 brouard 5565: if((outcmd=system(plotcmd)) != 0){
5566: printf(" Problem with gnuplot\n");
5567: }
1.75 brouard 5568: printf(" Wait...");
1.53 brouard 5569: while (z[0] != 'q') {
5570: /* chdir(path); */
1.91 brouard 5571: printf("\nType e to edit output files, g to graph again and q for exiting: ");
1.53 brouard 5572: scanf("%s",z);
1.91 brouard 5573: /* if (z[0] == 'c') system("./imach"); */
1.99 brouard 5574: if (z[0] == 'e') {
5575: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5576: system(optionfilehtm);
5577: }
1.53 brouard 5578: else if (z[0] == 'g') system(plotcmd);
5579: else if (z[0] == 'q') exit(0);
5580: }
1.91 brouard 5581: end:
5582: while (z[0] != 'q') {
5583: printf("\nType q for exiting: ");
5584: scanf("%s",z);
5585: }
1.53 brouard 5586: }
1.88 brouard 5587:
1.53 brouard 5588:
5589:
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