1: /* $Id: imach.c,v 1.119 2006/03/15 17:42:26 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.119 2006/03/15 17:42:26 brouard
5: (Module): Bug if status = -2, the loglikelihood was
6: computed as likelihood omitting the logarithm. Version O.98e
7:
8: Revision 1.118 2006/03/14 18:20:07 brouard
9: (Module): varevsij Comments added explaining the second
10: table of variances if popbased=1 .
11: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
12: (Module): Function pstamp added
13: (Module): Version 0.98d
14:
15: Revision 1.117 2006/03/14 17:16:22 brouard
16: (Module): varevsij Comments added explaining the second
17: table of variances if popbased=1 .
18: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
19: (Module): Function pstamp added
20: (Module): Version 0.98d
21:
22: Revision 1.116 2006/03/06 10:29:27 brouard
23: (Module): Variance-covariance wrong links and
24: varian-covariance of ej. is needed (Saito).
25:
26: Revision 1.115 2006/02/27 12:17:45 brouard
27: (Module): One freematrix added in mlikeli! 0.98c
28:
29: Revision 1.114 2006/02/26 12:57:58 brouard
30: (Module): Some improvements in processing parameter
31: filename with strsep.
32:
33: Revision 1.113 2006/02/24 14:20:24 brouard
34: (Module): Memory leaks checks with valgrind and:
35: datafile was not closed, some imatrix were not freed and on matrix
36: allocation too.
37:
38: Revision 1.112 2006/01/30 09:55:26 brouard
39: (Module): Back to gnuplot.exe instead of wgnuplot.exe
40:
41: Revision 1.111 2006/01/25 20:38:18 brouard
42: (Module): Lots of cleaning and bugs added (Gompertz)
43: (Module): Comments can be added in data file. Missing date values
44: can be a simple dot '.'.
45:
46: Revision 1.110 2006/01/25 00:51:50 brouard
47: (Module): Lots of cleaning and bugs added (Gompertz)
48:
49: Revision 1.109 2006/01/24 19:37:15 brouard
50: (Module): Comments (lines starting with a #) are allowed in data.
51:
52: Revision 1.108 2006/01/19 18:05:42 lievre
53: Gnuplot problem appeared...
54: To be fixed
55:
56: Revision 1.107 2006/01/19 16:20:37 brouard
57: Test existence of gnuplot in imach path
58:
59: Revision 1.106 2006/01/19 13:24:36 brouard
60: Some cleaning and links added in html output
61:
62: Revision 1.105 2006/01/05 20:23:19 lievre
63: *** empty log message ***
64:
65: Revision 1.104 2005/09/30 16:11:43 lievre
66: (Module): sump fixed, loop imx fixed, and simplifications.
67: (Module): If the status is missing at the last wave but we know
68: that the person is alive, then we can code his/her status as -2
69: (instead of missing=-1 in earlier versions) and his/her
70: contributions to the likelihood is 1 - Prob of dying from last
71: health status (= 1-p13= p11+p12 in the easiest case of somebody in
72: the healthy state at last known wave). Version is 0.98
73:
74: Revision 1.103 2005/09/30 15:54:49 lievre
75: (Module): sump fixed, loop imx fixed, and simplifications.
76:
77: Revision 1.102 2004/09/15 17:31:30 brouard
78: Add the possibility to read data file including tab characters.
79:
80: Revision 1.101 2004/09/15 10:38:38 brouard
81: Fix on curr_time
82:
83: Revision 1.100 2004/07/12 18:29:06 brouard
84: Add version for Mac OS X. Just define UNIX in Makefile
85:
86: Revision 1.99 2004/06/05 08:57:40 brouard
87: *** empty log message ***
88:
89: Revision 1.98 2004/05/16 15:05:56 brouard
90: New version 0.97 . First attempt to estimate force of mortality
91: directly from the data i.e. without the need of knowing the health
92: state at each age, but using a Gompertz model: log u =a + b*age .
93: This is the basic analysis of mortality and should be done before any
94: other analysis, in order to test if the mortality estimated from the
95: cross-longitudinal survey is different from the mortality estimated
96: from other sources like vital statistic data.
97:
98: The same imach parameter file can be used but the option for mle should be -3.
99:
100: Agnès, who wrote this part of the code, tried to keep most of the
101: former routines in order to include the new code within the former code.
102:
103: The output is very simple: only an estimate of the intercept and of
104: the slope with 95% confident intervals.
105:
106: Current limitations:
107: A) Even if you enter covariates, i.e. with the
108: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
109: B) There is no computation of Life Expectancy nor Life Table.
110:
111: Revision 1.97 2004/02/20 13:25:42 lievre
112: Version 0.96d. Population forecasting command line is (temporarily)
113: suppressed.
114:
115: Revision 1.96 2003/07/15 15:38:55 brouard
116: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
117: rewritten within the same printf. Workaround: many printfs.
118:
119: Revision 1.95 2003/07/08 07:54:34 brouard
120: * imach.c (Repository):
121: (Repository): Using imachwizard code to output a more meaningful covariance
122: matrix (cov(a12,c31) instead of numbers.
123:
124: Revision 1.94 2003/06/27 13:00:02 brouard
125: Just cleaning
126:
127: Revision 1.93 2003/06/25 16:33:55 brouard
128: (Module): On windows (cygwin) function asctime_r doesn't
129: exist so I changed back to asctime which exists.
130: (Module): Version 0.96b
131:
132: Revision 1.92 2003/06/25 16:30:45 brouard
133: (Module): On windows (cygwin) function asctime_r doesn't
134: exist so I changed back to asctime which exists.
135:
136: Revision 1.91 2003/06/25 15:30:29 brouard
137: * imach.c (Repository): Duplicated warning errors corrected.
138: (Repository): Elapsed time after each iteration is now output. It
139: helps to forecast when convergence will be reached. Elapsed time
140: is stamped in powell. We created a new html file for the graphs
141: concerning matrix of covariance. It has extension -cov.htm.
142:
143: Revision 1.90 2003/06/24 12:34:15 brouard
144: (Module): Some bugs corrected for windows. Also, when
145: mle=-1 a template is output in file "or"mypar.txt with the design
146: of the covariance matrix to be input.
147:
148: Revision 1.89 2003/06/24 12:30:52 brouard
149: (Module): Some bugs corrected for windows. Also, when
150: mle=-1 a template is output in file "or"mypar.txt with the design
151: of the covariance matrix to be input.
152:
153: Revision 1.88 2003/06/23 17:54:56 brouard
154: * 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.
155:
156: Revision 1.87 2003/06/18 12:26:01 brouard
157: Version 0.96
158:
159: Revision 1.86 2003/06/17 20:04:08 brouard
160: (Module): Change position of html and gnuplot routines and added
161: routine fileappend.
162:
163: Revision 1.85 2003/06/17 13:12:43 brouard
164: * imach.c (Repository): Check when date of death was earlier that
165: current date of interview. It may happen when the death was just
166: prior to the death. In this case, dh was negative and likelihood
167: was wrong (infinity). We still send an "Error" but patch by
168: assuming that the date of death was just one stepm after the
169: interview.
170: (Repository): Because some people have very long ID (first column)
171: we changed int to long in num[] and we added a new lvector for
172: memory allocation. But we also truncated to 8 characters (left
173: truncation)
174: (Repository): No more line truncation errors.
175:
176: Revision 1.84 2003/06/13 21:44:43 brouard
177: * imach.c (Repository): Replace "freqsummary" at a correct
178: place. It differs from routine "prevalence" which may be called
179: many times. Probs is memory consuming and must be used with
180: parcimony.
181: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
182:
183: Revision 1.83 2003/06/10 13:39:11 lievre
184: *** empty log message ***
185:
186: Revision 1.82 2003/06/05 15:57:20 brouard
187: Add log in imach.c and fullversion number is now printed.
188:
189: */
190: /*
191: Interpolated Markov Chain
192:
193: Short summary of the programme:
194:
195: This program computes Healthy Life Expectancies from
196: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
197: first survey ("cross") where individuals from different ages are
198: interviewed on their health status or degree of disability (in the
199: case of a health survey which is our main interest) -2- at least a
200: second wave of interviews ("longitudinal") which measure each change
201: (if any) in individual health status. Health expectancies are
202: computed from the time spent in each health state according to a
203: model. More health states you consider, more time is necessary to reach the
204: Maximum Likelihood of the parameters involved in the model. The
205: simplest model is the multinomial logistic model where pij is the
206: probability to be observed in state j at the second wave
207: conditional to be observed in state i at the first wave. Therefore
208: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
209: 'age' is age and 'sex' is a covariate. If you want to have a more
210: complex model than "constant and age", you should modify the program
211: where the markup *Covariates have to be included here again* invites
212: you to do it. More covariates you add, slower the
213: convergence.
214:
215: The advantage of this computer programme, compared to a simple
216: multinomial logistic model, is clear when the delay between waves is not
217: identical for each individual. Also, if a individual missed an
218: intermediate interview, the information is lost, but taken into
219: account using an interpolation or extrapolation.
220:
221: hPijx is the probability to be observed in state i at age x+h
222: conditional to the observed state i at age x. The delay 'h' can be
223: split into an exact number (nh*stepm) of unobserved intermediate
224: states. This elementary transition (by month, quarter,
225: semester or year) is modelled as a multinomial logistic. The hPx
226: matrix is simply the matrix product of nh*stepm elementary matrices
227: and the contribution of each individual to the likelihood is simply
228: hPijx.
229:
230: Also this programme outputs the covariance matrix of the parameters but also
231: of the life expectancies. It also computes the period (stable) prevalence.
232:
233: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
234: Institut national d'études démographiques, Paris.
235: This software have been partly granted by Euro-REVES, a concerted action
236: from the European Union.
237: It is copyrighted identically to a GNU software product, ie programme and
238: software can be distributed freely for non commercial use. Latest version
239: can be accessed at http://euroreves.ined.fr/imach .
240:
241: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
242: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
243:
244: **********************************************************************/
245: /*
246: main
247: read parameterfile
248: read datafile
249: concatwav
250: freqsummary
251: if (mle >= 1)
252: mlikeli
253: print results files
254: if mle==1
255: computes hessian
256: read end of parameter file: agemin, agemax, bage, fage, estepm
257: begin-prev-date,...
258: open gnuplot file
259: open html file
260: period (stable) prevalence
261: for age prevalim()
262: h Pij x
263: variance of p varprob
264: forecasting if prevfcast==1 prevforecast call prevalence()
265: health expectancies
266: Variance-covariance of DFLE
267: prevalence()
268: movingaverage()
269: varevsij()
270: if popbased==1 varevsij(,popbased)
271: total life expectancies
272: Variance of period (stable) prevalence
273: end
274: */
275:
276:
277:
278:
279: #include <math.h>
280: #include <stdio.h>
281: #include <stdlib.h>
282: #include <string.h>
283: #include <unistd.h>
284:
285: #include <limits.h>
286: #include <sys/types.h>
287: #include <sys/stat.h>
288: #include <errno.h>
289: extern int errno;
290:
291: /* #include <sys/time.h> */
292: #include <time.h>
293: #include "timeval.h"
294:
295: /* #include <libintl.h> */
296: /* #define _(String) gettext (String) */
297:
298: #define MAXLINE 256
299:
300: #define GNUPLOTPROGRAM "gnuplot"
301: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
302: #define FILENAMELENGTH 132
303:
304: #define GLOCK_ERROR_NOPATH -1 /* empty path */
305: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
306:
307: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
308: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
309:
310: #define NINTERVMAX 8
311: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
312: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
313: #define NCOVMAX 8 /* Maximum number of covariates */
314: #define MAXN 20000
315: #define YEARM 12. /* Number of months per year */
316: #define AGESUP 130
317: #define AGEBASE 40
318: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
319: #ifdef UNIX
320: #define DIRSEPARATOR '/'
321: #define CHARSEPARATOR "/"
322: #define ODIRSEPARATOR '\\'
323: #else
324: #define DIRSEPARATOR '\\'
325: #define CHARSEPARATOR "\\"
326: #define ODIRSEPARATOR '/'
327: #endif
328:
329: /* $Id: imach.c,v 1.119 2006/03/15 17:42:26 brouard Exp $ */
330: /* $State: Exp $ */
331:
332: char version[]="Imach version 0.98e, March 2006, INED-EUROREVES-Institut de longevite ";
333: char fullversion[]="$Revision: 1.119 $ $Date: 2006/03/15 17:42:26 $";
334: char strstart[80];
335: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
336: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
337: int nvar;
338: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
339: int npar=NPARMAX;
340: int nlstate=2; /* Number of live states */
341: int ndeath=1; /* Number of dead states */
342: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
343: int popbased=0;
344:
345: int *wav; /* Number of waves for this individuual 0 is possible */
346: int maxwav; /* Maxim number of waves */
347: int jmin, jmax; /* min, max spacing between 2 waves */
348: int ijmin, ijmax; /* Individuals having jmin and jmax */
349: int gipmx, gsw; /* Global variables on the number of contributions
350: to the likelihood and the sum of weights (done by funcone)*/
351: int mle, weightopt;
352: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
353: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
354: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
355: * wave mi and wave mi+1 is not an exact multiple of stepm. */
356: double jmean; /* Mean space between 2 waves */
357: double **oldm, **newm, **savm; /* Working pointers to matrices */
358: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
359: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
360: FILE *ficlog, *ficrespow;
361: int globpr; /* Global variable for printing or not */
362: double fretone; /* Only one call to likelihood */
363: long ipmx; /* Number of contributions */
364: double sw; /* Sum of weights */
365: char filerespow[FILENAMELENGTH];
366: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
367: FILE *ficresilk;
368: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
369: FILE *ficresprobmorprev;
370: FILE *fichtm, *fichtmcov; /* Html File */
371: FILE *ficreseij;
372: char filerese[FILENAMELENGTH];
373: FILE *ficresstdeij;
374: char fileresstde[FILENAMELENGTH];
375: FILE *ficrescveij;
376: char filerescve[FILENAMELENGTH];
377: FILE *ficresvij;
378: char fileresv[FILENAMELENGTH];
379: FILE *ficresvpl;
380: char fileresvpl[FILENAMELENGTH];
381: char title[MAXLINE];
382: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
383: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
384: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
385: char command[FILENAMELENGTH];
386: int outcmd=0;
387:
388: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
389:
390: char filelog[FILENAMELENGTH]; /* Log file */
391: char filerest[FILENAMELENGTH];
392: char fileregp[FILENAMELENGTH];
393: char popfile[FILENAMELENGTH];
394:
395: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
396:
397: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
398: struct timezone tzp;
399: extern int gettimeofday();
400: struct tm tmg, tm, tmf, *gmtime(), *localtime();
401: long time_value;
402: extern long time();
403: char strcurr[80], strfor[80];
404:
405: char *endptr;
406: long lval;
407:
408: #define NR_END 1
409: #define FREE_ARG char*
410: #define FTOL 1.0e-10
411:
412: #define NRANSI
413: #define ITMAX 200
414:
415: #define TOL 2.0e-4
416:
417: #define CGOLD 0.3819660
418: #define ZEPS 1.0e-10
419: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
420:
421: #define GOLD 1.618034
422: #define GLIMIT 100.0
423: #define TINY 1.0e-20
424:
425: static double maxarg1,maxarg2;
426: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
427: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
428:
429: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
430: #define rint(a) floor(a+0.5)
431:
432: static double sqrarg;
433: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
434: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
435: int agegomp= AGEGOMP;
436:
437: int imx;
438: int stepm=1;
439: /* Stepm, step in month: minimum step interpolation*/
440:
441: int estepm;
442: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
443:
444: int m,nb;
445: long *num;
446: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
447: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
448: double **pmmij, ***probs;
449: double *ageexmed,*agecens;
450: double dateintmean=0;
451:
452: double *weight;
453: int **s; /* Status */
454: double *agedc, **covar, idx;
455: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
456: double *lsurv, *lpop, *tpop;
457:
458: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
459: double ftolhess; /* Tolerance for computing hessian */
460:
461: /**************** split *************************/
462: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
463: {
464: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
465: the name of the file (name), its extension only (ext) and its first part of the name (finame)
466: */
467: char *ss; /* pointer */
468: int l1, l2; /* length counters */
469:
470: l1 = strlen(path ); /* length of path */
471: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
472: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
473: if ( ss == NULL ) { /* no directory, so determine current directory */
474: strcpy( name, path ); /* we got the fullname name because no directory */
475: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
476: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
477: /* get current working directory */
478: /* extern char* getcwd ( char *buf , int len);*/
479: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
480: return( GLOCK_ERROR_GETCWD );
481: }
482: /* got dirc from getcwd*/
483: printf(" DIRC = %s \n",dirc);
484: } else { /* strip direcotry from path */
485: ss++; /* after this, the filename */
486: l2 = strlen( ss ); /* length of filename */
487: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
488: strcpy( name, ss ); /* save file name */
489: strncpy( dirc, path, l1 - l2 ); /* now the directory */
490: dirc[l1-l2] = 0; /* add zero */
491: printf(" DIRC2 = %s \n",dirc);
492: }
493: /* We add a separator at the end of dirc if not exists */
494: l1 = strlen( dirc ); /* length of directory */
495: if( dirc[l1-1] != DIRSEPARATOR ){
496: dirc[l1] = DIRSEPARATOR;
497: dirc[l1+1] = 0;
498: printf(" DIRC3 = %s \n",dirc);
499: }
500: ss = strrchr( name, '.' ); /* find last / */
501: if (ss >0){
502: ss++;
503: strcpy(ext,ss); /* save extension */
504: l1= strlen( name);
505: l2= strlen(ss)+1;
506: strncpy( finame, name, l1-l2);
507: finame[l1-l2]= 0;
508: }
509:
510: return( 0 ); /* we're done */
511: }
512:
513:
514: /******************************************/
515:
516: void replace_back_to_slash(char *s, char*t)
517: {
518: int i;
519: int lg=0;
520: i=0;
521: lg=strlen(t);
522: for(i=0; i<= lg; i++) {
523: (s[i] = t[i]);
524: if (t[i]== '\\') s[i]='/';
525: }
526: }
527:
528: int nbocc(char *s, char occ)
529: {
530: int i,j=0;
531: int lg=20;
532: i=0;
533: lg=strlen(s);
534: for(i=0; i<= lg; i++) {
535: if (s[i] == occ ) j++;
536: }
537: return j;
538: }
539:
540: void cutv(char *u,char *v, char*t, char occ)
541: {
542: /* cuts string t into u and v where u ends before first occurence of char 'occ'
543: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
544: gives u="abcedf" and v="ghi2j" */
545: int i,lg,j,p=0;
546: i=0;
547: for(j=0; j<=strlen(t)-1; j++) {
548: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
549: }
550:
551: lg=strlen(t);
552: for(j=0; j<p; j++) {
553: (u[j] = t[j]);
554: }
555: u[p]='\0';
556:
557: for(j=0; j<= lg; j++) {
558: if (j>=(p+1))(v[j-p-1] = t[j]);
559: }
560: }
561:
562: /********************** nrerror ********************/
563:
564: void nrerror(char error_text[])
565: {
566: fprintf(stderr,"ERREUR ...\n");
567: fprintf(stderr,"%s\n",error_text);
568: exit(EXIT_FAILURE);
569: }
570: /*********************** vector *******************/
571: double *vector(int nl, int nh)
572: {
573: double *v;
574: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
575: if (!v) nrerror("allocation failure in vector");
576: return v-nl+NR_END;
577: }
578:
579: /************************ free vector ******************/
580: void free_vector(double*v, int nl, int nh)
581: {
582: free((FREE_ARG)(v+nl-NR_END));
583: }
584:
585: /************************ivector *******************************/
586: int *ivector(long nl,long nh)
587: {
588: int *v;
589: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
590: if (!v) nrerror("allocation failure in ivector");
591: return v-nl+NR_END;
592: }
593:
594: /******************free ivector **************************/
595: void free_ivector(int *v, long nl, long nh)
596: {
597: free((FREE_ARG)(v+nl-NR_END));
598: }
599:
600: /************************lvector *******************************/
601: long *lvector(long nl,long nh)
602: {
603: long *v;
604: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
605: if (!v) nrerror("allocation failure in ivector");
606: return v-nl+NR_END;
607: }
608:
609: /******************free lvector **************************/
610: void free_lvector(long *v, long nl, long nh)
611: {
612: free((FREE_ARG)(v+nl-NR_END));
613: }
614:
615: /******************* imatrix *******************************/
616: int **imatrix(long nrl, long nrh, long ncl, long nch)
617: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
618: {
619: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
620: int **m;
621:
622: /* allocate pointers to rows */
623: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
624: if (!m) nrerror("allocation failure 1 in matrix()");
625: m += NR_END;
626: m -= nrl;
627:
628:
629: /* allocate rows and set pointers to them */
630: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
631: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
632: m[nrl] += NR_END;
633: m[nrl] -= ncl;
634:
635: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
636:
637: /* return pointer to array of pointers to rows */
638: return m;
639: }
640:
641: /****************** free_imatrix *************************/
642: void free_imatrix(m,nrl,nrh,ncl,nch)
643: int **m;
644: long nch,ncl,nrh,nrl;
645: /* free an int matrix allocated by imatrix() */
646: {
647: free((FREE_ARG) (m[nrl]+ncl-NR_END));
648: free((FREE_ARG) (m+nrl-NR_END));
649: }
650:
651: /******************* matrix *******************************/
652: double **matrix(long nrl, long nrh, long ncl, long nch)
653: {
654: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
655: double **m;
656:
657: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
658: if (!m) nrerror("allocation failure 1 in matrix()");
659: m += NR_END;
660: m -= nrl;
661:
662: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
663: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
664: m[nrl] += NR_END;
665: m[nrl] -= ncl;
666:
667: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
668: return m;
669: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
670: */
671: }
672:
673: /*************************free matrix ************************/
674: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
675: {
676: free((FREE_ARG)(m[nrl]+ncl-NR_END));
677: free((FREE_ARG)(m+nrl-NR_END));
678: }
679:
680: /******************* ma3x *******************************/
681: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
682: {
683: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
684: double ***m;
685:
686: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
687: if (!m) nrerror("allocation failure 1 in matrix()");
688: m += NR_END;
689: m -= nrl;
690:
691: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
692: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
693: m[nrl] += NR_END;
694: m[nrl] -= ncl;
695:
696: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
697:
698: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
699: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
700: m[nrl][ncl] += NR_END;
701: m[nrl][ncl] -= nll;
702: for (j=ncl+1; j<=nch; j++)
703: m[nrl][j]=m[nrl][j-1]+nlay;
704:
705: for (i=nrl+1; i<=nrh; i++) {
706: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
707: for (j=ncl+1; j<=nch; j++)
708: m[i][j]=m[i][j-1]+nlay;
709: }
710: return m;
711: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
712: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
713: */
714: }
715:
716: /*************************free ma3x ************************/
717: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
718: {
719: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
720: free((FREE_ARG)(m[nrl]+ncl-NR_END));
721: free((FREE_ARG)(m+nrl-NR_END));
722: }
723:
724: /*************** function subdirf ***********/
725: char *subdirf(char fileres[])
726: {
727: /* Caution optionfilefiname is hidden */
728: strcpy(tmpout,optionfilefiname);
729: strcat(tmpout,"/"); /* Add to the right */
730: strcat(tmpout,fileres);
731: return tmpout;
732: }
733:
734: /*************** function subdirf2 ***********/
735: char *subdirf2(char fileres[], char *preop)
736: {
737:
738: /* Caution optionfilefiname is hidden */
739: strcpy(tmpout,optionfilefiname);
740: strcat(tmpout,"/");
741: strcat(tmpout,preop);
742: strcat(tmpout,fileres);
743: return tmpout;
744: }
745:
746: /*************** function subdirf3 ***********/
747: char *subdirf3(char fileres[], char *preop, char *preop2)
748: {
749:
750: /* Caution optionfilefiname is hidden */
751: strcpy(tmpout,optionfilefiname);
752: strcat(tmpout,"/");
753: strcat(tmpout,preop);
754: strcat(tmpout,preop2);
755: strcat(tmpout,fileres);
756: return tmpout;
757: }
758:
759: /***************** f1dim *************************/
760: extern int ncom;
761: extern double *pcom,*xicom;
762: extern double (*nrfunc)(double []);
763:
764: double f1dim(double x)
765: {
766: int j;
767: double f;
768: double *xt;
769:
770: xt=vector(1,ncom);
771: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
772: f=(*nrfunc)(xt);
773: free_vector(xt,1,ncom);
774: return f;
775: }
776:
777: /*****************brent *************************/
778: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
779: {
780: int iter;
781: double a,b,d,etemp;
782: double fu,fv,fw,fx;
783: double ftemp;
784: double p,q,r,tol1,tol2,u,v,w,x,xm;
785: double e=0.0;
786:
787: a=(ax < cx ? ax : cx);
788: b=(ax > cx ? ax : cx);
789: x=w=v=bx;
790: fw=fv=fx=(*f)(x);
791: for (iter=1;iter<=ITMAX;iter++) {
792: xm=0.5*(a+b);
793: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
794: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
795: printf(".");fflush(stdout);
796: fprintf(ficlog,".");fflush(ficlog);
797: #ifdef DEBUG
798: 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);
799: 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);
800: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
801: #endif
802: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
803: *xmin=x;
804: return fx;
805: }
806: ftemp=fu;
807: if (fabs(e) > tol1) {
808: r=(x-w)*(fx-fv);
809: q=(x-v)*(fx-fw);
810: p=(x-v)*q-(x-w)*r;
811: q=2.0*(q-r);
812: if (q > 0.0) p = -p;
813: q=fabs(q);
814: etemp=e;
815: e=d;
816: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
817: d=CGOLD*(e=(x >= xm ? a-x : b-x));
818: else {
819: d=p/q;
820: u=x+d;
821: if (u-a < tol2 || b-u < tol2)
822: d=SIGN(tol1,xm-x);
823: }
824: } else {
825: d=CGOLD*(e=(x >= xm ? a-x : b-x));
826: }
827: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
828: fu=(*f)(u);
829: if (fu <= fx) {
830: if (u >= x) a=x; else b=x;
831: SHFT(v,w,x,u)
832: SHFT(fv,fw,fx,fu)
833: } else {
834: if (u < x) a=u; else b=u;
835: if (fu <= fw || w == x) {
836: v=w;
837: w=u;
838: fv=fw;
839: fw=fu;
840: } else if (fu <= fv || v == x || v == w) {
841: v=u;
842: fv=fu;
843: }
844: }
845: }
846: nrerror("Too many iterations in brent");
847: *xmin=x;
848: return fx;
849: }
850:
851: /****************** mnbrak ***********************/
852:
853: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
854: double (*func)(double))
855: {
856: double ulim,u,r,q, dum;
857: double fu;
858:
859: *fa=(*func)(*ax);
860: *fb=(*func)(*bx);
861: if (*fb > *fa) {
862: SHFT(dum,*ax,*bx,dum)
863: SHFT(dum,*fb,*fa,dum)
864: }
865: *cx=(*bx)+GOLD*(*bx-*ax);
866: *fc=(*func)(*cx);
867: while (*fb > *fc) {
868: r=(*bx-*ax)*(*fb-*fc);
869: q=(*bx-*cx)*(*fb-*fa);
870: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
871: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
872: ulim=(*bx)+GLIMIT*(*cx-*bx);
873: if ((*bx-u)*(u-*cx) > 0.0) {
874: fu=(*func)(u);
875: } else if ((*cx-u)*(u-ulim) > 0.0) {
876: fu=(*func)(u);
877: if (fu < *fc) {
878: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
879: SHFT(*fb,*fc,fu,(*func)(u))
880: }
881: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
882: u=ulim;
883: fu=(*func)(u);
884: } else {
885: u=(*cx)+GOLD*(*cx-*bx);
886: fu=(*func)(u);
887: }
888: SHFT(*ax,*bx,*cx,u)
889: SHFT(*fa,*fb,*fc,fu)
890: }
891: }
892:
893: /*************** linmin ************************/
894:
895: int ncom;
896: double *pcom,*xicom;
897: double (*nrfunc)(double []);
898:
899: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
900: {
901: double brent(double ax, double bx, double cx,
902: double (*f)(double), double tol, double *xmin);
903: double f1dim(double x);
904: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
905: double *fc, double (*func)(double));
906: int j;
907: double xx,xmin,bx,ax;
908: double fx,fb,fa;
909:
910: ncom=n;
911: pcom=vector(1,n);
912: xicom=vector(1,n);
913: nrfunc=func;
914: for (j=1;j<=n;j++) {
915: pcom[j]=p[j];
916: xicom[j]=xi[j];
917: }
918: ax=0.0;
919: xx=1.0;
920: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
921: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
922: #ifdef DEBUG
923: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
924: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
925: #endif
926: for (j=1;j<=n;j++) {
927: xi[j] *= xmin;
928: p[j] += xi[j];
929: }
930: free_vector(xicom,1,n);
931: free_vector(pcom,1,n);
932: }
933:
934: char *asc_diff_time(long time_sec, char ascdiff[])
935: {
936: long sec_left, days, hours, minutes;
937: days = (time_sec) / (60*60*24);
938: sec_left = (time_sec) % (60*60*24);
939: hours = (sec_left) / (60*60) ;
940: sec_left = (sec_left) %(60*60);
941: minutes = (sec_left) /60;
942: sec_left = (sec_left) % (60);
943: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
944: return ascdiff;
945: }
946:
947: /*************** powell ************************/
948: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
949: double (*func)(double []))
950: {
951: void linmin(double p[], double xi[], int n, double *fret,
952: double (*func)(double []));
953: int i,ibig,j;
954: double del,t,*pt,*ptt,*xit;
955: double fp,fptt;
956: double *xits;
957: int niterf, itmp;
958:
959: pt=vector(1,n);
960: ptt=vector(1,n);
961: xit=vector(1,n);
962: xits=vector(1,n);
963: *fret=(*func)(p);
964: for (j=1;j<=n;j++) pt[j]=p[j];
965: for (*iter=1;;++(*iter)) {
966: fp=(*fret);
967: ibig=0;
968: del=0.0;
969: last_time=curr_time;
970: (void) gettimeofday(&curr_time,&tzp);
971: 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);
972: /* 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);
973: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
974: */
975: for (i=1;i<=n;i++) {
976: printf(" %d %.12f",i, p[i]);
977: fprintf(ficlog," %d %.12lf",i, p[i]);
978: fprintf(ficrespow," %.12lf", p[i]);
979: }
980: printf("\n");
981: fprintf(ficlog,"\n");
982: fprintf(ficrespow,"\n");fflush(ficrespow);
983: if(*iter <=3){
984: tm = *localtime(&curr_time.tv_sec);
985: strcpy(strcurr,asctime(&tm));
986: /* asctime_r(&tm,strcurr); */
987: forecast_time=curr_time;
988: itmp = strlen(strcurr);
989: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
990: strcurr[itmp-1]='\0';
991: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
992: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
993: for(niterf=10;niterf<=30;niterf+=10){
994: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
995: tmf = *localtime(&forecast_time.tv_sec);
996: /* asctime_r(&tmf,strfor); */
997: strcpy(strfor,asctime(&tmf));
998: itmp = strlen(strfor);
999: if(strfor[itmp-1]=='\n')
1000: strfor[itmp-1]='\0';
1001: 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);
1002: 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);
1003: }
1004: }
1005: for (i=1;i<=n;i++) {
1006: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1007: fptt=(*fret);
1008: #ifdef DEBUG
1009: printf("fret=%lf \n",*fret);
1010: fprintf(ficlog,"fret=%lf \n",*fret);
1011: #endif
1012: printf("%d",i);fflush(stdout);
1013: fprintf(ficlog,"%d",i);fflush(ficlog);
1014: linmin(p,xit,n,fret,func);
1015: if (fabs(fptt-(*fret)) > del) {
1016: del=fabs(fptt-(*fret));
1017: ibig=i;
1018: }
1019: #ifdef DEBUG
1020: printf("%d %.12e",i,(*fret));
1021: fprintf(ficlog,"%d %.12e",i,(*fret));
1022: for (j=1;j<=n;j++) {
1023: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1024: printf(" x(%d)=%.12e",j,xit[j]);
1025: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1026: }
1027: for(j=1;j<=n;j++) {
1028: printf(" p=%.12e",p[j]);
1029: fprintf(ficlog," p=%.12e",p[j]);
1030: }
1031: printf("\n");
1032: fprintf(ficlog,"\n");
1033: #endif
1034: }
1035: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1036: #ifdef DEBUG
1037: int k[2],l;
1038: k[0]=1;
1039: k[1]=-1;
1040: printf("Max: %.12e",(*func)(p));
1041: fprintf(ficlog,"Max: %.12e",(*func)(p));
1042: for (j=1;j<=n;j++) {
1043: printf(" %.12e",p[j]);
1044: fprintf(ficlog," %.12e",p[j]);
1045: }
1046: printf("\n");
1047: fprintf(ficlog,"\n");
1048: for(l=0;l<=1;l++) {
1049: for (j=1;j<=n;j++) {
1050: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1051: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1052: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1053: }
1054: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1055: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1056: }
1057: #endif
1058:
1059:
1060: free_vector(xit,1,n);
1061: free_vector(xits,1,n);
1062: free_vector(ptt,1,n);
1063: free_vector(pt,1,n);
1064: return;
1065: }
1066: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1067: for (j=1;j<=n;j++) {
1068: ptt[j]=2.0*p[j]-pt[j];
1069: xit[j]=p[j]-pt[j];
1070: pt[j]=p[j];
1071: }
1072: fptt=(*func)(ptt);
1073: if (fptt < fp) {
1074: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1075: if (t < 0.0) {
1076: linmin(p,xit,n,fret,func);
1077: for (j=1;j<=n;j++) {
1078: xi[j][ibig]=xi[j][n];
1079: xi[j][n]=xit[j];
1080: }
1081: #ifdef DEBUG
1082: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1083: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1084: for(j=1;j<=n;j++){
1085: printf(" %.12e",xit[j]);
1086: fprintf(ficlog," %.12e",xit[j]);
1087: }
1088: printf("\n");
1089: fprintf(ficlog,"\n");
1090: #endif
1091: }
1092: }
1093: }
1094: }
1095:
1096: /**** Prevalence limit (stable or period prevalence) ****************/
1097:
1098: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1099: {
1100: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1101: matrix by transitions matrix until convergence is reached */
1102:
1103: int i, ii,j,k;
1104: double min, max, maxmin, maxmax,sumnew=0.;
1105: double **matprod2();
1106: double **out, cov[NCOVMAX], **pmij();
1107: double **newm;
1108: double agefin, delaymax=50 ; /* Max number of years to converge */
1109:
1110: for (ii=1;ii<=nlstate+ndeath;ii++)
1111: for (j=1;j<=nlstate+ndeath;j++){
1112: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1113: }
1114:
1115: cov[1]=1.;
1116:
1117: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1118: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1119: newm=savm;
1120: /* Covariates have to be included here again */
1121: cov[2]=agefin;
1122:
1123: for (k=1; k<=cptcovn;k++) {
1124: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1125: /* 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]]);*/
1126: }
1127: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1128: for (k=1; k<=cptcovprod;k++)
1129: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1130:
1131: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1132: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1133: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1134: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1135:
1136: savm=oldm;
1137: oldm=newm;
1138: maxmax=0.;
1139: for(j=1;j<=nlstate;j++){
1140: min=1.;
1141: max=0.;
1142: for(i=1; i<=nlstate; i++) {
1143: sumnew=0;
1144: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1145: prlim[i][j]= newm[i][j]/(1-sumnew);
1146: max=FMAX(max,prlim[i][j]);
1147: min=FMIN(min,prlim[i][j]);
1148: }
1149: maxmin=max-min;
1150: maxmax=FMAX(maxmax,maxmin);
1151: }
1152: if(maxmax < ftolpl){
1153: return prlim;
1154: }
1155: }
1156: }
1157:
1158: /*************** transition probabilities ***************/
1159:
1160: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1161: {
1162: double s1, s2;
1163: /*double t34;*/
1164: int i,j,j1, nc, ii, jj;
1165:
1166: for(i=1; i<= nlstate; i++){
1167: for(j=1; j<i;j++){
1168: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1169: /*s2 += param[i][j][nc]*cov[nc];*/
1170: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1171: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1172: }
1173: ps[i][j]=s2;
1174: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1175: }
1176: for(j=i+1; j<=nlstate+ndeath;j++){
1177: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1178: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1179: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1180: }
1181: ps[i][j]=s2;
1182: }
1183: }
1184: /*ps[3][2]=1;*/
1185:
1186: for(i=1; i<= nlstate; i++){
1187: s1=0;
1188: for(j=1; j<i; j++)
1189: s1+=exp(ps[i][j]);
1190: for(j=i+1; j<=nlstate+ndeath; j++)
1191: s1+=exp(ps[i][j]);
1192: ps[i][i]=1./(s1+1.);
1193: for(j=1; j<i; j++)
1194: ps[i][j]= exp(ps[i][j])*ps[i][i];
1195: for(j=i+1; j<=nlstate+ndeath; j++)
1196: ps[i][j]= exp(ps[i][j])*ps[i][i];
1197: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1198: } /* end i */
1199:
1200: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1201: for(jj=1; jj<= nlstate+ndeath; jj++){
1202: ps[ii][jj]=0;
1203: ps[ii][ii]=1;
1204: }
1205: }
1206:
1207:
1208: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1209: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1210: /* printf("ddd %lf ",ps[ii][jj]); */
1211: /* } */
1212: /* printf("\n "); */
1213: /* } */
1214: /* printf("\n ");printf("%lf ",cov[2]); */
1215: /*
1216: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1217: goto end;*/
1218: return ps;
1219: }
1220:
1221: /**************** Product of 2 matrices ******************/
1222:
1223: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1224: {
1225: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1226: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1227: /* in, b, out are matrice of pointers which should have been initialized
1228: before: only the contents of out is modified. The function returns
1229: a pointer to pointers identical to out */
1230: long i, j, k;
1231: for(i=nrl; i<= nrh; i++)
1232: for(k=ncolol; k<=ncoloh; k++)
1233: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1234: out[i][k] +=in[i][j]*b[j][k];
1235:
1236: return out;
1237: }
1238:
1239:
1240: /************* Higher Matrix Product ***************/
1241:
1242: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1243: {
1244: /* Computes the transition matrix starting at age 'age' over
1245: 'nhstepm*hstepm*stepm' months (i.e. until
1246: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1247: nhstepm*hstepm matrices.
1248: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1249: (typically every 2 years instead of every month which is too big
1250: for the memory).
1251: Model is determined by parameters x and covariates have to be
1252: included manually here.
1253:
1254: */
1255:
1256: int i, j, d, h, k;
1257: double **out, cov[NCOVMAX];
1258: double **newm;
1259:
1260: /* Hstepm could be zero and should return the unit matrix */
1261: for (i=1;i<=nlstate+ndeath;i++)
1262: for (j=1;j<=nlstate+ndeath;j++){
1263: oldm[i][j]=(i==j ? 1.0 : 0.0);
1264: po[i][j][0]=(i==j ? 1.0 : 0.0);
1265: }
1266: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1267: for(h=1; h <=nhstepm; h++){
1268: for(d=1; d <=hstepm; d++){
1269: newm=savm;
1270: /* Covariates have to be included here again */
1271: cov[1]=1.;
1272: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1273: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1274: for (k=1; k<=cptcovage;k++)
1275: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1276: for (k=1; k<=cptcovprod;k++)
1277: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1278:
1279:
1280: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1281: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1282: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1283: pmij(pmmij,cov,ncovmodel,x,nlstate));
1284: savm=oldm;
1285: oldm=newm;
1286: }
1287: for(i=1; i<=nlstate+ndeath; i++)
1288: for(j=1;j<=nlstate+ndeath;j++) {
1289: po[i][j][h]=newm[i][j];
1290: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1291: */
1292: }
1293: } /* end h */
1294: return po;
1295: }
1296:
1297:
1298: /*************** log-likelihood *************/
1299: double func( double *x)
1300: {
1301: int i, ii, j, k, mi, d, kk;
1302: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1303: double **out;
1304: double sw; /* Sum of weights */
1305: double lli; /* Individual log likelihood */
1306: int s1, s2;
1307: double bbh, survp;
1308: long ipmx;
1309: /*extern weight */
1310: /* We are differentiating ll according to initial status */
1311: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1312: /*for(i=1;i<imx;i++)
1313: printf(" %d\n",s[4][i]);
1314: */
1315: cov[1]=1.;
1316:
1317: for(k=1; k<=nlstate; k++) ll[k]=0.;
1318:
1319: if(mle==1){
1320: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1321: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1322: for(mi=1; mi<= wav[i]-1; mi++){
1323: for (ii=1;ii<=nlstate+ndeath;ii++)
1324: for (j=1;j<=nlstate+ndeath;j++){
1325: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1326: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1327: }
1328: for(d=0; d<dh[mi][i]; d++){
1329: newm=savm;
1330: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1331: for (kk=1; kk<=cptcovage;kk++) {
1332: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1333: }
1334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1335: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1336: savm=oldm;
1337: oldm=newm;
1338: } /* end mult */
1339:
1340: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1341: /* But now since version 0.9 we anticipate for bias at large stepm.
1342: * If stepm is larger than one month (smallest stepm) and if the exact delay
1343: * (in months) between two waves is not a multiple of stepm, we rounded to
1344: * the nearest (and in case of equal distance, to the lowest) interval but now
1345: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1346: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1347: * probability in order to take into account the bias as a fraction of the way
1348: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1349: * -stepm/2 to stepm/2 .
1350: * For stepm=1 the results are the same as for previous versions of Imach.
1351: * For stepm > 1 the results are less biased than in previous versions.
1352: */
1353: s1=s[mw[mi][i]][i];
1354: s2=s[mw[mi+1][i]][i];
1355: bbh=(double)bh[mi][i]/(double)stepm;
1356: /* bias bh is positive if real duration
1357: * is higher than the multiple of stepm and negative otherwise.
1358: */
1359: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1360: if( s2 > nlstate){
1361: /* i.e. if s2 is a death state and if the date of death is known
1362: then the contribution to the likelihood is the probability to
1363: die between last step unit time and current step unit time,
1364: which is also equal to probability to die before dh
1365: minus probability to die before dh-stepm .
1366: In version up to 0.92 likelihood was computed
1367: as if date of death was unknown. Death was treated as any other
1368: health state: the date of the interview describes the actual state
1369: and not the date of a change in health state. The former idea was
1370: to consider that at each interview the state was recorded
1371: (healthy, disable or death) and IMaCh was corrected; but when we
1372: introduced the exact date of death then we should have modified
1373: the contribution of an exact death to the likelihood. This new
1374: contribution is smaller and very dependent of the step unit
1375: stepm. It is no more the probability to die between last interview
1376: and month of death but the probability to survive from last
1377: interview up to one month before death multiplied by the
1378: probability to die within a month. Thanks to Chris
1379: Jackson for correcting this bug. Former versions increased
1380: mortality artificially. The bad side is that we add another loop
1381: which slows down the processing. The difference can be up to 10%
1382: lower mortality.
1383: */
1384: lli=log(out[s1][s2] - savm[s1][s2]);
1385:
1386:
1387: } else if (s2==-2) {
1388: for (j=1,survp=0. ; j<=nlstate; j++)
1389: survp += out[s1][j];
1390: lli= log(survp);
1391: }
1392:
1393: /* else if (s2==-4) { */
1394: /* for (j=3,survp=0. ; j<=nlstate; j++) */
1395: /* survp += out[s1][j]; */
1396: /* lli= survp; */
1397: /* } */
1398:
1399: /* else if (s2==-5) { */
1400: /* for (j=1,survp=0. ; j<=2; j++) */
1401: /* survp += out[s1][j]; */
1402: /* lli= survp; */
1403: /* } */
1404:
1405:
1406: else{
1407: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1408: /* 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 */
1409: }
1410: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1411: /*if(lli ==000.0)*/
1412: /*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); */
1413: ipmx +=1;
1414: sw += weight[i];
1415: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1416: } /* end of wave */
1417: } /* end of individual */
1418: } else if(mle==2){
1419: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1420: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1421: for(mi=1; mi<= wav[i]-1; mi++){
1422: for (ii=1;ii<=nlstate+ndeath;ii++)
1423: for (j=1;j<=nlstate+ndeath;j++){
1424: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1425: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1426: }
1427: for(d=0; d<=dh[mi][i]; d++){
1428: newm=savm;
1429: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1430: for (kk=1; kk<=cptcovage;kk++) {
1431: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1432: }
1433: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1434: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1435: savm=oldm;
1436: oldm=newm;
1437: } /* end mult */
1438:
1439: s1=s[mw[mi][i]][i];
1440: s2=s[mw[mi+1][i]][i];
1441: bbh=(double)bh[mi][i]/(double)stepm;
1442: 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 */
1443: ipmx +=1;
1444: sw += weight[i];
1445: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1446: } /* end of wave */
1447: } /* end of individual */
1448: } else if(mle==3){ /* exponential inter-extrapolation */
1449: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1450: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1451: for(mi=1; mi<= wav[i]-1; mi++){
1452: for (ii=1;ii<=nlstate+ndeath;ii++)
1453: for (j=1;j<=nlstate+ndeath;j++){
1454: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1455: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1456: }
1457: for(d=0; d<dh[mi][i]; d++){
1458: newm=savm;
1459: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1460: for (kk=1; kk<=cptcovage;kk++) {
1461: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
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];
1471: bbh=(double)bh[mi][i]/(double)stepm;
1472: 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 */
1473: ipmx +=1;
1474: sw += weight[i];
1475: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1476: } /* end of wave */
1477: } /* end of individual */
1478: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1479: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1480: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1481: for(mi=1; mi<= wav[i]-1; mi++){
1482: for (ii=1;ii<=nlstate+ndeath;ii++)
1483: for (j=1;j<=nlstate+ndeath;j++){
1484: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1485: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1486: }
1487: for(d=0; d<dh[mi][i]; d++){
1488: newm=savm;
1489: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1490: for (kk=1; kk<=cptcovage;kk++) {
1491: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1492: }
1493:
1494: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1495: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1496: savm=oldm;
1497: oldm=newm;
1498: } /* end mult */
1499:
1500: s1=s[mw[mi][i]][i];
1501: s2=s[mw[mi+1][i]][i];
1502: if( s2 > nlstate){
1503: lli=log(out[s1][s2] - savm[s1][s2]);
1504: }else{
1505: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1506: }
1507: ipmx +=1;
1508: sw += weight[i];
1509: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1510: /* 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]); */
1511: } /* end of wave */
1512: } /* end of individual */
1513: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1514: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1515: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1516: for(mi=1; mi<= wav[i]-1; mi++){
1517: for (ii=1;ii<=nlstate+ndeath;ii++)
1518: for (j=1;j<=nlstate+ndeath;j++){
1519: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1520: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1521: }
1522: for(d=0; d<dh[mi][i]; d++){
1523: newm=savm;
1524: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1525: for (kk=1; kk<=cptcovage;kk++) {
1526: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1527: }
1528:
1529: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1530: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1531: savm=oldm;
1532: oldm=newm;
1533: } /* end mult */
1534:
1535: s1=s[mw[mi][i]][i];
1536: s2=s[mw[mi+1][i]][i];
1537: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1538: ipmx +=1;
1539: sw += weight[i];
1540: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1541: /*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]);*/
1542: } /* end of wave */
1543: } /* end of individual */
1544: } /* End of if */
1545: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1546: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1547: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1548: return -l;
1549: }
1550:
1551: /*************** log-likelihood *************/
1552: double funcone( double *x)
1553: {
1554: /* Same as likeli but slower because of a lot of printf and if */
1555: int i, ii, j, k, mi, d, kk;
1556: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1557: double **out;
1558: double lli; /* Individual log likelihood */
1559: double llt;
1560: int s1, s2;
1561: double bbh, survp;
1562: /*extern weight */
1563: /* We are differentiating ll according to initial status */
1564: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1565: /*for(i=1;i<imx;i++)
1566: printf(" %d\n",s[4][i]);
1567: */
1568: cov[1]=1.;
1569:
1570: for(k=1; k<=nlstate; k++) ll[k]=0.;
1571:
1572: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1573: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1574: for(mi=1; mi<= wav[i]-1; mi++){
1575: for (ii=1;ii<=nlstate+ndeath;ii++)
1576: for (j=1;j<=nlstate+ndeath;j++){
1577: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1578: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1579: }
1580: for(d=0; d<dh[mi][i]; d++){
1581: newm=savm;
1582: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1583: for (kk=1; kk<=cptcovage;kk++) {
1584: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1585: }
1586: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1587: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1588: savm=oldm;
1589: oldm=newm;
1590: } /* end mult */
1591:
1592: s1=s[mw[mi][i]][i];
1593: s2=s[mw[mi+1][i]][i];
1594: bbh=(double)bh[mi][i]/(double)stepm;
1595: /* bias is positive if real duration
1596: * is higher than the multiple of stepm and negative otherwise.
1597: */
1598: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1599: lli=log(out[s1][s2] - savm[s1][s2]);
1600: } else if (s2==-2) {
1601: for (j=1,survp=0. ; j<=nlstate; j++)
1602: survp += out[s1][j];
1603: lli= log(survp);
1604: }else if (mle==1){
1605: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1606: } else if(mle==2){
1607: 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 */
1608: } else if(mle==3){ /* exponential inter-extrapolation */
1609: 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 */
1610: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1611: lli=log(out[s1][s2]); /* Original formula */
1612: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1613: lli=log(out[s1][s2]); /* Original formula */
1614: } /* End of if */
1615: ipmx +=1;
1616: sw += weight[i];
1617: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1618: /* 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]); */
1619: if(globpr){
1620: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1621: %11.6f %11.6f %11.6f ", \
1622: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1623: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1624: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1625: llt +=ll[k]*gipmx/gsw;
1626: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1627: }
1628: fprintf(ficresilk," %10.6f\n", -llt);
1629: }
1630: } /* end of wave */
1631: } /* end of individual */
1632: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1633: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1634: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1635: if(globpr==0){ /* First time we count the contributions and weights */
1636: gipmx=ipmx;
1637: gsw=sw;
1638: }
1639: return -l;
1640: }
1641:
1642:
1643: /*************** function likelione ***********/
1644: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1645: {
1646: /* This routine should help understanding what is done with
1647: the selection of individuals/waves and
1648: to check the exact contribution to the likelihood.
1649: Plotting could be done.
1650: */
1651: int k;
1652:
1653: if(*globpri !=0){ /* Just counts and sums, no printings */
1654: strcpy(fileresilk,"ilk");
1655: strcat(fileresilk,fileres);
1656: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1657: printf("Problem with resultfile: %s\n", fileresilk);
1658: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1659: }
1660: 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");
1661: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1662: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1663: for(k=1; k<=nlstate; k++)
1664: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1665: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1666: }
1667:
1668: *fretone=(*funcone)(p);
1669: if(*globpri !=0){
1670: fclose(ficresilk);
1671: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1672: fflush(fichtm);
1673: }
1674: return;
1675: }
1676:
1677:
1678: /*********** Maximum Likelihood Estimation ***************/
1679:
1680: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1681: {
1682: int i,j, iter;
1683: double **xi;
1684: double fret;
1685: double fretone; /* Only one call to likelihood */
1686: /* char filerespow[FILENAMELENGTH];*/
1687: xi=matrix(1,npar,1,npar);
1688: for (i=1;i<=npar;i++)
1689: for (j=1;j<=npar;j++)
1690: xi[i][j]=(i==j ? 1.0 : 0.0);
1691: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1692: strcpy(filerespow,"pow");
1693: strcat(filerespow,fileres);
1694: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1695: printf("Problem with resultfile: %s\n", filerespow);
1696: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1697: }
1698: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1699: for (i=1;i<=nlstate;i++)
1700: for(j=1;j<=nlstate+ndeath;j++)
1701: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1702: fprintf(ficrespow,"\n");
1703:
1704: powell(p,xi,npar,ftol,&iter,&fret,func);
1705:
1706: free_matrix(xi,1,npar,1,npar);
1707: fclose(ficrespow);
1708: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1709: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1710: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1711:
1712: }
1713:
1714: /**** Computes Hessian and covariance matrix ***/
1715: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1716: {
1717: double **a,**y,*x,pd;
1718: double **hess;
1719: int i, j,jk;
1720: int *indx;
1721:
1722: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1723: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1724: void lubksb(double **a, int npar, int *indx, double b[]) ;
1725: void ludcmp(double **a, int npar, int *indx, double *d) ;
1726: double gompertz(double p[]);
1727: hess=matrix(1,npar,1,npar);
1728:
1729: printf("\nCalculation of the hessian matrix. Wait...\n");
1730: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1731: for (i=1;i<=npar;i++){
1732: printf("%d",i);fflush(stdout);
1733: fprintf(ficlog,"%d",i);fflush(ficlog);
1734:
1735: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1736:
1737: /* printf(" %f ",p[i]);
1738: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1739: }
1740:
1741: for (i=1;i<=npar;i++) {
1742: for (j=1;j<=npar;j++) {
1743: if (j>i) {
1744: printf(".%d%d",i,j);fflush(stdout);
1745: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1746: hess[i][j]=hessij(p,delti,i,j,func,npar);
1747:
1748: hess[j][i]=hess[i][j];
1749: /*printf(" %lf ",hess[i][j]);*/
1750: }
1751: }
1752: }
1753: printf("\n");
1754: fprintf(ficlog,"\n");
1755:
1756: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1757: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1758:
1759: a=matrix(1,npar,1,npar);
1760: y=matrix(1,npar,1,npar);
1761: x=vector(1,npar);
1762: indx=ivector(1,npar);
1763: for (i=1;i<=npar;i++)
1764: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1765: ludcmp(a,npar,indx,&pd);
1766:
1767: for (j=1;j<=npar;j++) {
1768: for (i=1;i<=npar;i++) x[i]=0;
1769: x[j]=1;
1770: lubksb(a,npar,indx,x);
1771: for (i=1;i<=npar;i++){
1772: matcov[i][j]=x[i];
1773: }
1774: }
1775:
1776: printf("\n#Hessian matrix#\n");
1777: fprintf(ficlog,"\n#Hessian matrix#\n");
1778: for (i=1;i<=npar;i++) {
1779: for (j=1;j<=npar;j++) {
1780: printf("%.3e ",hess[i][j]);
1781: fprintf(ficlog,"%.3e ",hess[i][j]);
1782: }
1783: printf("\n");
1784: fprintf(ficlog,"\n");
1785: }
1786:
1787: /* Recompute Inverse */
1788: for (i=1;i<=npar;i++)
1789: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1790: ludcmp(a,npar,indx,&pd);
1791:
1792: /* printf("\n#Hessian matrix recomputed#\n");
1793:
1794: for (j=1;j<=npar;j++) {
1795: for (i=1;i<=npar;i++) x[i]=0;
1796: x[j]=1;
1797: lubksb(a,npar,indx,x);
1798: for (i=1;i<=npar;i++){
1799: y[i][j]=x[i];
1800: printf("%.3e ",y[i][j]);
1801: fprintf(ficlog,"%.3e ",y[i][j]);
1802: }
1803: printf("\n");
1804: fprintf(ficlog,"\n");
1805: }
1806: */
1807:
1808: free_matrix(a,1,npar,1,npar);
1809: free_matrix(y,1,npar,1,npar);
1810: free_vector(x,1,npar);
1811: free_ivector(indx,1,npar);
1812: free_matrix(hess,1,npar,1,npar);
1813:
1814:
1815: }
1816:
1817: /*************** hessian matrix ****************/
1818: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1819: {
1820: int i;
1821: int l=1, lmax=20;
1822: double k1,k2;
1823: double p2[NPARMAX+1];
1824: double res;
1825: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1826: double fx;
1827: int k=0,kmax=10;
1828: double l1;
1829:
1830: fx=func(x);
1831: for (i=1;i<=npar;i++) p2[i]=x[i];
1832: for(l=0 ; l <=lmax; l++){
1833: l1=pow(10,l);
1834: delts=delt;
1835: for(k=1 ; k <kmax; k=k+1){
1836: delt = delta*(l1*k);
1837: p2[theta]=x[theta] +delt;
1838: k1=func(p2)-fx;
1839: p2[theta]=x[theta]-delt;
1840: k2=func(p2)-fx;
1841: /*res= (k1-2.0*fx+k2)/delt/delt; */
1842: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1843:
1844: #ifdef DEBUG
1845: 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);
1846: 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);
1847: #endif
1848: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1849: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1850: k=kmax;
1851: }
1852: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1853: k=kmax; l=lmax*10.;
1854: }
1855: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1856: delts=delt;
1857: }
1858: }
1859: }
1860: delti[theta]=delts;
1861: return res;
1862:
1863: }
1864:
1865: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1866: {
1867: int i;
1868: int l=1, l1, lmax=20;
1869: double k1,k2,k3,k4,res,fx;
1870: double p2[NPARMAX+1];
1871: int k;
1872:
1873: fx=func(x);
1874: for (k=1; k<=2; k++) {
1875: for (i=1;i<=npar;i++) p2[i]=x[i];
1876: p2[thetai]=x[thetai]+delti[thetai]/k;
1877: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1878: k1=func(p2)-fx;
1879:
1880: p2[thetai]=x[thetai]+delti[thetai]/k;
1881: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1882: k2=func(p2)-fx;
1883:
1884: p2[thetai]=x[thetai]-delti[thetai]/k;
1885: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1886: k3=func(p2)-fx;
1887:
1888: p2[thetai]=x[thetai]-delti[thetai]/k;
1889: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1890: k4=func(p2)-fx;
1891: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1892: #ifdef DEBUG
1893: 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);
1894: 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);
1895: #endif
1896: }
1897: return res;
1898: }
1899:
1900: /************** Inverse of matrix **************/
1901: void ludcmp(double **a, int n, int *indx, double *d)
1902: {
1903: int i,imax,j,k;
1904: double big,dum,sum,temp;
1905: double *vv;
1906:
1907: vv=vector(1,n);
1908: *d=1.0;
1909: for (i=1;i<=n;i++) {
1910: big=0.0;
1911: for (j=1;j<=n;j++)
1912: if ((temp=fabs(a[i][j])) > big) big=temp;
1913: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1914: vv[i]=1.0/big;
1915: }
1916: for (j=1;j<=n;j++) {
1917: for (i=1;i<j;i++) {
1918: sum=a[i][j];
1919: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1920: a[i][j]=sum;
1921: }
1922: big=0.0;
1923: for (i=j;i<=n;i++) {
1924: sum=a[i][j];
1925: for (k=1;k<j;k++)
1926: sum -= a[i][k]*a[k][j];
1927: a[i][j]=sum;
1928: if ( (dum=vv[i]*fabs(sum)) >= big) {
1929: big=dum;
1930: imax=i;
1931: }
1932: }
1933: if (j != imax) {
1934: for (k=1;k<=n;k++) {
1935: dum=a[imax][k];
1936: a[imax][k]=a[j][k];
1937: a[j][k]=dum;
1938: }
1939: *d = -(*d);
1940: vv[imax]=vv[j];
1941: }
1942: indx[j]=imax;
1943: if (a[j][j] == 0.0) a[j][j]=TINY;
1944: if (j != n) {
1945: dum=1.0/(a[j][j]);
1946: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1947: }
1948: }
1949: free_vector(vv,1,n); /* Doesn't work */
1950: ;
1951: }
1952:
1953: void lubksb(double **a, int n, int *indx, double b[])
1954: {
1955: int i,ii=0,ip,j;
1956: double sum;
1957:
1958: for (i=1;i<=n;i++) {
1959: ip=indx[i];
1960: sum=b[ip];
1961: b[ip]=b[i];
1962: if (ii)
1963: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1964: else if (sum) ii=i;
1965: b[i]=sum;
1966: }
1967: for (i=n;i>=1;i--) {
1968: sum=b[i];
1969: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1970: b[i]=sum/a[i][i];
1971: }
1972: }
1973:
1974: void pstamp(FILE *fichier)
1975: {
1976: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1977: }
1978:
1979: /************ Frequencies ********************/
1980: 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[])
1981: { /* Some frequencies */
1982:
1983: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1984: int first;
1985: double ***freq; /* Frequencies */
1986: double *pp, **prop;
1987: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1988: char fileresp[FILENAMELENGTH];
1989:
1990: pp=vector(1,nlstate);
1991: prop=matrix(1,nlstate,iagemin,iagemax+3);
1992: strcpy(fileresp,"p");
1993: strcat(fileresp,fileres);
1994: if((ficresp=fopen(fileresp,"w"))==NULL) {
1995: printf("Problem with prevalence resultfile: %s\n", fileresp);
1996: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1997: exit(0);
1998: }
1999: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2000: j1=0;
2001:
2002: j=cptcoveff;
2003: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2004:
2005: first=1;
2006:
2007: for(k1=1; k1<=j;k1++){
2008: for(i1=1; i1<=ncodemax[k1];i1++){
2009: j1++;
2010: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2011: scanf("%d", i);*/
2012: for (i=-5; i<=nlstate+ndeath; i++)
2013: for (jk=-5; jk<=nlstate+ndeath; jk++)
2014: for(m=iagemin; m <= iagemax+3; m++)
2015: freq[i][jk][m]=0;
2016:
2017: for (i=1; i<=nlstate; i++)
2018: for(m=iagemin; m <= iagemax+3; m++)
2019: prop[i][m]=0;
2020:
2021: dateintsum=0;
2022: k2cpt=0;
2023: for (i=1; i<=imx; i++) {
2024: bool=1;
2025: if (cptcovn>0) {
2026: for (z1=1; z1<=cptcoveff; z1++)
2027: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2028: bool=0;
2029: }
2030: if (bool==1){
2031: for(m=firstpass; m<=lastpass; m++){
2032: k2=anint[m][i]+(mint[m][i]/12.);
2033: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2034: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2035: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2036: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2037: if (m<lastpass) {
2038: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2039: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2040: }
2041:
2042: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2043: dateintsum=dateintsum+k2;
2044: k2cpt++;
2045: }
2046: /*}*/
2047: }
2048: }
2049: }
2050:
2051: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2052: pstamp(ficresp);
2053: if (cptcovn>0) {
2054: fprintf(ficresp, "\n#********** Variable ");
2055: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2056: fprintf(ficresp, "**********\n#");
2057: }
2058: for(i=1; i<=nlstate;i++)
2059: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2060: fprintf(ficresp, "\n");
2061:
2062: for(i=iagemin; i <= iagemax+3; i++){
2063: if(i==iagemax+3){
2064: fprintf(ficlog,"Total");
2065: }else{
2066: if(first==1){
2067: first=0;
2068: printf("See log file for details...\n");
2069: }
2070: fprintf(ficlog,"Age %d", i);
2071: }
2072: for(jk=1; jk <=nlstate ; jk++){
2073: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2074: pp[jk] += freq[jk][m][i];
2075: }
2076: for(jk=1; jk <=nlstate ; jk++){
2077: for(m=-1, pos=0; m <=0 ; m++)
2078: pos += freq[jk][m][i];
2079: if(pp[jk]>=1.e-10){
2080: if(first==1){
2081: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2082: }
2083: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2084: }else{
2085: if(first==1)
2086: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2087: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2088: }
2089: }
2090:
2091: for(jk=1; jk <=nlstate ; jk++){
2092: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2093: pp[jk] += freq[jk][m][i];
2094: }
2095: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2096: pos += pp[jk];
2097: posprop += prop[jk][i];
2098: }
2099: for(jk=1; jk <=nlstate ; jk++){
2100: if(pos>=1.e-5){
2101: if(first==1)
2102: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2103: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2104: }else{
2105: if(first==1)
2106: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2107: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2108: }
2109: if( i <= iagemax){
2110: if(pos>=1.e-5){
2111: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2112: /*probs[i][jk][j1]= pp[jk]/pos;*/
2113: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2114: }
2115: else
2116: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2117: }
2118: }
2119:
2120: for(jk=-1; jk <=nlstate+ndeath; jk++)
2121: for(m=-1; m <=nlstate+ndeath; m++)
2122: if(freq[jk][m][i] !=0 ) {
2123: if(first==1)
2124: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2125: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2126: }
2127: if(i <= iagemax)
2128: fprintf(ficresp,"\n");
2129: if(first==1)
2130: printf("Others in log...\n");
2131: fprintf(ficlog,"\n");
2132: }
2133: }
2134: }
2135: dateintmean=dateintsum/k2cpt;
2136:
2137: fclose(ficresp);
2138: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2139: free_vector(pp,1,nlstate);
2140: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2141: /* End of Freq */
2142: }
2143:
2144: /************ Prevalence ********************/
2145: 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)
2146: {
2147: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2148: in each health status at the date of interview (if between dateprev1 and dateprev2).
2149: We still use firstpass and lastpass as another selection.
2150: */
2151:
2152: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2153: double ***freq; /* Frequencies */
2154: double *pp, **prop;
2155: double pos,posprop;
2156: double y2; /* in fractional years */
2157: int iagemin, iagemax;
2158:
2159: iagemin= (int) agemin;
2160: iagemax= (int) agemax;
2161: /*pp=vector(1,nlstate);*/
2162: prop=matrix(1,nlstate,iagemin,iagemax+3);
2163: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2164: j1=0;
2165:
2166: j=cptcoveff;
2167: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2168:
2169: for(k1=1; k1<=j;k1++){
2170: for(i1=1; i1<=ncodemax[k1];i1++){
2171: j1++;
2172:
2173: for (i=1; i<=nlstate; i++)
2174: for(m=iagemin; m <= iagemax+3; m++)
2175: prop[i][m]=0.0;
2176:
2177: for (i=1; i<=imx; i++) { /* Each individual */
2178: bool=1;
2179: if (cptcovn>0) {
2180: for (z1=1; z1<=cptcoveff; z1++)
2181: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2182: bool=0;
2183: }
2184: if (bool==1) {
2185: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2186: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2187: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2188: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2189: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2190: 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);
2191: if (s[m][i]>0 && s[m][i]<=nlstate) {
2192: /*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]]);*/
2193: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2194: prop[s[m][i]][iagemax+3] += weight[i];
2195: }
2196: }
2197: } /* end selection of waves */
2198: }
2199: }
2200: for(i=iagemin; i <= iagemax+3; i++){
2201:
2202: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2203: posprop += prop[jk][i];
2204: }
2205:
2206: for(jk=1; jk <=nlstate ; jk++){
2207: if( i <= iagemax){
2208: if(posprop>=1.e-5){
2209: probs[i][jk][j1]= prop[jk][i]/posprop;
2210: }
2211: }
2212: }/* end jk */
2213: }/* end i */
2214: } /* end i1 */
2215: } /* end k1 */
2216:
2217: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2218: /*free_vector(pp,1,nlstate);*/
2219: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2220: } /* End of prevalence */
2221:
2222: /************* Waves Concatenation ***************/
2223:
2224: 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)
2225: {
2226: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2227: Death is a valid wave (if date is known).
2228: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2229: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2230: and mw[mi+1][i]. dh depends on stepm.
2231: */
2232:
2233: int i, mi, m;
2234: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2235: double sum=0., jmean=0.;*/
2236: int first;
2237: int j, k=0,jk, ju, jl;
2238: double sum=0.;
2239: first=0;
2240: jmin=1e+5;
2241: jmax=-1;
2242: jmean=0.;
2243: for(i=1; i<=imx; i++){
2244: mi=0;
2245: m=firstpass;
2246: while(s[m][i] <= nlstate){
2247: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2248: mw[++mi][i]=m;
2249: if(m >=lastpass)
2250: break;
2251: else
2252: m++;
2253: }/* end while */
2254: if (s[m][i] > nlstate){
2255: mi++; /* Death is another wave */
2256: /* if(mi==0) never been interviewed correctly before death */
2257: /* Only death is a correct wave */
2258: mw[mi][i]=m;
2259: }
2260:
2261: wav[i]=mi;
2262: if(mi==0){
2263: nbwarn++;
2264: if(first==0){
2265: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2266: first=1;
2267: }
2268: if(first==1){
2269: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2270: }
2271: } /* end mi==0 */
2272: } /* End individuals */
2273:
2274: for(i=1; i<=imx; i++){
2275: for(mi=1; mi<wav[i];mi++){
2276: if (stepm <=0)
2277: dh[mi][i]=1;
2278: else{
2279: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2280: if (agedc[i] < 2*AGESUP) {
2281: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2282: if(j==0) j=1; /* Survives at least one month after exam */
2283: else if(j<0){
2284: nberr++;
2285: 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]);
2286: j=1; /* Temporary Dangerous patch */
2287: 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);
2288: 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]);
2289: 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);
2290: }
2291: k=k+1;
2292: if (j >= jmax){
2293: jmax=j;
2294: ijmax=i;
2295: }
2296: if (j <= jmin){
2297: jmin=j;
2298: ijmin=i;
2299: }
2300: sum=sum+j;
2301: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2302: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2303: }
2304: }
2305: else{
2306: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2307: /* 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]); */
2308:
2309: k=k+1;
2310: if (j >= jmax) {
2311: jmax=j;
2312: ijmax=i;
2313: }
2314: else if (j <= jmin){
2315: jmin=j;
2316: ijmin=i;
2317: }
2318: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2319: /*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]);*/
2320: if(j<0){
2321: nberr++;
2322: 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]);
2323: 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]);
2324: }
2325: sum=sum+j;
2326: }
2327: jk= j/stepm;
2328: jl= j -jk*stepm;
2329: ju= j -(jk+1)*stepm;
2330: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2331: if(jl==0){
2332: dh[mi][i]=jk;
2333: bh[mi][i]=0;
2334: }else{ /* We want a negative bias in order to only have interpolation ie
2335: * at the price of an extra matrix product in likelihood */
2336: dh[mi][i]=jk+1;
2337: bh[mi][i]=ju;
2338: }
2339: }else{
2340: if(jl <= -ju){
2341: dh[mi][i]=jk;
2342: bh[mi][i]=jl; /* bias is positive if real duration
2343: * is higher than the multiple of stepm and negative otherwise.
2344: */
2345: }
2346: else{
2347: dh[mi][i]=jk+1;
2348: bh[mi][i]=ju;
2349: }
2350: if(dh[mi][i]==0){
2351: dh[mi][i]=1; /* At least one step */
2352: bh[mi][i]=ju; /* At least one step */
2353: /* 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);*/
2354: }
2355: } /* end if mle */
2356: }
2357: } /* end wave */
2358: }
2359: jmean=sum/k;
2360: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
2361: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2362: }
2363:
2364: /*********** Tricode ****************************/
2365: void tricode(int *Tvar, int **nbcode, int imx)
2366: {
2367:
2368: int Ndum[20],ij=1, k, j, i, maxncov=19;
2369: int cptcode=0;
2370: cptcoveff=0;
2371:
2372: for (k=0; k<maxncov; k++) Ndum[k]=0;
2373: for (k=1; k<=7; k++) ncodemax[k]=0;
2374:
2375: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2376: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2377: modality*/
2378: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2379: Ndum[ij]++; /*store the modality */
2380: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2381: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2382: Tvar[j]. If V=sex and male is 0 and
2383: female is 1, then cptcode=1.*/
2384: }
2385:
2386: for (i=0; i<=cptcode; i++) {
2387: 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 */
2388: }
2389:
2390: ij=1;
2391: for (i=1; i<=ncodemax[j]; i++) {
2392: for (k=0; k<= maxncov; k++) {
2393: if (Ndum[k] != 0) {
2394: nbcode[Tvar[j]][ij]=k;
2395: /* 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; */
2396:
2397: ij++;
2398: }
2399: if (ij > ncodemax[j]) break;
2400: }
2401: }
2402: }
2403:
2404: for (k=0; k< maxncov; k++) Ndum[k]=0;
2405:
2406: for (i=1; i<=ncovmodel-2; i++) {
2407: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2408: ij=Tvar[i];
2409: Ndum[ij]++;
2410: }
2411:
2412: ij=1;
2413: for (i=1; i<= maxncov; i++) {
2414: if((Ndum[i]!=0) && (i<=ncovcol)){
2415: Tvaraff[ij]=i; /*For printing */
2416: ij++;
2417: }
2418: }
2419:
2420: cptcoveff=ij-1; /*Number of simple covariates*/
2421: }
2422:
2423: /*********** Health Expectancies ****************/
2424:
2425: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2426:
2427: {
2428: /* Health expectancies, no variances */
2429: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2430: double age, agelim, hf;
2431: double ***p3mat;
2432: double eip;
2433:
2434: pstamp(ficreseij);
2435: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2436: fprintf(ficreseij,"# Age");
2437: for(i=1; i<=nlstate;i++){
2438: for(j=1; j<=nlstate;j++){
2439: fprintf(ficreseij," e%1d%1d ",i,j);
2440: }
2441: fprintf(ficreseij," e%1d. ",i);
2442: }
2443: fprintf(ficreseij,"\n");
2444:
2445:
2446: if(estepm < stepm){
2447: printf ("Problem %d lower than %d\n",estepm, stepm);
2448: }
2449: else hstepm=estepm;
2450: /* We compute the life expectancy from trapezoids spaced every estepm months
2451: * This is mainly to measure the difference between two models: for example
2452: * if stepm=24 months pijx are given only every 2 years and by summing them
2453: * we are calculating an estimate of the Life Expectancy assuming a linear
2454: * progression in between and thus overestimating or underestimating according
2455: * to the curvature of the survival function. If, for the same date, we
2456: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2457: * to compare the new estimate of Life expectancy with the same linear
2458: * hypothesis. A more precise result, taking into account a more precise
2459: * curvature will be obtained if estepm is as small as stepm. */
2460:
2461: /* For example we decided to compute the life expectancy with the smallest unit */
2462: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2463: nhstepm is the number of hstepm from age to agelim
2464: nstepm is the number of stepm from age to agelin.
2465: Look at hpijx to understand the reason of that which relies in memory size
2466: and note for a fixed period like estepm months */
2467: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2468: survival function given by stepm (the optimization length). Unfortunately it
2469: means that if the survival funtion is printed only each two years of age and if
2470: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2471: results. So we changed our mind and took the option of the best precision.
2472: */
2473: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2474:
2475: agelim=AGESUP;
2476: /* nhstepm age range expressed in number of stepm */
2477: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2478: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2479: /* if (stepm >= YEARM) hstepm=1;*/
2480: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2481: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2482:
2483: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2484: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2485: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2486:
2487: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2488:
2489: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2490:
2491: printf("%d|",(int)age);fflush(stdout);
2492: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2493:
2494: /* Computing expectancies */
2495: for(i=1; i<=nlstate;i++)
2496: for(j=1; j<=nlstate;j++)
2497: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2498: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2499:
2500: /* 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]);*/
2501:
2502: }
2503:
2504: fprintf(ficreseij,"%3.0f",age );
2505: for(i=1; i<=nlstate;i++){
2506: eip=0;
2507: for(j=1; j<=nlstate;j++){
2508: eip +=eij[i][j][(int)age];
2509: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2510: }
2511: fprintf(ficreseij,"%9.4f", eip );
2512: }
2513: fprintf(ficreseij,"\n");
2514:
2515: }
2516: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2517: printf("\n");
2518: fprintf(ficlog,"\n");
2519:
2520: }
2521:
2522: void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
2523:
2524: {
2525: /* Covariances of health expectancies eij and of total life expectancies according
2526: to initial status i, ei. .
2527: */
2528: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2529: double age, agelim, hf;
2530: double ***p3matp, ***p3matm, ***varhe;
2531: double **dnewm,**doldm;
2532: double *xp, *xm;
2533: double **gp, **gm;
2534: double ***gradg, ***trgradg;
2535: int theta;
2536:
2537: double eip, vip;
2538:
2539: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2540: xp=vector(1,npar);
2541: xm=vector(1,npar);
2542: dnewm=matrix(1,nlstate*nlstate,1,npar);
2543: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2544:
2545: pstamp(ficresstdeij);
2546: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2547: fprintf(ficresstdeij,"# Age");
2548: for(i=1; i<=nlstate;i++){
2549: for(j=1; j<=nlstate;j++)
2550: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2551: fprintf(ficresstdeij," e%1d. ",i);
2552: }
2553: fprintf(ficresstdeij,"\n");
2554:
2555: pstamp(ficrescveij);
2556: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2557: fprintf(ficrescveij,"# Age");
2558: for(i=1; i<=nlstate;i++)
2559: for(j=1; j<=nlstate;j++){
2560: cptj= (j-1)*nlstate+i;
2561: for(i2=1; i2<=nlstate;i2++)
2562: for(j2=1; j2<=nlstate;j2++){
2563: cptj2= (j2-1)*nlstate+i2;
2564: if(cptj2 <= cptj)
2565: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2566: }
2567: }
2568: fprintf(ficrescveij,"\n");
2569:
2570: if(estepm < stepm){
2571: printf ("Problem %d lower than %d\n",estepm, stepm);
2572: }
2573: else hstepm=estepm;
2574: /* We compute the life expectancy from trapezoids spaced every estepm months
2575: * This is mainly to measure the difference between two models: for example
2576: * if stepm=24 months pijx are given only every 2 years and by summing them
2577: * we are calculating an estimate of the Life Expectancy assuming a linear
2578: * progression in between and thus overestimating or underestimating according
2579: * to the curvature of the survival function. If, for the same date, we
2580: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2581: * to compare the new estimate of Life expectancy with the same linear
2582: * hypothesis. A more precise result, taking into account a more precise
2583: * curvature will be obtained if estepm is as small as stepm. */
2584:
2585: /* For example we decided to compute the life expectancy with the smallest unit */
2586: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2587: nhstepm is the number of hstepm from age to agelim
2588: nstepm is the number of stepm from age to agelin.
2589: Look at hpijx to understand the reason of that which relies in memory size
2590: and note for a fixed period like estepm months */
2591: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2592: survival function given by stepm (the optimization length). Unfortunately it
2593: means that if the survival funtion is printed only each two years of age and if
2594: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2595: results. So we changed our mind and took the option of the best precision.
2596: */
2597: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2598:
2599: /* If stepm=6 months */
2600: /* nhstepm age range expressed in number of stepm */
2601: agelim=AGESUP;
2602: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2603: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2604: /* if (stepm >= YEARM) hstepm=1;*/
2605: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2606:
2607: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2608: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2609: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2610: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2611: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2612: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2613:
2614: for (age=bage; age<=fage; age ++){
2615:
2616: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2617: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2618:
2619: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2620:
2621: /* Computing Variances of health expectancies */
2622: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2623: decrease memory allocation */
2624: for(theta=1; theta <=npar; theta++){
2625: for(i=1; i<=npar; i++){
2626: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2627: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2628: }
2629: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2630: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2631:
2632: for(j=1; j<= nlstate; j++){
2633: for(i=1; i<=nlstate; i++){
2634: for(h=0; h<=nhstepm-1; h++){
2635: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2636: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2637: }
2638: }
2639: }
2640:
2641: for(ij=1; ij<= nlstate*nlstate; ij++)
2642: for(h=0; h<=nhstepm-1; h++){
2643: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2644: }
2645: }/* End theta */
2646:
2647:
2648: for(h=0; h<=nhstepm-1; h++)
2649: for(j=1; j<=nlstate*nlstate;j++)
2650: for(theta=1; theta <=npar; theta++)
2651: trgradg[h][j][theta]=gradg[h][theta][j];
2652:
2653:
2654: for(ij=1;ij<=nlstate*nlstate;ij++)
2655: for(ji=1;ji<=nlstate*nlstate;ji++)
2656: varhe[ij][ji][(int)age] =0.;
2657:
2658: printf("%d|",(int)age);fflush(stdout);
2659: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2660: for(h=0;h<=nhstepm-1;h++){
2661: for(k=0;k<=nhstepm-1;k++){
2662: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2663: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2664: for(ij=1;ij<=nlstate*nlstate;ij++)
2665: for(ji=1;ji<=nlstate*nlstate;ji++)
2666: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2667: }
2668: }
2669: /* Computing expectancies */
2670: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2671: for(i=1; i<=nlstate;i++)
2672: for(j=1; j<=nlstate;j++)
2673: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2674: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2675:
2676: /* 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]);*/
2677:
2678: }
2679:
2680: fprintf(ficresstdeij,"%3.0f",age );
2681: for(i=1; i<=nlstate;i++){
2682: eip=0.;
2683: vip=0.;
2684: for(j=1; j<=nlstate;j++){
2685: eip += eij[i][j][(int)age];
2686: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2687: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2688: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2689: }
2690: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2691: }
2692: fprintf(ficresstdeij,"\n");
2693:
2694: fprintf(ficrescveij,"%3.0f",age );
2695: for(i=1; i<=nlstate;i++)
2696: for(j=1; j<=nlstate;j++){
2697: cptj= (j-1)*nlstate+i;
2698: for(i2=1; i2<=nlstate;i2++)
2699: for(j2=1; j2<=nlstate;j2++){
2700: cptj2= (j2-1)*nlstate+i2;
2701: if(cptj2 <= cptj)
2702: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2703: }
2704: }
2705: fprintf(ficrescveij,"\n");
2706:
2707: }
2708: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2709: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2710: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2711: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2712: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2713: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2714: printf("\n");
2715: fprintf(ficlog,"\n");
2716:
2717: free_vector(xm,1,npar);
2718: free_vector(xp,1,npar);
2719: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2720: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2721: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2722: }
2723:
2724: /************ Variance ******************/
2725: 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[])
2726: {
2727: /* Variance of health expectancies */
2728: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2729: /* double **newm;*/
2730: double **dnewm,**doldm;
2731: double **dnewmp,**doldmp;
2732: int i, j, nhstepm, hstepm, h, nstepm ;
2733: int k, cptcode;
2734: double *xp;
2735: double **gp, **gm; /* for var eij */
2736: double ***gradg, ***trgradg; /*for var eij */
2737: double **gradgp, **trgradgp; /* for var p point j */
2738: double *gpp, *gmp; /* for var p point j */
2739: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2740: double ***p3mat;
2741: double age,agelim, hf;
2742: double ***mobaverage;
2743: int theta;
2744: char digit[4];
2745: char digitp[25];
2746:
2747: char fileresprobmorprev[FILENAMELENGTH];
2748:
2749: if(popbased==1){
2750: if(mobilav!=0)
2751: strcpy(digitp,"-populbased-mobilav-");
2752: else strcpy(digitp,"-populbased-nomobil-");
2753: }
2754: else
2755: strcpy(digitp,"-stablbased-");
2756:
2757: if (mobilav!=0) {
2758: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2759: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2760: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2761: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2762: }
2763: }
2764:
2765: strcpy(fileresprobmorprev,"prmorprev");
2766: sprintf(digit,"%-d",ij);
2767: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2768: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2769: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2770: strcat(fileresprobmorprev,fileres);
2771: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2772: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2773: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2774: }
2775: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2776:
2777: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2778: pstamp(ficresprobmorprev);
2779: 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);
2780: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2781: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2782: fprintf(ficresprobmorprev," p.%-d SE",j);
2783: for(i=1; i<=nlstate;i++)
2784: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2785: }
2786: fprintf(ficresprobmorprev,"\n");
2787: fprintf(ficgp,"\n# Routine varevsij");
2788: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2789: 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");
2790: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2791: /* } */
2792: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2793: pstamp(ficresvij);
2794: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2795: if(popbased==1)
2796: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2797: else
2798: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2799: fprintf(ficresvij,"# Age");
2800: for(i=1; i<=nlstate;i++)
2801: for(j=1; j<=nlstate;j++)
2802: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2803: fprintf(ficresvij,"\n");
2804:
2805: xp=vector(1,npar);
2806: dnewm=matrix(1,nlstate,1,npar);
2807: doldm=matrix(1,nlstate,1,nlstate);
2808: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2809: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2810:
2811: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2812: gpp=vector(nlstate+1,nlstate+ndeath);
2813: gmp=vector(nlstate+1,nlstate+ndeath);
2814: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2815:
2816: if(estepm < stepm){
2817: printf ("Problem %d lower than %d\n",estepm, stepm);
2818: }
2819: else hstepm=estepm;
2820: /* For example we decided to compute the life expectancy with the smallest unit */
2821: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2822: nhstepm is the number of hstepm from age to agelim
2823: nstepm is the number of stepm from age to agelin.
2824: Look at hpijx to understand the reason of that which relies in memory size
2825: and note for a fixed period like k years */
2826: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2827: survival function given by stepm (the optimization length). Unfortunately it
2828: means that if the survival funtion is printed every two years of age and if
2829: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2830: results. So we changed our mind and took the option of the best precision.
2831: */
2832: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2833: agelim = AGESUP;
2834: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2835: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2836: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2837: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2838: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2839: gp=matrix(0,nhstepm,1,nlstate);
2840: gm=matrix(0,nhstepm,1,nlstate);
2841:
2842:
2843: for(theta=1; theta <=npar; theta++){
2844: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2845: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2846: }
2847: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2848: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2849:
2850: if (popbased==1) {
2851: if(mobilav ==0){
2852: for(i=1; i<=nlstate;i++)
2853: prlim[i][i]=probs[(int)age][i][ij];
2854: }else{ /* mobilav */
2855: for(i=1; i<=nlstate;i++)
2856: prlim[i][i]=mobaverage[(int)age][i][ij];
2857: }
2858: }
2859:
2860: for(j=1; j<= nlstate; j++){
2861: for(h=0; h<=nhstepm; h++){
2862: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2863: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2864: }
2865: }
2866: /* This for computing probability of death (h=1 means
2867: computed over hstepm matrices product = hstepm*stepm months)
2868: as a weighted average of prlim.
2869: */
2870: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2871: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2872: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2873: }
2874: /* end probability of death */
2875:
2876: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2877: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2878: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2879: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2880:
2881: if (popbased==1) {
2882: if(mobilav ==0){
2883: for(i=1; i<=nlstate;i++)
2884: prlim[i][i]=probs[(int)age][i][ij];
2885: }else{ /* mobilav */
2886: for(i=1; i<=nlstate;i++)
2887: prlim[i][i]=mobaverage[(int)age][i][ij];
2888: }
2889: }
2890:
2891: for(j=1; j<= nlstate; j++){
2892: for(h=0; h<=nhstepm; h++){
2893: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2894: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2895: }
2896: }
2897: /* This for computing probability of death (h=1 means
2898: computed over hstepm matrices product = hstepm*stepm months)
2899: as a weighted average of prlim.
2900: */
2901: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2902: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2903: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2904: }
2905: /* end probability of death */
2906:
2907: for(j=1; j<= nlstate; j++) /* vareij */
2908: for(h=0; h<=nhstepm; h++){
2909: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2910: }
2911:
2912: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2913: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2914: }
2915:
2916: } /* End theta */
2917:
2918: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2919:
2920: for(h=0; h<=nhstepm; h++) /* veij */
2921: for(j=1; j<=nlstate;j++)
2922: for(theta=1; theta <=npar; theta++)
2923: trgradg[h][j][theta]=gradg[h][theta][j];
2924:
2925: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2926: for(theta=1; theta <=npar; theta++)
2927: trgradgp[j][theta]=gradgp[theta][j];
2928:
2929:
2930: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2931: for(i=1;i<=nlstate;i++)
2932: for(j=1;j<=nlstate;j++)
2933: vareij[i][j][(int)age] =0.;
2934:
2935: for(h=0;h<=nhstepm;h++){
2936: for(k=0;k<=nhstepm;k++){
2937: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2938: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2939: for(i=1;i<=nlstate;i++)
2940: for(j=1;j<=nlstate;j++)
2941: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2942: }
2943: }
2944:
2945: /* pptj */
2946: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2947: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2948: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2949: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2950: varppt[j][i]=doldmp[j][i];
2951: /* end ppptj */
2952: /* x centered again */
2953: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2954: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2955:
2956: if (popbased==1) {
2957: if(mobilav ==0){
2958: for(i=1; i<=nlstate;i++)
2959: prlim[i][i]=probs[(int)age][i][ij];
2960: }else{ /* mobilav */
2961: for(i=1; i<=nlstate;i++)
2962: prlim[i][i]=mobaverage[(int)age][i][ij];
2963: }
2964: }
2965:
2966: /* This for computing probability of death (h=1 means
2967: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2968: as a weighted average of prlim.
2969: */
2970: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2971: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2972: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2973: }
2974: /* end probability of death */
2975:
2976: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2977: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2978: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2979: for(i=1; i<=nlstate;i++){
2980: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2981: }
2982: }
2983: fprintf(ficresprobmorprev,"\n");
2984:
2985: fprintf(ficresvij,"%.0f ",age );
2986: for(i=1; i<=nlstate;i++)
2987: for(j=1; j<=nlstate;j++){
2988: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2989: }
2990: fprintf(ficresvij,"\n");
2991: free_matrix(gp,0,nhstepm,1,nlstate);
2992: free_matrix(gm,0,nhstepm,1,nlstate);
2993: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2994: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2995: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2996: } /* End age */
2997: free_vector(gpp,nlstate+1,nlstate+ndeath);
2998: free_vector(gmp,nlstate+1,nlstate+ndeath);
2999: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3000: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3001: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3002: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3003: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3004: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3005: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3006: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3007: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3008: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3009: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3010: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3011: 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);
3012: /* 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);
3013: */
3014: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3015: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3016:
3017: free_vector(xp,1,npar);
3018: free_matrix(doldm,1,nlstate,1,nlstate);
3019: free_matrix(dnewm,1,nlstate,1,npar);
3020: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3021: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3022: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3023: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3024: fclose(ficresprobmorprev);
3025: fflush(ficgp);
3026: fflush(fichtm);
3027: } /* end varevsij */
3028:
3029: /************ Variance of prevlim ******************/
3030: 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[])
3031: {
3032: /* Variance of prevalence limit */
3033: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3034: double **newm;
3035: double **dnewm,**doldm;
3036: int i, j, nhstepm, hstepm;
3037: int k, cptcode;
3038: double *xp;
3039: double *gp, *gm;
3040: double **gradg, **trgradg;
3041: double age,agelim;
3042: int theta;
3043:
3044: pstamp(ficresvpl);
3045: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3046: fprintf(ficresvpl,"# Age");
3047: for(i=1; i<=nlstate;i++)
3048: fprintf(ficresvpl," %1d-%1d",i,i);
3049: fprintf(ficresvpl,"\n");
3050:
3051: xp=vector(1,npar);
3052: dnewm=matrix(1,nlstate,1,npar);
3053: doldm=matrix(1,nlstate,1,nlstate);
3054:
3055: hstepm=1*YEARM; /* Every year of age */
3056: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3057: agelim = AGESUP;
3058: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3059: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3060: if (stepm >= YEARM) hstepm=1;
3061: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3062: gradg=matrix(1,npar,1,nlstate);
3063: gp=vector(1,nlstate);
3064: gm=vector(1,nlstate);
3065:
3066: for(theta=1; theta <=npar; theta++){
3067: for(i=1; i<=npar; i++){ /* Computes gradient */
3068: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3069: }
3070: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3071: for(i=1;i<=nlstate;i++)
3072: gp[i] = prlim[i][i];
3073:
3074: for(i=1; i<=npar; i++) /* Computes gradient */
3075: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3076: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3077: for(i=1;i<=nlstate;i++)
3078: gm[i] = prlim[i][i];
3079:
3080: for(i=1;i<=nlstate;i++)
3081: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3082: } /* End theta */
3083:
3084: trgradg =matrix(1,nlstate,1,npar);
3085:
3086: for(j=1; j<=nlstate;j++)
3087: for(theta=1; theta <=npar; theta++)
3088: trgradg[j][theta]=gradg[theta][j];
3089:
3090: for(i=1;i<=nlstate;i++)
3091: varpl[i][(int)age] =0.;
3092: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3093: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3094: for(i=1;i<=nlstate;i++)
3095: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3096:
3097: fprintf(ficresvpl,"%.0f ",age );
3098: for(i=1; i<=nlstate;i++)
3099: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3100: fprintf(ficresvpl,"\n");
3101: free_vector(gp,1,nlstate);
3102: free_vector(gm,1,nlstate);
3103: free_matrix(gradg,1,npar,1,nlstate);
3104: free_matrix(trgradg,1,nlstate,1,npar);
3105: } /* End age */
3106:
3107: free_vector(xp,1,npar);
3108: free_matrix(doldm,1,nlstate,1,npar);
3109: free_matrix(dnewm,1,nlstate,1,nlstate);
3110:
3111: }
3112:
3113: /************ Variance of one-step probabilities ******************/
3114: 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[])
3115: {
3116: int i, j=0, i1, k1, l1, t, tj;
3117: int k2, l2, j1, z1;
3118: int k=0,l, cptcode;
3119: int first=1, first1;
3120: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3121: double **dnewm,**doldm;
3122: double *xp;
3123: double *gp, *gm;
3124: double **gradg, **trgradg;
3125: double **mu;
3126: double age,agelim, cov[NCOVMAX];
3127: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3128: int theta;
3129: char fileresprob[FILENAMELENGTH];
3130: char fileresprobcov[FILENAMELENGTH];
3131: char fileresprobcor[FILENAMELENGTH];
3132:
3133: double ***varpij;
3134:
3135: strcpy(fileresprob,"prob");
3136: strcat(fileresprob,fileres);
3137: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3138: printf("Problem with resultfile: %s\n", fileresprob);
3139: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3140: }
3141: strcpy(fileresprobcov,"probcov");
3142: strcat(fileresprobcov,fileres);
3143: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3144: printf("Problem with resultfile: %s\n", fileresprobcov);
3145: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3146: }
3147: strcpy(fileresprobcor,"probcor");
3148: strcat(fileresprobcor,fileres);
3149: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3150: printf("Problem with resultfile: %s\n", fileresprobcor);
3151: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3152: }
3153: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3154: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3155: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3156: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3157: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3158: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3159: pstamp(ficresprob);
3160: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3161: fprintf(ficresprob,"# Age");
3162: pstamp(ficresprobcov);
3163: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3164: fprintf(ficresprobcov,"# Age");
3165: pstamp(ficresprobcor);
3166: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3167: fprintf(ficresprobcor,"# Age");
3168:
3169:
3170: for(i=1; i<=nlstate;i++)
3171: for(j=1; j<=(nlstate+ndeath);j++){
3172: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3173: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3174: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3175: }
3176: /* fprintf(ficresprob,"\n");
3177: fprintf(ficresprobcov,"\n");
3178: fprintf(ficresprobcor,"\n");
3179: */
3180: xp=vector(1,npar);
3181: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3182: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3183: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3184: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3185: first=1;
3186: fprintf(ficgp,"\n# Routine varprob");
3187: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3188: fprintf(fichtm,"\n");
3189:
3190: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3191: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3192: file %s<br>\n",optionfilehtmcov);
3193: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3194: and drawn. It helps understanding how is the covariance between two incidences.\
3195: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3196: 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. \
3197: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3198: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3199: standard deviations wide on each axis. <br>\
3200: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3201: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3202: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3203:
3204: cov[1]=1;
3205: tj=cptcoveff;
3206: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3207: j1=0;
3208: for(t=1; t<=tj;t++){
3209: for(i1=1; i1<=ncodemax[t];i1++){
3210: j1++;
3211: if (cptcovn>0) {
3212: fprintf(ficresprob, "\n#********** Variable ");
3213: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3214: fprintf(ficresprob, "**********\n#\n");
3215: fprintf(ficresprobcov, "\n#********** Variable ");
3216: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3217: fprintf(ficresprobcov, "**********\n#\n");
3218:
3219: fprintf(ficgp, "\n#********** Variable ");
3220: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3221: fprintf(ficgp, "**********\n#\n");
3222:
3223:
3224: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3225: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3226: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3227:
3228: fprintf(ficresprobcor, "\n#********** Variable ");
3229: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3230: fprintf(ficresprobcor, "**********\n#");
3231: }
3232:
3233: for (age=bage; age<=fage; age ++){
3234: cov[2]=age;
3235: for (k=1; k<=cptcovn;k++) {
3236: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3237: }
3238: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3239: for (k=1; k<=cptcovprod;k++)
3240: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3241:
3242: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3243: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3244: gp=vector(1,(nlstate)*(nlstate+ndeath));
3245: gm=vector(1,(nlstate)*(nlstate+ndeath));
3246:
3247: for(theta=1; theta <=npar; theta++){
3248: for(i=1; i<=npar; i++)
3249: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3250:
3251: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3252:
3253: k=0;
3254: for(i=1; i<= (nlstate); i++){
3255: for(j=1; j<=(nlstate+ndeath);j++){
3256: k=k+1;
3257: gp[k]=pmmij[i][j];
3258: }
3259: }
3260:
3261: for(i=1; i<=npar; i++)
3262: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3263:
3264: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3265: k=0;
3266: for(i=1; i<=(nlstate); i++){
3267: for(j=1; j<=(nlstate+ndeath);j++){
3268: k=k+1;
3269: gm[k]=pmmij[i][j];
3270: }
3271: }
3272:
3273: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3274: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3275: }
3276:
3277: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3278: for(theta=1; theta <=npar; theta++)
3279: trgradg[j][theta]=gradg[theta][j];
3280:
3281: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3282: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3283: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3284: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3285: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3286: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3287:
3288: pmij(pmmij,cov,ncovmodel,x,nlstate);
3289:
3290: k=0;
3291: for(i=1; i<=(nlstate); i++){
3292: for(j=1; j<=(nlstate+ndeath);j++){
3293: k=k+1;
3294: mu[k][(int) age]=pmmij[i][j];
3295: }
3296: }
3297: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3298: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3299: varpij[i][j][(int)age] = doldm[i][j];
3300:
3301: /*printf("\n%d ",(int)age);
3302: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3303: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3304: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3305: }*/
3306:
3307: fprintf(ficresprob,"\n%d ",(int)age);
3308: fprintf(ficresprobcov,"\n%d ",(int)age);
3309: fprintf(ficresprobcor,"\n%d ",(int)age);
3310:
3311: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3312: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3313: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3314: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3315: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3316: }
3317: i=0;
3318: for (k=1; k<=(nlstate);k++){
3319: for (l=1; l<=(nlstate+ndeath);l++){
3320: i=i++;
3321: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3322: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3323: for (j=1; j<=i;j++){
3324: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3325: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3326: }
3327: }
3328: }/* end of loop for state */
3329: } /* end of loop for age */
3330:
3331: /* Confidence intervalle of pij */
3332: /*
3333: fprintf(ficgp,"\nset noparametric;unset label");
3334: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3335: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3336: 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);
3337: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3338: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3339: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3340: */
3341:
3342: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3343: first1=1;
3344: for (k2=1; k2<=(nlstate);k2++){
3345: for (l2=1; l2<=(nlstate+ndeath);l2++){
3346: if(l2==k2) continue;
3347: j=(k2-1)*(nlstate+ndeath)+l2;
3348: for (k1=1; k1<=(nlstate);k1++){
3349: for (l1=1; l1<=(nlstate+ndeath);l1++){
3350: if(l1==k1) continue;
3351: i=(k1-1)*(nlstate+ndeath)+l1;
3352: if(i<=j) continue;
3353: for (age=bage; age<=fage; age ++){
3354: if ((int)age %5==0){
3355: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3356: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3357: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3358: mu1=mu[i][(int) age]/stepm*YEARM ;
3359: mu2=mu[j][(int) age]/stepm*YEARM;
3360: c12=cv12/sqrt(v1*v2);
3361: /* Computing eigen value of matrix of covariance */
3362: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3363: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3364: /* Eigen vectors */
3365: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3366: /*v21=sqrt(1.-v11*v11); *//* error */
3367: v21=(lc1-v1)/cv12*v11;
3368: v12=-v21;
3369: v22=v11;
3370: tnalp=v21/v11;
3371: if(first1==1){
3372: first1=0;
3373: 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);
3374: }
3375: 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);
3376: /*printf(fignu*/
3377: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3378: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3379: if(first==1){
3380: first=0;
3381: fprintf(ficgp,"\nset parametric;unset label");
3382: 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);
3383: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3384: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3385: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3386: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3387: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3388: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3389: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3390: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3391: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3392: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3393: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3394: 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",\
3395: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3396: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3397: }else{
3398: first=0;
3399: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3400: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3401: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3402: 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",\
3403: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3404: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3405: }/* if first */
3406: } /* age mod 5 */
3407: } /* end loop age */
3408: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3409: first=1;
3410: } /*l12 */
3411: } /* k12 */
3412: } /*l1 */
3413: }/* k1 */
3414: } /* loop covariates */
3415: }
3416: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3417: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3418: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3419: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3420: free_vector(xp,1,npar);
3421: fclose(ficresprob);
3422: fclose(ficresprobcov);
3423: fclose(ficresprobcor);
3424: fflush(ficgp);
3425: fflush(fichtmcov);
3426: }
3427:
3428:
3429: /******************* Printing html file ***********/
3430: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3431: int lastpass, int stepm, int weightopt, char model[],\
3432: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3433: int popforecast, int estepm ,\
3434: double jprev1, double mprev1,double anprev1, \
3435: double jprev2, double mprev2,double anprev2){
3436: int jj1, k1, i1, cpt;
3437:
3438: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3439: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3440: </ul>");
3441: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3442: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3443: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3444: fprintf(fichtm,"\
3445: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3446: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3447: fprintf(fichtm,"\
3448: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3449: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3450: fprintf(fichtm,"\
3451: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \
3452: <a href=\"%s\">%s</a> <br>\n</li>",
3453: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3454:
3455:
3456: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3457:
3458: m=cptcoveff;
3459: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3460:
3461: jj1=0;
3462: for(k1=1; k1<=m;k1++){
3463: for(i1=1; i1<=ncodemax[k1];i1++){
3464: jj1++;
3465: if (cptcovn > 0) {
3466: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3467: for (cpt=1; cpt<=cptcoveff;cpt++)
3468: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3469: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3470: }
3471: /* Pij */
3472: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
3473: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3474: /* Quasi-incidences */
3475: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3476: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
3477: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3478: /* Period (stable) prevalence in each health state */
3479: for(cpt=1; cpt<nlstate;cpt++){
3480: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3481: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3482: }
3483: for(cpt=1; cpt<=nlstate;cpt++) {
3484: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3485: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3486: }
3487: } /* end i1 */
3488: }/* End k1 */
3489: fprintf(fichtm,"</ul>");
3490:
3491:
3492: fprintf(fichtm,"\
3493: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3494: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3495:
3496: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3497: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3498: fprintf(fichtm,"\
3499: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3500: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3501:
3502: fprintf(fichtm,"\
3503: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3504: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3505: fprintf(fichtm,"\
3506: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
3507: <a href=\"%s\">%s</a> <br>\n</li>",
3508: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3509: fprintf(fichtm,"\
3510: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
3511: <a href=\"%s\">%s</a> <br>\n</li>",
3512: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3513: fprintf(fichtm,"\
3514: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3515: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3516: fprintf(fichtm,"\
3517: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
3518: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3519: fprintf(fichtm,"\
3520: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3521: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3522:
3523: /* if(popforecast==1) fprintf(fichtm,"\n */
3524: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3525: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3526: /* <br>",fileres,fileres,fileres,fileres); */
3527: /* else */
3528: /* 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); */
3529: fflush(fichtm);
3530: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3531:
3532: m=cptcoveff;
3533: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3534:
3535: jj1=0;
3536: for(k1=1; k1<=m;k1++){
3537: for(i1=1; i1<=ncodemax[k1];i1++){
3538: jj1++;
3539: if (cptcovn > 0) {
3540: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3541: for (cpt=1; cpt<=cptcoveff;cpt++)
3542: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3543: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3544: }
3545: for(cpt=1; cpt<=nlstate;cpt++) {
3546: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3547: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3548: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3549: }
3550: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3551: health expectancies in states (1) and (2): %s%d.png<br>\
3552: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3553: } /* end i1 */
3554: }/* End k1 */
3555: fprintf(fichtm,"</ul>");
3556: fflush(fichtm);
3557: }
3558:
3559: /******************* Gnuplot file **************/
3560: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3561:
3562: char dirfileres[132],optfileres[132];
3563: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3564: int ng;
3565: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3566: /* printf("Problem with file %s",optionfilegnuplot); */
3567: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3568: /* } */
3569:
3570: /*#ifdef windows */
3571: fprintf(ficgp,"cd \"%s\" \n",pathc);
3572: /*#endif */
3573: m=pow(2,cptcoveff);
3574:
3575: strcpy(dirfileres,optionfilefiname);
3576: strcpy(optfileres,"vpl");
3577: /* 1eme*/
3578: for (cpt=1; cpt<= nlstate ; cpt ++) {
3579: for (k1=1; k1<= m ; k1 ++) {
3580: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3581: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3582: fprintf(ficgp,"set xlabel \"Age\" \n\
3583: set ylabel \"Probability\" \n\
3584: set ter png small\n\
3585: set size 0.65,0.65\n\
3586: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3587:
3588: for (i=1; i<= nlstate ; i ++) {
3589: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3590: else fprintf(ficgp," \%%*lf (\%%*lf)");
3591: }
3592: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3593: for (i=1; i<= nlstate ; i ++) {
3594: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3595: else fprintf(ficgp," \%%*lf (\%%*lf)");
3596: }
3597: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3598: for (i=1; i<= nlstate ; i ++) {
3599: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3600: else fprintf(ficgp," \%%*lf (\%%*lf)");
3601: }
3602: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3603: }
3604: }
3605: /*2 eme*/
3606:
3607: for (k1=1; k1<= m ; k1 ++) {
3608: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3609: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3610:
3611: for (i=1; i<= nlstate+1 ; i ++) {
3612: k=2*i;
3613: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3614: for (j=1; j<= nlstate+1 ; j ++) {
3615: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3616: else fprintf(ficgp," \%%*lf (\%%*lf)");
3617: }
3618: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3619: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3620: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3621: for (j=1; j<= nlstate+1 ; j ++) {
3622: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3623: else fprintf(ficgp," \%%*lf (\%%*lf)");
3624: }
3625: fprintf(ficgp,"\" t\"\" w l 0,");
3626: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3627: for (j=1; j<= nlstate+1 ; j ++) {
3628: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3629: else fprintf(ficgp," \%%*lf (\%%*lf)");
3630: }
3631: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3632: else fprintf(ficgp,"\" t\"\" w l 0,");
3633: }
3634: }
3635:
3636: /*3eme*/
3637:
3638: for (k1=1; k1<= m ; k1 ++) {
3639: for (cpt=1; cpt<= nlstate ; cpt ++) {
3640: /* k=2+nlstate*(2*cpt-2); */
3641: k=2+(nlstate+1)*(cpt-1);
3642: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3643: fprintf(ficgp,"set ter png small\n\
3644: set size 0.65,0.65\n\
3645: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3646: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3647: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3648: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3649: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3650: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3651: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3652:
3653: */
3654: for (i=1; i< nlstate ; i ++) {
3655: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
3656: /* 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);*/
3657:
3658: }
3659: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3660: }
3661: }
3662:
3663: /* CV preval stable (period) */
3664: for (k1=1; k1<= m ; k1 ++) {
3665: for (cpt=1; cpt<=nlstate ; cpt ++) {
3666: k=3;
3667: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3668: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3669: set ter png small\nset size 0.65,0.65\n\
3670: unset log y\n\
3671: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3672:
3673: for (i=1; i< nlstate ; i ++)
3674: fprintf(ficgp,"+$%d",k+i+1);
3675: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3676:
3677: l=3+(nlstate+ndeath)*cpt;
3678: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3679: for (i=1; i< nlstate ; i ++) {
3680: l=3+(nlstate+ndeath)*cpt;
3681: fprintf(ficgp,"+$%d",l+i+1);
3682: }
3683: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3684: }
3685: }
3686:
3687: /* proba elementaires */
3688: for(i=1,jk=1; i <=nlstate; i++){
3689: for(k=1; k <=(nlstate+ndeath); k++){
3690: if (k != i) {
3691: for(j=1; j <=ncovmodel; j++){
3692: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3693: jk++;
3694: fprintf(ficgp,"\n");
3695: }
3696: }
3697: }
3698: }
3699:
3700: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3701: for(jk=1; jk <=m; jk++) {
3702: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3703: if (ng==2)
3704: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3705: else
3706: fprintf(ficgp,"\nset title \"Probability\"\n");
3707: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3708: i=1;
3709: for(k2=1; k2<=nlstate; k2++) {
3710: k3=i;
3711: for(k=1; k<=(nlstate+ndeath); k++) {
3712: if (k != k2){
3713: if(ng==2)
3714: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3715: else
3716: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3717: ij=1;
3718: for(j=3; j <=ncovmodel; j++) {
3719: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3720: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3721: ij++;
3722: }
3723: else
3724: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3725: }
3726: fprintf(ficgp,")/(1");
3727:
3728: for(k1=1; k1 <=nlstate; k1++){
3729: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3730: ij=1;
3731: for(j=3; j <=ncovmodel; j++){
3732: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3733: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3734: ij++;
3735: }
3736: else
3737: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3738: }
3739: fprintf(ficgp,")");
3740: }
3741: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3742: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3743: i=i+ncovmodel;
3744: }
3745: } /* end k */
3746: } /* end k2 */
3747: } /* end jk */
3748: } /* end ng */
3749: fflush(ficgp);
3750: } /* end gnuplot */
3751:
3752:
3753: /*************** Moving average **************/
3754: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3755:
3756: int i, cpt, cptcod;
3757: int modcovmax =1;
3758: int mobilavrange, mob;
3759: double age;
3760:
3761: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3762: a covariate has 2 modalities */
3763: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3764:
3765: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3766: if(mobilav==1) mobilavrange=5; /* default */
3767: else mobilavrange=mobilav;
3768: for (age=bage; age<=fage; age++)
3769: for (i=1; i<=nlstate;i++)
3770: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3771: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3772: /* We keep the original values on the extreme ages bage, fage and for
3773: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3774: we use a 5 terms etc. until the borders are no more concerned.
3775: */
3776: for (mob=3;mob <=mobilavrange;mob=mob+2){
3777: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3778: for (i=1; i<=nlstate;i++){
3779: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3780: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3781: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3782: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3783: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3784: }
3785: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3786: }
3787: }
3788: }/* end age */
3789: }/* end mob */
3790: }else return -1;
3791: return 0;
3792: }/* End movingaverage */
3793:
3794:
3795: /************** Forecasting ******************/
3796: 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){
3797: /* proj1, year, month, day of starting projection
3798: agemin, agemax range of age
3799: dateprev1 dateprev2 range of dates during which prevalence is computed
3800: anproj2 year of en of projection (same day and month as proj1).
3801: */
3802: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3803: int *popage;
3804: double agec; /* generic age */
3805: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3806: double *popeffectif,*popcount;
3807: double ***p3mat;
3808: double ***mobaverage;
3809: char fileresf[FILENAMELENGTH];
3810:
3811: agelim=AGESUP;
3812: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3813:
3814: strcpy(fileresf,"f");
3815: strcat(fileresf,fileres);
3816: if((ficresf=fopen(fileresf,"w"))==NULL) {
3817: printf("Problem with forecast resultfile: %s\n", fileresf);
3818: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3819: }
3820: printf("Computing forecasting: result on file '%s' \n", fileresf);
3821: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3822:
3823: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3824:
3825: if (mobilav!=0) {
3826: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3827: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3828: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3829: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3830: }
3831: }
3832:
3833: stepsize=(int) (stepm+YEARM-1)/YEARM;
3834: if (stepm<=12) stepsize=1;
3835: if(estepm < stepm){
3836: printf ("Problem %d lower than %d\n",estepm, stepm);
3837: }
3838: else hstepm=estepm;
3839:
3840: hstepm=hstepm/stepm;
3841: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3842: fractional in yp1 */
3843: anprojmean=yp;
3844: yp2=modf((yp1*12),&yp);
3845: mprojmean=yp;
3846: yp1=modf((yp2*30.5),&yp);
3847: jprojmean=yp;
3848: if(jprojmean==0) jprojmean=1;
3849: if(mprojmean==0) jprojmean=1;
3850:
3851: i1=cptcoveff;
3852: if (cptcovn < 1){i1=1;}
3853:
3854: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3855:
3856: fprintf(ficresf,"#****** Routine prevforecast **\n");
3857:
3858: /* if (h==(int)(YEARM*yearp)){ */
3859: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3860: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3861: k=k+1;
3862: fprintf(ficresf,"\n#******");
3863: for(j=1;j<=cptcoveff;j++) {
3864: 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]]);
3865: }
3866: fprintf(ficresf,"******\n");
3867: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3868: for(j=1; j<=nlstate+ndeath;j++){
3869: for(i=1; i<=nlstate;i++)
3870: fprintf(ficresf," p%d%d",i,j);
3871: fprintf(ficresf," p.%d",j);
3872: }
3873: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3874: fprintf(ficresf,"\n");
3875: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3876:
3877: for (agec=fage; agec>=(ageminpar-1); agec--){
3878: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3879: nhstepm = nhstepm/hstepm;
3880: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3881: oldm=oldms;savm=savms;
3882: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3883:
3884: for (h=0; h<=nhstepm; h++){
3885: if (h*hstepm/YEARM*stepm ==yearp) {
3886: fprintf(ficresf,"\n");
3887: for(j=1;j<=cptcoveff;j++)
3888: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3889: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3890: }
3891: for(j=1; j<=nlstate+ndeath;j++) {
3892: ppij=0.;
3893: for(i=1; i<=nlstate;i++) {
3894: if (mobilav==1)
3895: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3896: else {
3897: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3898: }
3899: if (h*hstepm/YEARM*stepm== yearp) {
3900: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3901: }
3902: } /* end i */
3903: if (h*hstepm/YEARM*stepm==yearp) {
3904: fprintf(ficresf," %.3f", ppij);
3905: }
3906: }/* end j */
3907: } /* end h */
3908: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3909: } /* end agec */
3910: } /* end yearp */
3911: } /* end cptcod */
3912: } /* end cptcov */
3913:
3914: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3915:
3916: fclose(ficresf);
3917: }
3918:
3919: /************** Forecasting *****not tested NB*************/
3920: 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){
3921:
3922: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3923: int *popage;
3924: double calagedatem, agelim, kk1, kk2;
3925: double *popeffectif,*popcount;
3926: double ***p3mat,***tabpop,***tabpopprev;
3927: double ***mobaverage;
3928: char filerespop[FILENAMELENGTH];
3929:
3930: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3931: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3932: agelim=AGESUP;
3933: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3934:
3935: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3936:
3937:
3938: strcpy(filerespop,"pop");
3939: strcat(filerespop,fileres);
3940: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3941: printf("Problem with forecast resultfile: %s\n", filerespop);
3942: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3943: }
3944: printf("Computing forecasting: result on file '%s' \n", filerespop);
3945: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3946:
3947: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3948:
3949: if (mobilav!=0) {
3950: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3951: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3952: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3953: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3954: }
3955: }
3956:
3957: stepsize=(int) (stepm+YEARM-1)/YEARM;
3958: if (stepm<=12) stepsize=1;
3959:
3960: agelim=AGESUP;
3961:
3962: hstepm=1;
3963: hstepm=hstepm/stepm;
3964:
3965: if (popforecast==1) {
3966: if((ficpop=fopen(popfile,"r"))==NULL) {
3967: printf("Problem with population file : %s\n",popfile);exit(0);
3968: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3969: }
3970: popage=ivector(0,AGESUP);
3971: popeffectif=vector(0,AGESUP);
3972: popcount=vector(0,AGESUP);
3973:
3974: i=1;
3975: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3976:
3977: imx=i;
3978: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3979: }
3980:
3981: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3982: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3983: k=k+1;
3984: fprintf(ficrespop,"\n#******");
3985: for(j=1;j<=cptcoveff;j++) {
3986: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3987: }
3988: fprintf(ficrespop,"******\n");
3989: fprintf(ficrespop,"# Age");
3990: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3991: if (popforecast==1) fprintf(ficrespop," [Population]");
3992:
3993: for (cpt=0; cpt<=0;cpt++) {
3994: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3995:
3996: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3997: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3998: nhstepm = nhstepm/hstepm;
3999:
4000: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4001: oldm=oldms;savm=savms;
4002: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4003:
4004: for (h=0; h<=nhstepm; h++){
4005: if (h==(int) (calagedatem+YEARM*cpt)) {
4006: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4007: }
4008: for(j=1; j<=nlstate+ndeath;j++) {
4009: kk1=0.;kk2=0;
4010: for(i=1; i<=nlstate;i++) {
4011: if (mobilav==1)
4012: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4013: else {
4014: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4015: }
4016: }
4017: if (h==(int)(calagedatem+12*cpt)){
4018: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4019: /*fprintf(ficrespop," %.3f", kk1);
4020: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4021: }
4022: }
4023: for(i=1; i<=nlstate;i++){
4024: kk1=0.;
4025: for(j=1; j<=nlstate;j++){
4026: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4027: }
4028: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4029: }
4030:
4031: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4032: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4033: }
4034: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4035: }
4036: }
4037:
4038: /******/
4039:
4040: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4041: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4042: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4043: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4044: nhstepm = nhstepm/hstepm;
4045:
4046: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4047: oldm=oldms;savm=savms;
4048: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4049: for (h=0; h<=nhstepm; h++){
4050: if (h==(int) (calagedatem+YEARM*cpt)) {
4051: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4052: }
4053: for(j=1; j<=nlstate+ndeath;j++) {
4054: kk1=0.;kk2=0;
4055: for(i=1; i<=nlstate;i++) {
4056: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4057: }
4058: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4059: }
4060: }
4061: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4062: }
4063: }
4064: }
4065: }
4066:
4067: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4068:
4069: if (popforecast==1) {
4070: free_ivector(popage,0,AGESUP);
4071: free_vector(popeffectif,0,AGESUP);
4072: free_vector(popcount,0,AGESUP);
4073: }
4074: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4075: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4076: fclose(ficrespop);
4077: } /* End of popforecast */
4078:
4079: int fileappend(FILE *fichier, char *optionfich)
4080: {
4081: if((fichier=fopen(optionfich,"a"))==NULL) {
4082: printf("Problem with file: %s\n", optionfich);
4083: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4084: return (0);
4085: }
4086: fflush(fichier);
4087: return (1);
4088: }
4089:
4090:
4091: /**************** function prwizard **********************/
4092: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4093: {
4094:
4095: /* Wizard to print covariance matrix template */
4096:
4097: char ca[32], cb[32], cc[32];
4098: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4099: int numlinepar;
4100:
4101: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4102: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4103: for(i=1; i <=nlstate; i++){
4104: jj=0;
4105: for(j=1; j <=nlstate+ndeath; j++){
4106: if(j==i) continue;
4107: jj++;
4108: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4109: printf("%1d%1d",i,j);
4110: fprintf(ficparo,"%1d%1d",i,j);
4111: for(k=1; k<=ncovmodel;k++){
4112: /* printf(" %lf",param[i][j][k]); */
4113: /* fprintf(ficparo," %lf",param[i][j][k]); */
4114: printf(" 0.");
4115: fprintf(ficparo," 0.");
4116: }
4117: printf("\n");
4118: fprintf(ficparo,"\n");
4119: }
4120: }
4121: printf("# Scales (for hessian or gradient estimation)\n");
4122: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4123: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4124: for(i=1; i <=nlstate; i++){
4125: jj=0;
4126: for(j=1; j <=nlstate+ndeath; j++){
4127: if(j==i) continue;
4128: jj++;
4129: fprintf(ficparo,"%1d%1d",i,j);
4130: printf("%1d%1d",i,j);
4131: fflush(stdout);
4132: for(k=1; k<=ncovmodel;k++){
4133: /* printf(" %le",delti3[i][j][k]); */
4134: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4135: printf(" 0.");
4136: fprintf(ficparo," 0.");
4137: }
4138: numlinepar++;
4139: printf("\n");
4140: fprintf(ficparo,"\n");
4141: }
4142: }
4143: printf("# Covariance matrix\n");
4144: /* # 121 Var(a12)\n\ */
4145: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4146: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4147: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4148: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4149: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4150: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4151: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4152: fflush(stdout);
4153: fprintf(ficparo,"# Covariance matrix\n");
4154: /* # 121 Var(a12)\n\ */
4155: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4156: /* # ...\n\ */
4157: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4158:
4159: for(itimes=1;itimes<=2;itimes++){
4160: jj=0;
4161: for(i=1; i <=nlstate; i++){
4162: for(j=1; j <=nlstate+ndeath; j++){
4163: if(j==i) continue;
4164: for(k=1; k<=ncovmodel;k++){
4165: jj++;
4166: ca[0]= k+'a'-1;ca[1]='\0';
4167: if(itimes==1){
4168: printf("#%1d%1d%d",i,j,k);
4169: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4170: }else{
4171: printf("%1d%1d%d",i,j,k);
4172: fprintf(ficparo,"%1d%1d%d",i,j,k);
4173: /* printf(" %.5le",matcov[i][j]); */
4174: }
4175: ll=0;
4176: for(li=1;li <=nlstate; li++){
4177: for(lj=1;lj <=nlstate+ndeath; lj++){
4178: if(lj==li) continue;
4179: for(lk=1;lk<=ncovmodel;lk++){
4180: ll++;
4181: if(ll<=jj){
4182: cb[0]= lk +'a'-1;cb[1]='\0';
4183: if(ll<jj){
4184: if(itimes==1){
4185: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4186: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4187: }else{
4188: printf(" 0.");
4189: fprintf(ficparo," 0.");
4190: }
4191: }else{
4192: if(itimes==1){
4193: printf(" Var(%s%1d%1d)",ca,i,j);
4194: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4195: }else{
4196: printf(" 0.");
4197: fprintf(ficparo," 0.");
4198: }
4199: }
4200: }
4201: } /* end lk */
4202: } /* end lj */
4203: } /* end li */
4204: printf("\n");
4205: fprintf(ficparo,"\n");
4206: numlinepar++;
4207: } /* end k*/
4208: } /*end j */
4209: } /* end i */
4210: } /* end itimes */
4211:
4212: } /* end of prwizard */
4213: /******************* Gompertz Likelihood ******************************/
4214: double gompertz(double x[])
4215: {
4216: double A,B,L=0.0,sump=0.,num=0.;
4217: int i,n=0; /* n is the size of the sample */
4218:
4219: for (i=0;i<=imx-1 ; i++) {
4220: sump=sump+weight[i];
4221: /* sump=sump+1;*/
4222: num=num+1;
4223: }
4224:
4225:
4226: /* for (i=0; i<=imx; i++)
4227: 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]);*/
4228:
4229: for (i=1;i<=imx ; i++)
4230: {
4231: if (cens[i] == 1 && wav[i]>1)
4232: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4233:
4234: if (cens[i] == 0 && wav[i]>1)
4235: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4236: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4237:
4238: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4239: if (wav[i] > 1 ) { /* ??? */
4240: L=L+A*weight[i];
4241: /* 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]);*/
4242: }
4243: }
4244:
4245: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4246:
4247: return -2*L*num/sump;
4248: }
4249:
4250: /******************* Printing html file ***********/
4251: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4252: int lastpass, int stepm, int weightopt, char model[],\
4253: int imx, double p[],double **matcov,double agemortsup){
4254: int i,k;
4255:
4256: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4257: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4258: for (i=1;i<=2;i++)
4259: 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]));
4260: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4261: fprintf(fichtm,"</ul>");
4262:
4263: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4264:
4265: 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>");
4266:
4267: for (k=agegomp;k<(agemortsup-2);k++)
4268: 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]);
4269:
4270:
4271: fflush(fichtm);
4272: }
4273:
4274: /******************* Gnuplot file **************/
4275: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4276:
4277: char dirfileres[132],optfileres[132];
4278: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4279: int ng;
4280:
4281:
4282: /*#ifdef windows */
4283: fprintf(ficgp,"cd \"%s\" \n",pathc);
4284: /*#endif */
4285:
4286:
4287: strcpy(dirfileres,optionfilefiname);
4288: strcpy(optfileres,"vpl");
4289: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4290: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4291: fprintf(ficgp, "set ter png small\n set log y\n");
4292: fprintf(ficgp, "set size 0.65,0.65\n");
4293: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4294:
4295: }
4296:
4297:
4298:
4299:
4300:
4301: /***********************************************/
4302: /**************** Main Program *****************/
4303: /***********************************************/
4304:
4305: int main(int argc, char *argv[])
4306: {
4307: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4308: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4309: int linei, month, year,iout;
4310: int jj, ll, li, lj, lk, imk;
4311: int numlinepar=0; /* Current linenumber of parameter file */
4312: int itimes;
4313: int NDIM=2;
4314:
4315: char ca[32], cb[32], cc[32];
4316: char dummy[]=" ";
4317: /* FILE *fichtm; *//* Html File */
4318: /* FILE *ficgp;*/ /*Gnuplot File */
4319: struct stat info;
4320: double agedeb, agefin,hf;
4321: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4322:
4323: double fret;
4324: double **xi,tmp,delta;
4325:
4326: double dum; /* Dummy variable */
4327: double ***p3mat;
4328: double ***mobaverage;
4329: int *indx;
4330: char line[MAXLINE], linepar[MAXLINE];
4331: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4332: char pathr[MAXLINE], pathimach[MAXLINE];
4333: char **bp, *tok, *val; /* pathtot */
4334: int firstobs=1, lastobs=10;
4335: int sdeb, sfin; /* Status at beginning and end */
4336: int c, h , cpt,l;
4337: int ju,jl, mi;
4338: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4339: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4340: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4341: int mobilav=0,popforecast=0;
4342: int hstepm, nhstepm;
4343: int agemortsup;
4344: float sumlpop=0.;
4345: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4346: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4347:
4348: double bage, fage, age, agelim, agebase;
4349: double ftolpl=FTOL;
4350: double **prlim;
4351: double *severity;
4352: double ***param; /* Matrix of parameters */
4353: double *p;
4354: double **matcov; /* Matrix of covariance */
4355: double ***delti3; /* Scale */
4356: double *delti; /* Scale */
4357: double ***eij, ***vareij;
4358: double **varpl; /* Variances of prevalence limits by age */
4359: double *epj, vepp;
4360: double kk1, kk2;
4361: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4362: double **ximort;
4363: char *alph[]={"a","a","b","c","d","e"}, str[4];
4364: int *dcwave;
4365:
4366: char z[1]="c", occ;
4367:
4368: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4369: char *strt, strtend[80];
4370: char *stratrunc;
4371: int lstra;
4372:
4373: long total_usecs;
4374:
4375: /* setlocale (LC_ALL, ""); */
4376: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4377: /* textdomain (PACKAGE); */
4378: /* setlocale (LC_CTYPE, ""); */
4379: /* setlocale (LC_MESSAGES, ""); */
4380:
4381: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4382: (void) gettimeofday(&start_time,&tzp);
4383: curr_time=start_time;
4384: tm = *localtime(&start_time.tv_sec);
4385: tmg = *gmtime(&start_time.tv_sec);
4386: strcpy(strstart,asctime(&tm));
4387:
4388: /* printf("Localtime (at start)=%s",strstart); */
4389: /* tp.tv_sec = tp.tv_sec +86400; */
4390: /* tm = *localtime(&start_time.tv_sec); */
4391: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4392: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4393: /* tmg.tm_hour=tmg.tm_hour + 1; */
4394: /* tp.tv_sec = mktime(&tmg); */
4395: /* strt=asctime(&tmg); */
4396: /* printf("Time(after) =%s",strstart); */
4397: /* (void) time (&time_value);
4398: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4399: * tm = *localtime(&time_value);
4400: * strstart=asctime(&tm);
4401: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4402: */
4403:
4404: nberr=0; /* Number of errors and warnings */
4405: nbwarn=0;
4406: getcwd(pathcd, size);
4407:
4408: printf("\n%s\n%s",version,fullversion);
4409: if(argc <=1){
4410: printf("\nEnter the parameter file name: ");
4411: fgets(pathr,FILENAMELENGTH,stdin);
4412: i=strlen(pathr);
4413: if(pathr[i-1]=='\n')
4414: pathr[i-1]='\0';
4415: for (tok = pathr; tok != NULL; ){
4416: printf("Pathr |%s|\n",pathr);
4417: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4418: printf("val= |%s| pathr=%s\n",val,pathr);
4419: strcpy (pathtot, val);
4420: if(pathr[0] == '\0') break; /* Dirty */
4421: }
4422: }
4423: else{
4424: strcpy(pathtot,argv[1]);
4425: }
4426: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4427: /*cygwin_split_path(pathtot,path,optionfile);
4428: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4429: /* cutv(path,optionfile,pathtot,'\\');*/
4430:
4431: /* Split argv[0], imach program to get pathimach */
4432: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4433: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4434: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4435: /* strcpy(pathimach,argv[0]); */
4436: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4437: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4438: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4439: chdir(path); /* Can be a relative path */
4440: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4441: printf("Current directory %s!\n",pathcd);
4442: strcpy(command,"mkdir ");
4443: strcat(command,optionfilefiname);
4444: if((outcmd=system(command)) != 0){
4445: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4446: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4447: /* fclose(ficlog); */
4448: /* exit(1); */
4449: }
4450: /* if((imk=mkdir(optionfilefiname))<0){ */
4451: /* perror("mkdir"); */
4452: /* } */
4453:
4454: /*-------- arguments in the command line --------*/
4455:
4456: /* Log file */
4457: strcat(filelog, optionfilefiname);
4458: strcat(filelog,".log"); /* */
4459: if((ficlog=fopen(filelog,"w"))==NULL) {
4460: printf("Problem with logfile %s\n",filelog);
4461: goto end;
4462: }
4463: fprintf(ficlog,"Log filename:%s\n",filelog);
4464: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4465: fprintf(ficlog,"\nEnter the parameter file name: \n");
4466: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4467: path=%s \n\
4468: optionfile=%s\n\
4469: optionfilext=%s\n\
4470: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4471:
4472: printf("Local time (at start):%s",strstart);
4473: fprintf(ficlog,"Local time (at start): %s",strstart);
4474: fflush(ficlog);
4475: /* (void) gettimeofday(&curr_time,&tzp); */
4476: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4477:
4478: /* */
4479: strcpy(fileres,"r");
4480: strcat(fileres, optionfilefiname);
4481: strcat(fileres,".txt"); /* Other files have txt extension */
4482:
4483: /*---------arguments file --------*/
4484:
4485: if((ficpar=fopen(optionfile,"r"))==NULL) {
4486: printf("Problem with optionfile %s\n",optionfile);
4487: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4488: fflush(ficlog);
4489: goto end;
4490: }
4491:
4492:
4493:
4494: strcpy(filereso,"o");
4495: strcat(filereso,fileres);
4496: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4497: printf("Problem with Output resultfile: %s\n", filereso);
4498: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4499: fflush(ficlog);
4500: goto end;
4501: }
4502:
4503: /* Reads comments: lines beginning with '#' */
4504: numlinepar=0;
4505: while((c=getc(ficpar))=='#' && c!= EOF){
4506: ungetc(c,ficpar);
4507: fgets(line, MAXLINE, ficpar);
4508: numlinepar++;
4509: puts(line);
4510: fputs(line,ficparo);
4511: fputs(line,ficlog);
4512: }
4513: ungetc(c,ficpar);
4514:
4515: 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);
4516: numlinepar++;
4517: 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);
4518: 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);
4519: 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);
4520: fflush(ficlog);
4521: while((c=getc(ficpar))=='#' && c!= EOF){
4522: ungetc(c,ficpar);
4523: fgets(line, MAXLINE, ficpar);
4524: numlinepar++;
4525: puts(line);
4526: fputs(line,ficparo);
4527: fputs(line,ficlog);
4528: }
4529: ungetc(c,ficpar);
4530:
4531:
4532: covar=matrix(0,NCOVMAX,1,n);
4533: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4534: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4535:
4536: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4537: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4538: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4539:
4540: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4541: delti=delti3[1][1];
4542: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4543: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4544: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4545: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4546: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4547: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4548: fclose (ficparo);
4549: fclose (ficlog);
4550: exit(0);
4551: }
4552: else if(mle==-3) {
4553: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4554: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4555: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4556: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4557: matcov=matrix(1,npar,1,npar);
4558: }
4559: else{
4560: /* Read guess parameters */
4561: /* Reads comments: lines beginning with '#' */
4562: while((c=getc(ficpar))=='#' && c!= EOF){
4563: ungetc(c,ficpar);
4564: fgets(line, MAXLINE, ficpar);
4565: numlinepar++;
4566: puts(line);
4567: fputs(line,ficparo);
4568: fputs(line,ficlog);
4569: }
4570: ungetc(c,ficpar);
4571:
4572: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4573: for(i=1; i <=nlstate; i++){
4574: j=0;
4575: for(jj=1; jj <=nlstate+ndeath; jj++){
4576: if(jj==i) continue;
4577: j++;
4578: fscanf(ficpar,"%1d%1d",&i1,&j1);
4579: if ((i1 != i) && (j1 != j)){
4580: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4581: exit(1);
4582: }
4583: fprintf(ficparo,"%1d%1d",i1,j1);
4584: if(mle==1)
4585: printf("%1d%1d",i,j);
4586: fprintf(ficlog,"%1d%1d",i,j);
4587: for(k=1; k<=ncovmodel;k++){
4588: fscanf(ficpar," %lf",¶m[i][j][k]);
4589: if(mle==1){
4590: printf(" %lf",param[i][j][k]);
4591: fprintf(ficlog," %lf",param[i][j][k]);
4592: }
4593: else
4594: fprintf(ficlog," %lf",param[i][j][k]);
4595: fprintf(ficparo," %lf",param[i][j][k]);
4596: }
4597: fscanf(ficpar,"\n");
4598: numlinepar++;
4599: if(mle==1)
4600: printf("\n");
4601: fprintf(ficlog,"\n");
4602: fprintf(ficparo,"\n");
4603: }
4604: }
4605: fflush(ficlog);
4606:
4607: p=param[1][1];
4608:
4609: /* Reads comments: lines beginning with '#' */
4610: while((c=getc(ficpar))=='#' && c!= EOF){
4611: ungetc(c,ficpar);
4612: fgets(line, MAXLINE, ficpar);
4613: numlinepar++;
4614: puts(line);
4615: fputs(line,ficparo);
4616: fputs(line,ficlog);
4617: }
4618: ungetc(c,ficpar);
4619:
4620: for(i=1; i <=nlstate; i++){
4621: for(j=1; j <=nlstate+ndeath-1; j++){
4622: fscanf(ficpar,"%1d%1d",&i1,&j1);
4623: if ((i1-i)*(j1-j)!=0){
4624: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4625: exit(1);
4626: }
4627: printf("%1d%1d",i,j);
4628: fprintf(ficparo,"%1d%1d",i1,j1);
4629: fprintf(ficlog,"%1d%1d",i1,j1);
4630: for(k=1; k<=ncovmodel;k++){
4631: fscanf(ficpar,"%le",&delti3[i][j][k]);
4632: printf(" %le",delti3[i][j][k]);
4633: fprintf(ficparo," %le",delti3[i][j][k]);
4634: fprintf(ficlog," %le",delti3[i][j][k]);
4635: }
4636: fscanf(ficpar,"\n");
4637: numlinepar++;
4638: printf("\n");
4639: fprintf(ficparo,"\n");
4640: fprintf(ficlog,"\n");
4641: }
4642: }
4643: fflush(ficlog);
4644:
4645: delti=delti3[1][1];
4646:
4647:
4648: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4649:
4650: /* Reads comments: lines beginning with '#' */
4651: while((c=getc(ficpar))=='#' && c!= EOF){
4652: ungetc(c,ficpar);
4653: fgets(line, MAXLINE, ficpar);
4654: numlinepar++;
4655: puts(line);
4656: fputs(line,ficparo);
4657: fputs(line,ficlog);
4658: }
4659: ungetc(c,ficpar);
4660:
4661: matcov=matrix(1,npar,1,npar);
4662: for(i=1; i <=npar; i++){
4663: fscanf(ficpar,"%s",&str);
4664: if(mle==1)
4665: printf("%s",str);
4666: fprintf(ficlog,"%s",str);
4667: fprintf(ficparo,"%s",str);
4668: for(j=1; j <=i; j++){
4669: fscanf(ficpar," %le",&matcov[i][j]);
4670: if(mle==1){
4671: printf(" %.5le",matcov[i][j]);
4672: }
4673: fprintf(ficlog," %.5le",matcov[i][j]);
4674: fprintf(ficparo," %.5le",matcov[i][j]);
4675: }
4676: fscanf(ficpar,"\n");
4677: numlinepar++;
4678: if(mle==1)
4679: printf("\n");
4680: fprintf(ficlog,"\n");
4681: fprintf(ficparo,"\n");
4682: }
4683: for(i=1; i <=npar; i++)
4684: for(j=i+1;j<=npar;j++)
4685: matcov[i][j]=matcov[j][i];
4686:
4687: if(mle==1)
4688: printf("\n");
4689: fprintf(ficlog,"\n");
4690:
4691: fflush(ficlog);
4692:
4693: /*-------- Rewriting parameter file ----------*/
4694: strcpy(rfileres,"r"); /* "Rparameterfile */
4695: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4696: strcat(rfileres,"."); /* */
4697: strcat(rfileres,optionfilext); /* Other files have txt extension */
4698: if((ficres =fopen(rfileres,"w"))==NULL) {
4699: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4700: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4701: }
4702: fprintf(ficres,"#%s\n",version);
4703: } /* End of mle != -3 */
4704:
4705: /*-------- data file ----------*/
4706: if((fic=fopen(datafile,"r"))==NULL) {
4707: printf("Problem while opening datafile: %s\n", datafile);goto end;
4708: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4709: }
4710:
4711: n= lastobs;
4712: severity = vector(1,maxwav);
4713: outcome=imatrix(1,maxwav+1,1,n);
4714: num=lvector(1,n);
4715: moisnais=vector(1,n);
4716: annais=vector(1,n);
4717: moisdc=vector(1,n);
4718: andc=vector(1,n);
4719: agedc=vector(1,n);
4720: cod=ivector(1,n);
4721: weight=vector(1,n);
4722: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4723: mint=matrix(1,maxwav,1,n);
4724: anint=matrix(1,maxwav,1,n);
4725: s=imatrix(1,maxwav+1,1,n);
4726: tab=ivector(1,NCOVMAX);
4727: ncodemax=ivector(1,8);
4728:
4729: i=1;
4730: linei=0;
4731: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4732: linei=linei+1;
4733: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4734: if(line[j] == '\t')
4735: line[j] = ' ';
4736: }
4737: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4738: ;
4739: };
4740: line[j+1]=0; /* Trims blanks at end of line */
4741: if(line[0]=='#'){
4742: fprintf(ficlog,"Comment line\n%s\n",line);
4743: printf("Comment line\n%s\n",line);
4744: continue;
4745: }
4746:
4747: for (j=maxwav;j>=1;j--){
4748: cutv(stra, strb,line,' ');
4749: errno=0;
4750: lval=strtol(strb,&endptr,10);
4751: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4752: if( strb[0]=='\0' || (*endptr != '\0')){
4753: printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
4754: exit(1);
4755: }
4756: s[j][i]=lval;
4757:
4758: strcpy(line,stra);
4759: cutv(stra, strb,line,' ');
4760: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4761: }
4762: else if(iout=sscanf(strb,"%s.") != 0){
4763: month=99;
4764: year=9999;
4765: }else{
4766: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4767: exit(1);
4768: }
4769: anint[j][i]= (double) year;
4770: mint[j][i]= (double)month;
4771: strcpy(line,stra);
4772: } /* ENd Waves */
4773:
4774: cutv(stra, strb,line,' ');
4775: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4776: }
4777: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4778: month=99;
4779: year=9999;
4780: }else{
4781: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4782: exit(1);
4783: }
4784: andc[i]=(double) year;
4785: moisdc[i]=(double) month;
4786: strcpy(line,stra);
4787:
4788: cutv(stra, strb,line,' ');
4789: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4790: }
4791: else if(iout=sscanf(strb,"%s.") != 0){
4792: month=99;
4793: year=9999;
4794: }else{
4795: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4796: exit(1);
4797: }
4798: annais[i]=(double)(year);
4799: moisnais[i]=(double)(month);
4800: strcpy(line,stra);
4801:
4802: cutv(stra, strb,line,' ');
4803: errno=0;
4804: lval=strtol(strb,&endptr,10);
4805: if( strb[0]=='\0' || (*endptr != '\0')){
4806: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4807: exit(1);
4808: }
4809: weight[i]=(double)(lval);
4810: strcpy(line,stra);
4811:
4812: for (j=ncovcol;j>=1;j--){
4813: cutv(stra, strb,line,' ');
4814: errno=0;
4815: lval=strtol(strb,&endptr,10);
4816: if( strb[0]=='\0' || (*endptr != '\0')){
4817: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4818: exit(1);
4819: }
4820: if(lval <-1 || lval >1){
4821: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
4822: exit(1);
4823: }
4824: covar[j][i]=(double)(lval);
4825: strcpy(line,stra);
4826: }
4827: lstra=strlen(stra);
4828:
4829: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4830: stratrunc = &(stra[lstra-9]);
4831: num[i]=atol(stratrunc);
4832: }
4833: else
4834: num[i]=atol(stra);
4835: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4836: 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;}*/
4837:
4838: i=i+1;
4839: } /* End loop reading data */
4840: fclose(fic);
4841: /* printf("ii=%d", ij);
4842: scanf("%d",i);*/
4843: imx=i-1; /* Number of individuals */
4844:
4845: /* for (i=1; i<=imx; i++){
4846: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4847: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4848: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4849: }*/
4850: /* for (i=1; i<=imx; i++){
4851: if (s[4][i]==9) s[4][i]=-1;
4852: 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]));}*/
4853:
4854: /* for (i=1; i<=imx; i++) */
4855:
4856: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4857: else weight[i]=1;*/
4858:
4859: /* Calculation of the number of parameters from char model */
4860: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4861: Tprod=ivector(1,15);
4862: Tvaraff=ivector(1,15);
4863: Tvard=imatrix(1,15,1,2);
4864: Tage=ivector(1,15);
4865:
4866: if (strlen(model) >1){ /* If there is at least 1 covariate */
4867: j=0, j1=0, k1=1, k2=1;
4868: j=nbocc(model,'+'); /* j=Number of '+' */
4869: j1=nbocc(model,'*'); /* j1=Number of '*' */
4870: cptcovn=j+1;
4871: cptcovprod=j1; /*Number of products */
4872:
4873: strcpy(modelsav,model);
4874: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4875: printf("Error. Non available option model=%s ",model);
4876: fprintf(ficlog,"Error. Non available option model=%s ",model);
4877: goto end;
4878: }
4879:
4880: /* This loop fills the array Tvar from the string 'model'.*/
4881:
4882: for(i=(j+1); i>=1;i--){
4883: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4884: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4885: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4886: /*scanf("%d",i);*/
4887: if (strchr(strb,'*')) { /* Model includes a product */
4888: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4889: if (strcmp(strc,"age")==0) { /* Vn*age */
4890: cptcovprod--;
4891: cutv(strb,stre,strd,'V');
4892: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4893: cptcovage++;
4894: Tage[cptcovage]=i;
4895: /*printf("stre=%s ", stre);*/
4896: }
4897: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4898: cptcovprod--;
4899: cutv(strb,stre,strc,'V');
4900: Tvar[i]=atoi(stre);
4901: cptcovage++;
4902: Tage[cptcovage]=i;
4903: }
4904: else { /* Age is not in the model */
4905: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4906: Tvar[i]=ncovcol+k1;
4907: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4908: Tprod[k1]=i;
4909: Tvard[k1][1]=atoi(strc); /* m*/
4910: Tvard[k1][2]=atoi(stre); /* n */
4911: Tvar[cptcovn+k2]=Tvard[k1][1];
4912: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4913: for (k=1; k<=lastobs;k++)
4914: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4915: k1++;
4916: k2=k2+2;
4917: }
4918: }
4919: else { /* no more sum */
4920: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4921: /* scanf("%d",i);*/
4922: cutv(strd,strc,strb,'V');
4923: Tvar[i]=atoi(strc);
4924: }
4925: strcpy(modelsav,stra);
4926: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4927: scanf("%d",i);*/
4928: } /* end of loop + */
4929: } /* end model */
4930:
4931: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4932: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4933:
4934: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4935: printf("cptcovprod=%d ", cptcovprod);
4936: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4937:
4938: scanf("%d ",i);*/
4939:
4940: /* if(mle==1){*/
4941: if (weightopt != 1) { /* Maximisation without weights*/
4942: for(i=1;i<=n;i++) weight[i]=1.0;
4943: }
4944: /*-calculation of age at interview from date of interview and age at death -*/
4945: agev=matrix(1,maxwav,1,imx);
4946:
4947: for (i=1; i<=imx; i++) {
4948: for(m=2; (m<= maxwav); m++) {
4949: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4950: anint[m][i]=9999;
4951: s[m][i]=-1;
4952: }
4953: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4954: nberr++;
4955: 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);
4956: 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);
4957: s[m][i]=-1;
4958: }
4959: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4960: nberr++;
4961: 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]);
4962: 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]);
4963: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4964: }
4965: }
4966: }
4967:
4968: for (i=1; i<=imx; i++) {
4969: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4970: for(m=firstpass; (m<= lastpass); m++){
4971: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4972: if (s[m][i] >= nlstate+1) {
4973: if(agedc[i]>0)
4974: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4975: agev[m][i]=agedc[i];
4976: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4977: else {
4978: if ((int)andc[i]!=9999){
4979: nbwarn++;
4980: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4981: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4982: agev[m][i]=-1;
4983: }
4984: }
4985: }
4986: else if(s[m][i] !=9){ /* Standard case, age in fractional
4987: years but with the precision of a month */
4988: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4989: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4990: agev[m][i]=1;
4991: else if(agev[m][i] <agemin){
4992: agemin=agev[m][i];
4993: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4994: }
4995: else if(agev[m][i] >agemax){
4996: agemax=agev[m][i];
4997: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4998: }
4999: /*agev[m][i]=anint[m][i]-annais[i];*/
5000: /* agev[m][i] = age[i]+2*m;*/
5001: }
5002: else { /* =9 */
5003: agev[m][i]=1;
5004: s[m][i]=-1;
5005: }
5006: }
5007: else /*= 0 Unknown */
5008: agev[m][i]=1;
5009: }
5010:
5011: }
5012: for (i=1; i<=imx; i++) {
5013: for(m=firstpass; (m<=lastpass); m++){
5014: if (s[m][i] > (nlstate+ndeath)) {
5015: nberr++;
5016: 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);
5017: 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);
5018: goto end;
5019: }
5020: }
5021: }
5022:
5023: /*for (i=1; i<=imx; i++){
5024: for (m=firstpass; (m<lastpass); m++){
5025: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5026: }
5027:
5028: }*/
5029:
5030:
5031: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5032: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5033:
5034: agegomp=(int)agemin;
5035: free_vector(severity,1,maxwav);
5036: free_imatrix(outcome,1,maxwav+1,1,n);
5037: free_vector(moisnais,1,n);
5038: free_vector(annais,1,n);
5039: /* free_matrix(mint,1,maxwav,1,n);
5040: free_matrix(anint,1,maxwav,1,n);*/
5041: free_vector(moisdc,1,n);
5042: free_vector(andc,1,n);
5043:
5044:
5045: wav=ivector(1,imx);
5046: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5047: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5048: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5049:
5050: /* Concatenates waves */
5051: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5052:
5053: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5054:
5055: Tcode=ivector(1,100);
5056: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5057: ncodemax[1]=1;
5058: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5059:
5060: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5061: the estimations*/
5062: h=0;
5063: m=pow(2,cptcoveff);
5064:
5065: for(k=1;k<=cptcoveff; k++){
5066: for(i=1; i <=(m/pow(2,k));i++){
5067: for(j=1; j <= ncodemax[k]; j++){
5068: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5069: h++;
5070: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5071: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5072: }
5073: }
5074: }
5075: }
5076: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5077: codtab[1][2]=1;codtab[2][2]=2; */
5078: /* for(i=1; i <=m ;i++){
5079: for(k=1; k <=cptcovn; k++){
5080: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5081: }
5082: printf("\n");
5083: }
5084: scanf("%d",i);*/
5085:
5086: /*------------ gnuplot -------------*/
5087: strcpy(optionfilegnuplot,optionfilefiname);
5088: if(mle==-3)
5089: strcat(optionfilegnuplot,"-mort");
5090: strcat(optionfilegnuplot,".gp");
5091:
5092: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5093: printf("Problem with file %s",optionfilegnuplot);
5094: }
5095: else{
5096: fprintf(ficgp,"\n# %s\n", version);
5097: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5098: fprintf(ficgp,"set missing 'NaNq'\n");
5099: }
5100: /* fclose(ficgp);*/
5101: /*--------- index.htm --------*/
5102:
5103: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5104: if(mle==-3)
5105: strcat(optionfilehtm,"-mort");
5106: strcat(optionfilehtm,".htm");
5107: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5108: printf("Problem with %s \n",optionfilehtm), exit(0);
5109: }
5110:
5111: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5112: strcat(optionfilehtmcov,"-cov.htm");
5113: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5114: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5115: }
5116: else{
5117: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5118: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5119: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5120: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5121: }
5122:
5123: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
5124: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5125: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5126: \n\
5127: <hr size=\"2\" color=\"#EC5E5E\">\
5128: <ul><li><h4>Parameter files</h4>\n\
5129: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5130: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5131: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5132: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5133: - Date and time at start: %s</ul>\n",\
5134: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5135: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5136: fileres,fileres,\
5137: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5138: fflush(fichtm);
5139:
5140: strcpy(pathr,path);
5141: strcat(pathr,optionfilefiname);
5142: chdir(optionfilefiname); /* Move to directory named optionfile */
5143:
5144: /* Calculates basic frequencies. Computes observed prevalence at single age
5145: and prints on file fileres'p'. */
5146: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5147:
5148: fprintf(fichtm,"\n");
5149: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5150: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5151: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5152: imx,agemin,agemax,jmin,jmax,jmean);
5153: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5154: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5155: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5156: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5157: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5158:
5159:
5160: /* For Powell, parameters are in a vector p[] starting at p[1]
5161: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5162: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5163:
5164: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5165:
5166: if (mle==-3){
5167: ximort=matrix(1,NDIM,1,NDIM);
5168: cens=ivector(1,n);
5169: ageexmed=vector(1,n);
5170: agecens=vector(1,n);
5171: dcwave=ivector(1,n);
5172:
5173: for (i=1; i<=imx; i++){
5174: dcwave[i]=-1;
5175: for (m=firstpass; m<=lastpass; m++)
5176: if (s[m][i]>nlstate) {
5177: dcwave[i]=m;
5178: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5179: break;
5180: }
5181: }
5182:
5183: for (i=1; i<=imx; i++) {
5184: if (wav[i]>0){
5185: ageexmed[i]=agev[mw[1][i]][i];
5186: j=wav[i];
5187: agecens[i]=1.;
5188:
5189: if (ageexmed[i]> 1 && wav[i] > 0){
5190: agecens[i]=agev[mw[j][i]][i];
5191: cens[i]= 1;
5192: }else if (ageexmed[i]< 1)
5193: cens[i]= -1;
5194: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5195: cens[i]=0 ;
5196: }
5197: else cens[i]=-1;
5198: }
5199:
5200: for (i=1;i<=NDIM;i++) {
5201: for (j=1;j<=NDIM;j++)
5202: ximort[i][j]=(i == j ? 1.0 : 0.0);
5203: }
5204:
5205: p[1]=0.0268; p[NDIM]=0.083;
5206: /*printf("%lf %lf", p[1], p[2]);*/
5207:
5208:
5209: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5210: strcpy(filerespow,"pow-mort");
5211: strcat(filerespow,fileres);
5212: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5213: printf("Problem with resultfile: %s\n", filerespow);
5214: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5215: }
5216: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5217: /* for (i=1;i<=nlstate;i++)
5218: for(j=1;j<=nlstate+ndeath;j++)
5219: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5220: */
5221: fprintf(ficrespow,"\n");
5222:
5223: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5224: fclose(ficrespow);
5225:
5226: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5227:
5228: for(i=1; i <=NDIM; i++)
5229: for(j=i+1;j<=NDIM;j++)
5230: matcov[i][j]=matcov[j][i];
5231:
5232: printf("\nCovariance matrix\n ");
5233: for(i=1; i <=NDIM; i++) {
5234: for(j=1;j<=NDIM;j++){
5235: printf("%f ",matcov[i][j]);
5236: }
5237: printf("\n ");
5238: }
5239:
5240: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5241: for (i=1;i<=NDIM;i++)
5242: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5243:
5244: lsurv=vector(1,AGESUP);
5245: lpop=vector(1,AGESUP);
5246: tpop=vector(1,AGESUP);
5247: lsurv[agegomp]=100000;
5248:
5249: for (k=agegomp;k<=AGESUP;k++) {
5250: agemortsup=k;
5251: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5252: }
5253:
5254: for (k=agegomp;k<agemortsup;k++)
5255: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5256:
5257: for (k=agegomp;k<agemortsup;k++){
5258: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5259: sumlpop=sumlpop+lpop[k];
5260: }
5261:
5262: tpop[agegomp]=sumlpop;
5263: for (k=agegomp;k<(agemortsup-3);k++){
5264: /* tpop[k+1]=2;*/
5265: tpop[k+1]=tpop[k]-lpop[k];
5266: }
5267:
5268:
5269: printf("\nAge lx qx dx Lx Tx e(x)\n");
5270: for (k=agegomp;k<(agemortsup-2);k++)
5271: 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]);
5272:
5273:
5274: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5275: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5276:
5277: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5278: stepm, weightopt,\
5279: model,imx,p,matcov,agemortsup);
5280:
5281: free_vector(lsurv,1,AGESUP);
5282: free_vector(lpop,1,AGESUP);
5283: free_vector(tpop,1,AGESUP);
5284: } /* Endof if mle==-3 */
5285:
5286: else{ /* For mle >=1 */
5287:
5288: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5289: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5290: for (k=1; k<=npar;k++)
5291: printf(" %d %8.5f",k,p[k]);
5292: printf("\n");
5293: globpr=1; /* to print the contributions */
5294: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5295: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5296: for (k=1; k<=npar;k++)
5297: printf(" %d %8.5f",k,p[k]);
5298: printf("\n");
5299: if(mle>=1){ /* Could be 1 or 2 */
5300: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5301: }
5302:
5303: /*--------- results files --------------*/
5304: 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);
5305:
5306:
5307: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5308: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5309: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5310: for(i=1,jk=1; i <=nlstate; i++){
5311: for(k=1; k <=(nlstate+ndeath); k++){
5312: if (k != i) {
5313: printf("%d%d ",i,k);
5314: fprintf(ficlog,"%d%d ",i,k);
5315: fprintf(ficres,"%1d%1d ",i,k);
5316: for(j=1; j <=ncovmodel; j++){
5317: printf("%f ",p[jk]);
5318: fprintf(ficlog,"%f ",p[jk]);
5319: fprintf(ficres,"%f ",p[jk]);
5320: jk++;
5321: }
5322: printf("\n");
5323: fprintf(ficlog,"\n");
5324: fprintf(ficres,"\n");
5325: }
5326: }
5327: }
5328: if(mle!=0){
5329: /* Computing hessian and covariance matrix */
5330: ftolhess=ftol; /* Usually correct */
5331: hesscov(matcov, p, npar, delti, ftolhess, func);
5332: }
5333: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5334: printf("# Scales (for hessian or gradient estimation)\n");
5335: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5336: for(i=1,jk=1; i <=nlstate; i++){
5337: for(j=1; j <=nlstate+ndeath; j++){
5338: if (j!=i) {
5339: fprintf(ficres,"%1d%1d",i,j);
5340: printf("%1d%1d",i,j);
5341: fprintf(ficlog,"%1d%1d",i,j);
5342: for(k=1; k<=ncovmodel;k++){
5343: printf(" %.5e",delti[jk]);
5344: fprintf(ficlog," %.5e",delti[jk]);
5345: fprintf(ficres," %.5e",delti[jk]);
5346: jk++;
5347: }
5348: printf("\n");
5349: fprintf(ficlog,"\n");
5350: fprintf(ficres,"\n");
5351: }
5352: }
5353: }
5354:
5355: 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");
5356: if(mle>=1)
5357: 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");
5358: 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");
5359: /* # 121 Var(a12)\n\ */
5360: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5361: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5362: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5363: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5364: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5365: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5366: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5367:
5368:
5369: /* Just to have a covariance matrix which will be more understandable
5370: even is we still don't want to manage dictionary of variables
5371: */
5372: for(itimes=1;itimes<=2;itimes++){
5373: jj=0;
5374: for(i=1; i <=nlstate; i++){
5375: for(j=1; j <=nlstate+ndeath; j++){
5376: if(j==i) continue;
5377: for(k=1; k<=ncovmodel;k++){
5378: jj++;
5379: ca[0]= k+'a'-1;ca[1]='\0';
5380: if(itimes==1){
5381: if(mle>=1)
5382: printf("#%1d%1d%d",i,j,k);
5383: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5384: fprintf(ficres,"#%1d%1d%d",i,j,k);
5385: }else{
5386: if(mle>=1)
5387: printf("%1d%1d%d",i,j,k);
5388: fprintf(ficlog,"%1d%1d%d",i,j,k);
5389: fprintf(ficres,"%1d%1d%d",i,j,k);
5390: }
5391: ll=0;
5392: for(li=1;li <=nlstate; li++){
5393: for(lj=1;lj <=nlstate+ndeath; lj++){
5394: if(lj==li) continue;
5395: for(lk=1;lk<=ncovmodel;lk++){
5396: ll++;
5397: if(ll<=jj){
5398: cb[0]= lk +'a'-1;cb[1]='\0';
5399: if(ll<jj){
5400: if(itimes==1){
5401: if(mle>=1)
5402: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5403: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5404: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5405: }else{
5406: if(mle>=1)
5407: printf(" %.5e",matcov[jj][ll]);
5408: fprintf(ficlog," %.5e",matcov[jj][ll]);
5409: fprintf(ficres," %.5e",matcov[jj][ll]);
5410: }
5411: }else{
5412: if(itimes==1){
5413: if(mle>=1)
5414: printf(" Var(%s%1d%1d)",ca,i,j);
5415: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5416: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5417: }else{
5418: if(mle>=1)
5419: printf(" %.5e",matcov[jj][ll]);
5420: fprintf(ficlog," %.5e",matcov[jj][ll]);
5421: fprintf(ficres," %.5e",matcov[jj][ll]);
5422: }
5423: }
5424: }
5425: } /* end lk */
5426: } /* end lj */
5427: } /* end li */
5428: if(mle>=1)
5429: printf("\n");
5430: fprintf(ficlog,"\n");
5431: fprintf(ficres,"\n");
5432: numlinepar++;
5433: } /* end k*/
5434: } /*end j */
5435: } /* end i */
5436: } /* end itimes */
5437:
5438: fflush(ficlog);
5439: fflush(ficres);
5440:
5441: while((c=getc(ficpar))=='#' && c!= EOF){
5442: ungetc(c,ficpar);
5443: fgets(line, MAXLINE, ficpar);
5444: puts(line);
5445: fputs(line,ficparo);
5446: }
5447: ungetc(c,ficpar);
5448:
5449: estepm=0;
5450: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5451: if (estepm==0 || estepm < stepm) estepm=stepm;
5452: if (fage <= 2) {
5453: bage = ageminpar;
5454: fage = agemaxpar;
5455: }
5456:
5457: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5458: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5459: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5460:
5461: while((c=getc(ficpar))=='#' && c!= EOF){
5462: ungetc(c,ficpar);
5463: fgets(line, MAXLINE, ficpar);
5464: puts(line);
5465: fputs(line,ficparo);
5466: }
5467: ungetc(c,ficpar);
5468:
5469: 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);
5470: 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);
5471: 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);
5472: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5473: 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);
5474:
5475: while((c=getc(ficpar))=='#' && c!= EOF){
5476: ungetc(c,ficpar);
5477: fgets(line, MAXLINE, ficpar);
5478: puts(line);
5479: fputs(line,ficparo);
5480: }
5481: ungetc(c,ficpar);
5482:
5483:
5484: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5485: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5486:
5487: fscanf(ficpar,"pop_based=%d\n",&popbased);
5488: fprintf(ficparo,"pop_based=%d\n",popbased);
5489: fprintf(ficres,"pop_based=%d\n",popbased);
5490:
5491: while((c=getc(ficpar))=='#' && c!= EOF){
5492: ungetc(c,ficpar);
5493: fgets(line, MAXLINE, ficpar);
5494: puts(line);
5495: fputs(line,ficparo);
5496: }
5497: ungetc(c,ficpar);
5498:
5499: 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);
5500: 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);
5501: 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);
5502: 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);
5503: 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);
5504: /* day and month of proj2 are not used but only year anproj2.*/
5505:
5506:
5507:
5508: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5509: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5510:
5511: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5512: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5513:
5514: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5515: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5516: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5517:
5518: /*------------ free_vector -------------*/
5519: /* chdir(path); */
5520:
5521: free_ivector(wav,1,imx);
5522: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5523: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5524: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5525: free_lvector(num,1,n);
5526: free_vector(agedc,1,n);
5527: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5528: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5529: fclose(ficparo);
5530: fclose(ficres);
5531:
5532:
5533: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5534:
5535: strcpy(filerespl,"pl");
5536: strcat(filerespl,fileres);
5537: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5538: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5539: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5540: }
5541: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5542: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5543: pstamp(ficrespl);
5544: fprintf(ficrespl,"# Period (stable) prevalence \n");
5545: fprintf(ficrespl,"#Age ");
5546: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5547: fprintf(ficrespl,"\n");
5548:
5549: prlim=matrix(1,nlstate,1,nlstate);
5550:
5551: agebase=ageminpar;
5552: agelim=agemaxpar;
5553: ftolpl=1.e-10;
5554: i1=cptcoveff;
5555: if (cptcovn < 1){i1=1;}
5556:
5557: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5558: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5559: k=k+1;
5560: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5561: fprintf(ficrespl,"\n#******");
5562: printf("\n#******");
5563: fprintf(ficlog,"\n#******");
5564: for(j=1;j<=cptcoveff;j++) {
5565: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5566: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5567: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5568: }
5569: fprintf(ficrespl,"******\n");
5570: printf("******\n");
5571: fprintf(ficlog,"******\n");
5572:
5573: for (age=agebase; age<=agelim; age++){
5574: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5575: fprintf(ficrespl,"%.0f ",age );
5576: for(j=1;j<=cptcoveff;j++)
5577: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5578: for(i=1; i<=nlstate;i++)
5579: fprintf(ficrespl," %.5f", prlim[i][i]);
5580: fprintf(ficrespl,"\n");
5581: }
5582: }
5583: }
5584: fclose(ficrespl);
5585:
5586: /*------------- h Pij x at various ages ------------*/
5587:
5588: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5589: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5590: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5591: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5592: }
5593: printf("Computing pij: result on file '%s' \n", filerespij);
5594: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5595:
5596: stepsize=(int) (stepm+YEARM-1)/YEARM;
5597: /*if (stepm<=24) stepsize=2;*/
5598:
5599: agelim=AGESUP;
5600: hstepm=stepsize*YEARM; /* Every year of age */
5601: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5602:
5603: /* hstepm=1; aff par mois*/
5604: pstamp(ficrespij);
5605: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5606: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5607: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5608: k=k+1;
5609: fprintf(ficrespij,"\n#****** ");
5610: for(j=1;j<=cptcoveff;j++)
5611: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5612: fprintf(ficrespij,"******\n");
5613:
5614: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5615: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5616: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5617:
5618: /* nhstepm=nhstepm*YEARM; aff par mois*/
5619:
5620: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5621: oldm=oldms;savm=savms;
5622: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5623: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5624: for(i=1; i<=nlstate;i++)
5625: for(j=1; j<=nlstate+ndeath;j++)
5626: fprintf(ficrespij," %1d-%1d",i,j);
5627: fprintf(ficrespij,"\n");
5628: for (h=0; h<=nhstepm; h++){
5629: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5630: for(i=1; i<=nlstate;i++)
5631: for(j=1; j<=nlstate+ndeath;j++)
5632: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5633: fprintf(ficrespij,"\n");
5634: }
5635: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5636: fprintf(ficrespij,"\n");
5637: }
5638: }
5639: }
5640:
5641: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5642:
5643: fclose(ficrespij);
5644:
5645: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5646: for(i=1;i<=AGESUP;i++)
5647: for(j=1;j<=NCOVMAX;j++)
5648: for(k=1;k<=NCOVMAX;k++)
5649: probs[i][j][k]=0.;
5650:
5651: /*---------- Forecasting ------------------*/
5652: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5653: if(prevfcast==1){
5654: /* if(stepm ==1){*/
5655: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5656: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5657: /* } */
5658: /* else{ */
5659: /* erreur=108; */
5660: /* 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); */
5661: /* 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); */
5662: /* } */
5663: }
5664:
5665:
5666: /*---------- Health expectancies and variances ------------*/
5667:
5668: strcpy(filerest,"t");
5669: strcat(filerest,fileres);
5670: if((ficrest=fopen(filerest,"w"))==NULL) {
5671: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5672: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5673: }
5674: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5675: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5676:
5677:
5678: strcpy(filerese,"e");
5679: strcat(filerese,fileres);
5680: if((ficreseij=fopen(filerese,"w"))==NULL) {
5681: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5682: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5683: }
5684: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5685: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5686:
5687: strcpy(fileresstde,"stde");
5688: strcat(fileresstde,fileres);
5689: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5690: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5691: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5692: }
5693: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5694: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5695:
5696: strcpy(filerescve,"cve");
5697: strcat(filerescve,fileres);
5698: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5699: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5700: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5701: }
5702: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5703: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5704:
5705: strcpy(fileresv,"v");
5706: strcat(fileresv,fileres);
5707: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5708: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5709: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5710: }
5711: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5712: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5713:
5714: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5715: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5716: /* 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",\
5717: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5718: */
5719:
5720: if (mobilav!=0) {
5721: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5722: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5723: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5724: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5725: }
5726: }
5727:
5728: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5729: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5730: k=k+1;
5731: fprintf(ficrest,"\n#****** ");
5732: for(j=1;j<=cptcoveff;j++)
5733: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5734: fprintf(ficrest,"******\n");
5735:
5736: fprintf(ficreseij,"\n#****** ");
5737: fprintf(ficresstdeij,"\n#****** ");
5738: fprintf(ficrescveij,"\n#****** ");
5739: for(j=1;j<=cptcoveff;j++) {
5740: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5741: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5742: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5743: }
5744: fprintf(ficreseij,"******\n");
5745: fprintf(ficresstdeij,"******\n");
5746: fprintf(ficrescveij,"******\n");
5747:
5748: fprintf(ficresvij,"\n#****** ");
5749: for(j=1;j<=cptcoveff;j++)
5750: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5751: fprintf(ficresvij,"******\n");
5752:
5753: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5754: oldm=oldms;savm=savms;
5755: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5756: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5757:
5758: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5759: oldm=oldms;savm=savms;
5760: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5761: if(popbased==1){
5762: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5763: }
5764:
5765: pstamp(ficrest);
5766: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
5767: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5768: fprintf(ficrest,"\n");
5769:
5770: epj=vector(1,nlstate+1);
5771: for(age=bage; age <=fage ;age++){
5772: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5773: if (popbased==1) {
5774: if(mobilav ==0){
5775: for(i=1; i<=nlstate;i++)
5776: prlim[i][i]=probs[(int)age][i][k];
5777: }else{ /* mobilav */
5778: for(i=1; i<=nlstate;i++)
5779: prlim[i][i]=mobaverage[(int)age][i][k];
5780: }
5781: }
5782:
5783: fprintf(ficrest," %4.0f",age);
5784: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5785: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5786: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5787: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5788: }
5789: epj[nlstate+1] +=epj[j];
5790: }
5791:
5792: for(i=1, vepp=0.;i <=nlstate;i++)
5793: for(j=1;j <=nlstate;j++)
5794: vepp += vareij[i][j][(int)age];
5795: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5796: for(j=1;j <=nlstate;j++){
5797: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5798: }
5799: fprintf(ficrest,"\n");
5800: }
5801: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5802: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5803: free_vector(epj,1,nlstate+1);
5804: }
5805: }
5806: free_vector(weight,1,n);
5807: free_imatrix(Tvard,1,15,1,2);
5808: free_imatrix(s,1,maxwav+1,1,n);
5809: free_matrix(anint,1,maxwav,1,n);
5810: free_matrix(mint,1,maxwav,1,n);
5811: free_ivector(cod,1,n);
5812: free_ivector(tab,1,NCOVMAX);
5813: fclose(ficreseij);
5814: fclose(ficresstdeij);
5815: fclose(ficrescveij);
5816: fclose(ficresvij);
5817: fclose(ficrest);
5818: fclose(ficpar);
5819:
5820: /*------- Variance of period (stable) prevalence------*/
5821:
5822: strcpy(fileresvpl,"vpl");
5823: strcat(fileresvpl,fileres);
5824: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5825: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5826: exit(0);
5827: }
5828: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5829:
5830: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5831: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5832: k=k+1;
5833: fprintf(ficresvpl,"\n#****** ");
5834: for(j=1;j<=cptcoveff;j++)
5835: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5836: fprintf(ficresvpl,"******\n");
5837:
5838: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5839: oldm=oldms;savm=savms;
5840: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5841: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5842: }
5843: }
5844:
5845: fclose(ficresvpl);
5846:
5847: /*---------- End : free ----------------*/
5848: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5849: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5850:
5851: } /* mle==-3 arrives here for freeing */
5852: free_matrix(prlim,1,nlstate,1,nlstate);
5853: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5854: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5855: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5856: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5857: free_matrix(covar,0,NCOVMAX,1,n);
5858: free_matrix(matcov,1,npar,1,npar);
5859: /*free_vector(delti,1,npar);*/
5860: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5861: free_matrix(agev,1,maxwav,1,imx);
5862: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5863:
5864: free_ivector(ncodemax,1,8);
5865: free_ivector(Tvar,1,15);
5866: free_ivector(Tprod,1,15);
5867: free_ivector(Tvaraff,1,15);
5868: free_ivector(Tage,1,15);
5869: free_ivector(Tcode,1,100);
5870:
5871: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5872: free_imatrix(codtab,1,100,1,10);
5873: fflush(fichtm);
5874: fflush(ficgp);
5875:
5876:
5877: if((nberr >0) || (nbwarn>0)){
5878: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5879: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5880: }else{
5881: printf("End of Imach\n");
5882: fprintf(ficlog,"End of Imach\n");
5883: }
5884: printf("See log file on %s\n",filelog);
5885: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5886: (void) gettimeofday(&end_time,&tzp);
5887: tm = *localtime(&end_time.tv_sec);
5888: tmg = *gmtime(&end_time.tv_sec);
5889: strcpy(strtend,asctime(&tm));
5890: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5891: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5892: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5893:
5894: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5895: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5896: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5897: /* printf("Total time was %d uSec.\n", total_usecs);*/
5898: /* if(fileappend(fichtm,optionfilehtm)){ */
5899: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5900: fclose(fichtm);
5901: fclose(fichtmcov);
5902: fclose(ficgp);
5903: fclose(ficlog);
5904: /*------ End -----------*/
5905:
5906:
5907: printf("Before Current directory %s!\n",pathcd);
5908: if(chdir(pathcd) != 0)
5909: printf("Can't move to directory %s!\n",path);
5910: if(getcwd(pathcd,MAXLINE) > 0)
5911: printf("Current directory %s!\n",pathcd);
5912: /*strcat(plotcmd,CHARSEPARATOR);*/
5913: sprintf(plotcmd,"gnuplot");
5914: #ifndef UNIX
5915: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5916: #endif
5917: if(!stat(plotcmd,&info)){
5918: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5919: if(!stat(getenv("GNUPLOTBIN"),&info)){
5920: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5921: }else
5922: strcpy(pplotcmd,plotcmd);
5923: #ifdef UNIX
5924: strcpy(plotcmd,GNUPLOTPROGRAM);
5925: if(!stat(plotcmd,&info)){
5926: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5927: }else
5928: strcpy(pplotcmd,plotcmd);
5929: #endif
5930: }else
5931: strcpy(pplotcmd,plotcmd);
5932:
5933: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5934: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5935:
5936: if((outcmd=system(plotcmd)) != 0){
5937: printf("\n Problem with gnuplot\n");
5938: }
5939: printf(" Wait...");
5940: while (z[0] != 'q') {
5941: /* chdir(path); */
5942: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5943: scanf("%s",z);
5944: /* if (z[0] == 'c') system("./imach"); */
5945: if (z[0] == 'e') {
5946: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5947: system(optionfilehtm);
5948: }
5949: else if (z[0] == 'g') system(plotcmd);
5950: else if (z[0] == 'q') exit(0);
5951: }
5952: end:
5953: while (z[0] != 'q') {
5954: printf("\nType q for exiting: ");
5955: scanf("%s",z);
5956: }
5957: }
5958:
5959:
5960:
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