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Tue Mar 14 17:16:22 2006 UTC (18 years, 3 months ago) by
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(Module): varevsij Comments added explaining the second
table of variances if popbased=1 .
(Module): Covariances of eij, ekl added, graphs fixed, new html link.
(Module): Function pstamp added
(Module): Version 0.98d
1: /* $Id: imach.c,v 1.117 2006/03/14 17:16:22 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.117 2006/03/14 17:16:22 brouard
5: (Module): varevsij Comments added explaining the second
6: table of variances if popbased=1 .
7: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
8: (Module): Function pstamp added
9: (Module): Version 0.98d
10:
11: Revision 1.116 2006/03/06 10:29:27 brouard
12: (Module): Variance-covariance wrong links and
13: varian-covariance of ej. is needed (Saito).
14:
15: Revision 1.115 2006/02/27 12:17:45 brouard
16: (Module): One freematrix added in mlikeli! 0.98c
17:
18: Revision 1.114 2006/02/26 12:57:58 brouard
19: (Module): Some improvements in processing parameter
20: filename with strsep.
21:
22: Revision 1.113 2006/02/24 14:20:24 brouard
23: (Module): Memory leaks checks with valgrind and:
24: datafile was not closed, some imatrix were not freed and on matrix
25: allocation too.
26:
27: Revision 1.112 2006/01/30 09:55:26 brouard
28: (Module): Back to gnuplot.exe instead of wgnuplot.exe
29:
30: Revision 1.111 2006/01/25 20:38:18 brouard
31: (Module): Lots of cleaning and bugs added (Gompertz)
32: (Module): Comments can be added in data file. Missing date values
33: can be a simple dot '.'.
34:
35: Revision 1.110 2006/01/25 00:51:50 brouard
36: (Module): Lots of cleaning and bugs added (Gompertz)
37:
38: Revision 1.109 2006/01/24 19:37:15 brouard
39: (Module): Comments (lines starting with a #) are allowed in data.
40:
41: Revision 1.108 2006/01/19 18:05:42 lievre
42: Gnuplot problem appeared...
43: To be fixed
44:
45: Revision 1.107 2006/01/19 16:20:37 brouard
46: Test existence of gnuplot in imach path
47:
48: Revision 1.106 2006/01/19 13:24:36 brouard
49: Some cleaning and links added in html output
50:
51: Revision 1.105 2006/01/05 20:23:19 lievre
52: *** empty log message ***
53:
54: Revision 1.104 2005/09/30 16:11:43 lievre
55: (Module): sump fixed, loop imx fixed, and simplifications.
56: (Module): If the status is missing at the last wave but we know
57: that the person is alive, then we can code his/her status as -2
58: (instead of missing=-1 in earlier versions) and his/her
59: contributions to the likelihood is 1 - Prob of dying from last
60: health status (= 1-p13= p11+p12 in the easiest case of somebody in
61: the healthy state at last known wave). Version is 0.98
62:
63: Revision 1.103 2005/09/30 15:54:49 lievre
64: (Module): sump fixed, loop imx fixed, and simplifications.
65:
66: Revision 1.102 2004/09/15 17:31:30 brouard
67: Add the possibility to read data file including tab characters.
68:
69: Revision 1.101 2004/09/15 10:38:38 brouard
70: Fix on curr_time
71:
72: Revision 1.100 2004/07/12 18:29:06 brouard
73: Add version for Mac OS X. Just define UNIX in Makefile
74:
75: Revision 1.99 2004/06/05 08:57:40 brouard
76: *** empty log message ***
77:
78: Revision 1.98 2004/05/16 15:05:56 brouard
79: New version 0.97 . First attempt to estimate force of mortality
80: directly from the data i.e. without the need of knowing the health
81: state at each age, but using a Gompertz model: log u =a + b*age .
82: This is the basic analysis of mortality and should be done before any
83: other analysis, in order to test if the mortality estimated from the
84: cross-longitudinal survey is different from the mortality estimated
85: from other sources like vital statistic data.
86:
87: The same imach parameter file can be used but the option for mle should be -3.
88:
89: Agnès, who wrote this part of the code, tried to keep most of the
90: former routines in order to include the new code within the former code.
91:
92: The output is very simple: only an estimate of the intercept and of
93: the slope with 95% confident intervals.
94:
95: Current limitations:
96: A) Even if you enter covariates, i.e. with the
97: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
98: B) There is no computation of Life Expectancy nor Life Table.
99:
100: Revision 1.97 2004/02/20 13:25:42 lievre
101: Version 0.96d. Population forecasting command line is (temporarily)
102: suppressed.
103:
104: Revision 1.96 2003/07/15 15:38:55 brouard
105: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
106: rewritten within the same printf. Workaround: many printfs.
107:
108: Revision 1.95 2003/07/08 07:54:34 brouard
109: * imach.c (Repository):
110: (Repository): Using imachwizard code to output a more meaningful covariance
111: matrix (cov(a12,c31) instead of numbers.
112:
113: Revision 1.94 2003/06/27 13:00:02 brouard
114: Just cleaning
115:
116: Revision 1.93 2003/06/25 16:33:55 brouard
117: (Module): On windows (cygwin) function asctime_r doesn't
118: exist so I changed back to asctime which exists.
119: (Module): Version 0.96b
120:
121: Revision 1.92 2003/06/25 16:30:45 brouard
122: (Module): On windows (cygwin) function asctime_r doesn't
123: exist so I changed back to asctime which exists.
124:
125: Revision 1.91 2003/06/25 15:30:29 brouard
126: * imach.c (Repository): Duplicated warning errors corrected.
127: (Repository): Elapsed time after each iteration is now output. It
128: helps to forecast when convergence will be reached. Elapsed time
129: is stamped in powell. We created a new html file for the graphs
130: concerning matrix of covariance. It has extension -cov.htm.
131:
132: Revision 1.90 2003/06/24 12:34:15 brouard
133: (Module): Some bugs corrected for windows. Also, when
134: mle=-1 a template is output in file "or"mypar.txt with the design
135: of the covariance matrix to be input.
136:
137: Revision 1.89 2003/06/24 12:30:52 brouard
138: (Module): Some bugs corrected for windows. Also, when
139: mle=-1 a template is output in file "or"mypar.txt with the design
140: of the covariance matrix to be input.
141:
142: Revision 1.88 2003/06/23 17:54:56 brouard
143: * 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.
144:
145: Revision 1.87 2003/06/18 12:26:01 brouard
146: Version 0.96
147:
148: Revision 1.86 2003/06/17 20:04:08 brouard
149: (Module): Change position of html and gnuplot routines and added
150: routine fileappend.
151:
152: Revision 1.85 2003/06/17 13:12:43 brouard
153: * imach.c (Repository): Check when date of death was earlier that
154: current date of interview. It may happen when the death was just
155: prior to the death. In this case, dh was negative and likelihood
156: was wrong (infinity). We still send an "Error" but patch by
157: assuming that the date of death was just one stepm after the
158: interview.
159: (Repository): Because some people have very long ID (first column)
160: we changed int to long in num[] and we added a new lvector for
161: memory allocation. But we also truncated to 8 characters (left
162: truncation)
163: (Repository): No more line truncation errors.
164:
165: Revision 1.84 2003/06/13 21:44:43 brouard
166: * imach.c (Repository): Replace "freqsummary" at a correct
167: place. It differs from routine "prevalence" which may be called
168: many times. Probs is memory consuming and must be used with
169: parcimony.
170: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
171:
172: Revision 1.83 2003/06/10 13:39:11 lievre
173: *** empty log message ***
174:
175: Revision 1.82 2003/06/05 15:57:20 brouard
176: Add log in imach.c and fullversion number is now printed.
177:
178: */
179: /*
180: Interpolated Markov Chain
181:
182: Short summary of the programme:
183:
184: This program computes Healthy Life Expectancies from
185: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
186: first survey ("cross") where individuals from different ages are
187: interviewed on their health status or degree of disability (in the
188: case of a health survey which is our main interest) -2- at least a
189: second wave of interviews ("longitudinal") which measure each change
190: (if any) in individual health status. Health expectancies are
191: computed from the time spent in each health state according to a
192: model. More health states you consider, more time is necessary to reach the
193: Maximum Likelihood of the parameters involved in the model. The
194: simplest model is the multinomial logistic model where pij is the
195: probability to be observed in state j at the second wave
196: conditional to be observed in state i at the first wave. Therefore
197: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
198: 'age' is age and 'sex' is a covariate. If you want to have a more
199: complex model than "constant and age", you should modify the program
200: where the markup *Covariates have to be included here again* invites
201: you to do it. More covariates you add, slower the
202: convergence.
203:
204: The advantage of this computer programme, compared to a simple
205: multinomial logistic model, is clear when the delay between waves is not
206: identical for each individual. Also, if a individual missed an
207: intermediate interview, the information is lost, but taken into
208: account using an interpolation or extrapolation.
209:
210: hPijx is the probability to be observed in state i at age x+h
211: conditional to the observed state i at age x. The delay 'h' can be
212: split into an exact number (nh*stepm) of unobserved intermediate
213: states. This elementary transition (by month, quarter,
214: semester or year) is modelled as a multinomial logistic. The hPx
215: matrix is simply the matrix product of nh*stepm elementary matrices
216: and the contribution of each individual to the likelihood is simply
217: hPijx.
218:
219: Also this programme outputs the covariance matrix of the parameters but also
220: of the life expectancies. It also computes the period (stable) prevalence.
221:
222: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
223: Institut national d'études démographiques, Paris.
224: This software have been partly granted by Euro-REVES, a concerted action
225: from the European Union.
226: It is copyrighted identically to a GNU software product, ie programme and
227: software can be distributed freely for non commercial use. Latest version
228: can be accessed at http://euroreves.ined.fr/imach .
229:
230: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
231: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
232:
233: **********************************************************************/
234: /*
235: main
236: read parameterfile
237: read datafile
238: concatwav
239: freqsummary
240: if (mle >= 1)
241: mlikeli
242: print results files
243: if mle==1
244: computes hessian
245: read end of parameter file: agemin, agemax, bage, fage, estepm
246: begin-prev-date,...
247: open gnuplot file
248: open html file
249: period (stable) prevalence
250: for age prevalim()
251: h Pij x
252: variance of p varprob
253: forecasting if prevfcast==1 prevforecast call prevalence()
254: health expectancies
255: Variance-covariance of DFLE
256: prevalence()
257: movingaverage()
258: varevsij()
259: if popbased==1 varevsij(,popbased)
260: total life expectancies
261: Variance of period (stable) prevalence
262: end
263: */
264:
265:
266:
267:
268: #include <math.h>
269: #include <stdio.h>
270: #include <stdlib.h>
271: #include <string.h>
272: #include <unistd.h>
273:
274: #include <limits.h>
275: #include <sys/types.h>
276: #include <sys/stat.h>
277: #include <errno.h>
278: extern int errno;
279:
280: /* #include <sys/time.h> */
281: #include <time.h>
282: #include "timeval.h"
283:
284: /* #include <libintl.h> */
285: /* #define _(String) gettext (String) */
286:
287: #define MAXLINE 256
288:
289: #define GNUPLOTPROGRAM "gnuplot"
290: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
291: #define FILENAMELENGTH 132
292:
293: #define GLOCK_ERROR_NOPATH -1 /* empty path */
294: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
295:
296: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
297: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
298:
299: #define NINTERVMAX 8
300: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
301: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
302: #define NCOVMAX 8 /* Maximum number of covariates */
303: #define MAXN 20000
304: #define YEARM 12. /* Number of months per year */
305: #define AGESUP 130
306: #define AGEBASE 40
307: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
308: #ifdef UNIX
309: #define DIRSEPARATOR '/'
310: #define CHARSEPARATOR "/"
311: #define ODIRSEPARATOR '\\'
312: #else
313: #define DIRSEPARATOR '\\'
314: #define CHARSEPARATOR "\\"
315: #define ODIRSEPARATOR '/'
316: #endif
317:
318: /* $Id: imach.c,v 1.117 2006/03/14 17:16:22 brouard Exp $ */
319: /* $State: Exp $ */
320:
321: char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
322: char fullversion[]="$Revision: 1.117 $ $Date: 2006/03/14 17:16:22 $";
323: char strstart[80];
324: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
325: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
326: int nvar;
327: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
328: int npar=NPARMAX;
329: int nlstate=2; /* Number of live states */
330: int ndeath=1; /* Number of dead states */
331: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
332: int popbased=0;
333:
334: int *wav; /* Number of waves for this individuual 0 is possible */
335: int maxwav; /* Maxim number of waves */
336: int jmin, jmax; /* min, max spacing between 2 waves */
337: int ijmin, ijmax; /* Individuals having jmin and jmax */
338: int gipmx, gsw; /* Global variables on the number of contributions
339: to the likelihood and the sum of weights (done by funcone)*/
340: int mle, weightopt;
341: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
342: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
343: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
344: * wave mi and wave mi+1 is not an exact multiple of stepm. */
345: double jmean; /* Mean space between 2 waves */
346: double **oldm, **newm, **savm; /* Working pointers to matrices */
347: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
348: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
349: FILE *ficlog, *ficrespow;
350: int globpr; /* Global variable for printing or not */
351: double fretone; /* Only one call to likelihood */
352: long ipmx; /* Number of contributions */
353: double sw; /* Sum of weights */
354: char filerespow[FILENAMELENGTH];
355: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
356: FILE *ficresilk;
357: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
358: FILE *ficresprobmorprev;
359: FILE *fichtm, *fichtmcov; /* Html File */
360: FILE *ficreseij;
361: char filerese[FILENAMELENGTH];
362: FILE *ficresstdeij;
363: char fileresstde[FILENAMELENGTH];
364: FILE *ficrescveij;
365: char filerescve[FILENAMELENGTH];
366: FILE *ficresvij;
367: char fileresv[FILENAMELENGTH];
368: FILE *ficresvpl;
369: char fileresvpl[FILENAMELENGTH];
370: char title[MAXLINE];
371: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
372: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
373: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
374: char command[FILENAMELENGTH];
375: int outcmd=0;
376:
377: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
378:
379: char filelog[FILENAMELENGTH]; /* Log file */
380: char filerest[FILENAMELENGTH];
381: char fileregp[FILENAMELENGTH];
382: char popfile[FILENAMELENGTH];
383:
384: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
385:
386: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
387: struct timezone tzp;
388: extern int gettimeofday();
389: struct tm tmg, tm, tmf, *gmtime(), *localtime();
390: long time_value;
391: extern long time();
392: char strcurr[80], strfor[80];
393:
394: char *endptr;
395: long lval;
396:
397: #define NR_END 1
398: #define FREE_ARG char*
399: #define FTOL 1.0e-10
400:
401: #define NRANSI
402: #define ITMAX 200
403:
404: #define TOL 2.0e-4
405:
406: #define CGOLD 0.3819660
407: #define ZEPS 1.0e-10
408: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
409:
410: #define GOLD 1.618034
411: #define GLIMIT 100.0
412: #define TINY 1.0e-20
413:
414: static double maxarg1,maxarg2;
415: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
416: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
417:
418: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
419: #define rint(a) floor(a+0.5)
420:
421: static double sqrarg;
422: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
423: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
424: int agegomp= AGEGOMP;
425:
426: int imx;
427: int stepm=1;
428: /* Stepm, step in month: minimum step interpolation*/
429:
430: int estepm;
431: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
432:
433: int m,nb;
434: long *num;
435: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
436: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
437: double **pmmij, ***probs;
438: double *ageexmed,*agecens;
439: double dateintmean=0;
440:
441: double *weight;
442: int **s; /* Status */
443: double *agedc, **covar, idx;
444: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
445: double *lsurv, *lpop, *tpop;
446:
447: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
448: double ftolhess; /* Tolerance for computing hessian */
449:
450: /**************** split *************************/
451: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
452: {
453: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
454: the name of the file (name), its extension only (ext) and its first part of the name (finame)
455: */
456: char *ss; /* pointer */
457: int l1, l2; /* length counters */
458:
459: l1 = strlen(path ); /* length of path */
460: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
461: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
462: if ( ss == NULL ) { /* no directory, so determine current directory */
463: strcpy( name, path ); /* we got the fullname name because no directory */
464: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
465: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
466: /* get current working directory */
467: /* extern char* getcwd ( char *buf , int len);*/
468: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
469: return( GLOCK_ERROR_GETCWD );
470: }
471: /* got dirc from getcwd*/
472: printf(" DIRC = %s \n",dirc);
473: } else { /* strip direcotry from path */
474: ss++; /* after this, the filename */
475: l2 = strlen( ss ); /* length of filename */
476: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
477: strcpy( name, ss ); /* save file name */
478: strncpy( dirc, path, l1 - l2 ); /* now the directory */
479: dirc[l1-l2] = 0; /* add zero */
480: printf(" DIRC2 = %s \n",dirc);
481: }
482: /* We add a separator at the end of dirc if not exists */
483: l1 = strlen( dirc ); /* length of directory */
484: if( dirc[l1-1] != DIRSEPARATOR ){
485: dirc[l1] = DIRSEPARATOR;
486: dirc[l1+1] = 0;
487: printf(" DIRC3 = %s \n",dirc);
488: }
489: ss = strrchr( name, '.' ); /* find last / */
490: if (ss >0){
491: ss++;
492: strcpy(ext,ss); /* save extension */
493: l1= strlen( name);
494: l2= strlen(ss)+1;
495: strncpy( finame, name, l1-l2);
496: finame[l1-l2]= 0;
497: }
498:
499: return( 0 ); /* we're done */
500: }
501:
502:
503: /******************************************/
504:
505: void replace_back_to_slash(char *s, char*t)
506: {
507: int i;
508: int lg=0;
509: i=0;
510: lg=strlen(t);
511: for(i=0; i<= lg; i++) {
512: (s[i] = t[i]);
513: if (t[i]== '\\') s[i]='/';
514: }
515: }
516:
517: int nbocc(char *s, char occ)
518: {
519: int i,j=0;
520: int lg=20;
521: i=0;
522: lg=strlen(s);
523: for(i=0; i<= lg; i++) {
524: if (s[i] == occ ) j++;
525: }
526: return j;
527: }
528:
529: void cutv(char *u,char *v, char*t, char occ)
530: {
531: /* cuts string t into u and v where u ends before first occurence of char 'occ'
532: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
533: gives u="abcedf" and v="ghi2j" */
534: int i,lg,j,p=0;
535: i=0;
536: for(j=0; j<=strlen(t)-1; j++) {
537: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
538: }
539:
540: lg=strlen(t);
541: for(j=0; j<p; j++) {
542: (u[j] = t[j]);
543: }
544: u[p]='\0';
545:
546: for(j=0; j<= lg; j++) {
547: if (j>=(p+1))(v[j-p-1] = t[j]);
548: }
549: }
550:
551: /********************** nrerror ********************/
552:
553: void nrerror(char error_text[])
554: {
555: fprintf(stderr,"ERREUR ...\n");
556: fprintf(stderr,"%s\n",error_text);
557: exit(EXIT_FAILURE);
558: }
559: /*********************** vector *******************/
560: double *vector(int nl, int nh)
561: {
562: double *v;
563: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
564: if (!v) nrerror("allocation failure in vector");
565: return v-nl+NR_END;
566: }
567:
568: /************************ free vector ******************/
569: void free_vector(double*v, int nl, int nh)
570: {
571: free((FREE_ARG)(v+nl-NR_END));
572: }
573:
574: /************************ivector *******************************/
575: int *ivector(long nl,long nh)
576: {
577: int *v;
578: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
579: if (!v) nrerror("allocation failure in ivector");
580: return v-nl+NR_END;
581: }
582:
583: /******************free ivector **************************/
584: void free_ivector(int *v, long nl, long nh)
585: {
586: free((FREE_ARG)(v+nl-NR_END));
587: }
588:
589: /************************lvector *******************************/
590: long *lvector(long nl,long nh)
591: {
592: long *v;
593: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
594: if (!v) nrerror("allocation failure in ivector");
595: return v-nl+NR_END;
596: }
597:
598: /******************free lvector **************************/
599: void free_lvector(long *v, long nl, long nh)
600: {
601: free((FREE_ARG)(v+nl-NR_END));
602: }
603:
604: /******************* imatrix *******************************/
605: int **imatrix(long nrl, long nrh, long ncl, long nch)
606: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
607: {
608: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
609: int **m;
610:
611: /* allocate pointers to rows */
612: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
613: if (!m) nrerror("allocation failure 1 in matrix()");
614: m += NR_END;
615: m -= nrl;
616:
617:
618: /* allocate rows and set pointers to them */
619: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
620: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
621: m[nrl] += NR_END;
622: m[nrl] -= ncl;
623:
624: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
625:
626: /* return pointer to array of pointers to rows */
627: return m;
628: }
629:
630: /****************** free_imatrix *************************/
631: void free_imatrix(m,nrl,nrh,ncl,nch)
632: int **m;
633: long nch,ncl,nrh,nrl;
634: /* free an int matrix allocated by imatrix() */
635: {
636: free((FREE_ARG) (m[nrl]+ncl-NR_END));
637: free((FREE_ARG) (m+nrl-NR_END));
638: }
639:
640: /******************* matrix *******************************/
641: double **matrix(long nrl, long nrh, long ncl, long nch)
642: {
643: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
644: double **m;
645:
646: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
647: if (!m) nrerror("allocation failure 1 in matrix()");
648: m += NR_END;
649: m -= nrl;
650:
651: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
652: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
653: m[nrl] += NR_END;
654: m[nrl] -= ncl;
655:
656: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
657: return m;
658: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
659: */
660: }
661:
662: /*************************free matrix ************************/
663: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
664: {
665: free((FREE_ARG)(m[nrl]+ncl-NR_END));
666: free((FREE_ARG)(m+nrl-NR_END));
667: }
668:
669: /******************* ma3x *******************************/
670: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
671: {
672: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
673: double ***m;
674:
675: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
676: if (!m) nrerror("allocation failure 1 in matrix()");
677: m += NR_END;
678: m -= nrl;
679:
680: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
681: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
682: m[nrl] += NR_END;
683: m[nrl] -= ncl;
684:
685: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
686:
687: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
688: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
689: m[nrl][ncl] += NR_END;
690: m[nrl][ncl] -= nll;
691: for (j=ncl+1; j<=nch; j++)
692: m[nrl][j]=m[nrl][j-1]+nlay;
693:
694: for (i=nrl+1; i<=nrh; i++) {
695: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
696: for (j=ncl+1; j<=nch; j++)
697: m[i][j]=m[i][j-1]+nlay;
698: }
699: return m;
700: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
701: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
702: */
703: }
704:
705: /*************************free ma3x ************************/
706: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
707: {
708: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
709: free((FREE_ARG)(m[nrl]+ncl-NR_END));
710: free((FREE_ARG)(m+nrl-NR_END));
711: }
712:
713: /*************** function subdirf ***********/
714: char *subdirf(char fileres[])
715: {
716: /* Caution optionfilefiname is hidden */
717: strcpy(tmpout,optionfilefiname);
718: strcat(tmpout,"/"); /* Add to the right */
719: strcat(tmpout,fileres);
720: return tmpout;
721: }
722:
723: /*************** function subdirf2 ***********/
724: char *subdirf2(char fileres[], char *preop)
725: {
726:
727: /* Caution optionfilefiname is hidden */
728: strcpy(tmpout,optionfilefiname);
729: strcat(tmpout,"/");
730: strcat(tmpout,preop);
731: strcat(tmpout,fileres);
732: return tmpout;
733: }
734:
735: /*************** function subdirf3 ***********/
736: char *subdirf3(char fileres[], char *preop, char *preop2)
737: {
738:
739: /* Caution optionfilefiname is hidden */
740: strcpy(tmpout,optionfilefiname);
741: strcat(tmpout,"/");
742: strcat(tmpout,preop);
743: strcat(tmpout,preop2);
744: strcat(tmpout,fileres);
745: return tmpout;
746: }
747:
748: /***************** f1dim *************************/
749: extern int ncom;
750: extern double *pcom,*xicom;
751: extern double (*nrfunc)(double []);
752:
753: double f1dim(double x)
754: {
755: int j;
756: double f;
757: double *xt;
758:
759: xt=vector(1,ncom);
760: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
761: f=(*nrfunc)(xt);
762: free_vector(xt,1,ncom);
763: return f;
764: }
765:
766: /*****************brent *************************/
767: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
768: {
769: int iter;
770: double a,b,d,etemp;
771: double fu,fv,fw,fx;
772: double ftemp;
773: double p,q,r,tol1,tol2,u,v,w,x,xm;
774: double e=0.0;
775:
776: a=(ax < cx ? ax : cx);
777: b=(ax > cx ? ax : cx);
778: x=w=v=bx;
779: fw=fv=fx=(*f)(x);
780: for (iter=1;iter<=ITMAX;iter++) {
781: xm=0.5*(a+b);
782: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
783: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
784: printf(".");fflush(stdout);
785: fprintf(ficlog,".");fflush(ficlog);
786: #ifdef DEBUG
787: 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);
788: 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);
789: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
790: #endif
791: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
792: *xmin=x;
793: return fx;
794: }
795: ftemp=fu;
796: if (fabs(e) > tol1) {
797: r=(x-w)*(fx-fv);
798: q=(x-v)*(fx-fw);
799: p=(x-v)*q-(x-w)*r;
800: q=2.0*(q-r);
801: if (q > 0.0) p = -p;
802: q=fabs(q);
803: etemp=e;
804: e=d;
805: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
806: d=CGOLD*(e=(x >= xm ? a-x : b-x));
807: else {
808: d=p/q;
809: u=x+d;
810: if (u-a < tol2 || b-u < tol2)
811: d=SIGN(tol1,xm-x);
812: }
813: } else {
814: d=CGOLD*(e=(x >= xm ? a-x : b-x));
815: }
816: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
817: fu=(*f)(u);
818: if (fu <= fx) {
819: if (u >= x) a=x; else b=x;
820: SHFT(v,w,x,u)
821: SHFT(fv,fw,fx,fu)
822: } else {
823: if (u < x) a=u; else b=u;
824: if (fu <= fw || w == x) {
825: v=w;
826: w=u;
827: fv=fw;
828: fw=fu;
829: } else if (fu <= fv || v == x || v == w) {
830: v=u;
831: fv=fu;
832: }
833: }
834: }
835: nrerror("Too many iterations in brent");
836: *xmin=x;
837: return fx;
838: }
839:
840: /****************** mnbrak ***********************/
841:
842: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
843: double (*func)(double))
844: {
845: double ulim,u,r,q, dum;
846: double fu;
847:
848: *fa=(*func)(*ax);
849: *fb=(*func)(*bx);
850: if (*fb > *fa) {
851: SHFT(dum,*ax,*bx,dum)
852: SHFT(dum,*fb,*fa,dum)
853: }
854: *cx=(*bx)+GOLD*(*bx-*ax);
855: *fc=(*func)(*cx);
856: while (*fb > *fc) {
857: r=(*bx-*ax)*(*fb-*fc);
858: q=(*bx-*cx)*(*fb-*fa);
859: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
860: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
861: ulim=(*bx)+GLIMIT*(*cx-*bx);
862: if ((*bx-u)*(u-*cx) > 0.0) {
863: fu=(*func)(u);
864: } else if ((*cx-u)*(u-ulim) > 0.0) {
865: fu=(*func)(u);
866: if (fu < *fc) {
867: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
868: SHFT(*fb,*fc,fu,(*func)(u))
869: }
870: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
871: u=ulim;
872: fu=(*func)(u);
873: } else {
874: u=(*cx)+GOLD*(*cx-*bx);
875: fu=(*func)(u);
876: }
877: SHFT(*ax,*bx,*cx,u)
878: SHFT(*fa,*fb,*fc,fu)
879: }
880: }
881:
882: /*************** linmin ************************/
883:
884: int ncom;
885: double *pcom,*xicom;
886: double (*nrfunc)(double []);
887:
888: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
889: {
890: double brent(double ax, double bx, double cx,
891: double (*f)(double), double tol, double *xmin);
892: double f1dim(double x);
893: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
894: double *fc, double (*func)(double));
895: int j;
896: double xx,xmin,bx,ax;
897: double fx,fb,fa;
898:
899: ncom=n;
900: pcom=vector(1,n);
901: xicom=vector(1,n);
902: nrfunc=func;
903: for (j=1;j<=n;j++) {
904: pcom[j]=p[j];
905: xicom[j]=xi[j];
906: }
907: ax=0.0;
908: xx=1.0;
909: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
910: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
911: #ifdef DEBUG
912: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
913: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
914: #endif
915: for (j=1;j<=n;j++) {
916: xi[j] *= xmin;
917: p[j] += xi[j];
918: }
919: free_vector(xicom,1,n);
920: free_vector(pcom,1,n);
921: }
922:
923: char *asc_diff_time(long time_sec, char ascdiff[])
924: {
925: long sec_left, days, hours, minutes;
926: days = (time_sec) / (60*60*24);
927: sec_left = (time_sec) % (60*60*24);
928: hours = (sec_left) / (60*60) ;
929: sec_left = (sec_left) %(60*60);
930: minutes = (sec_left) /60;
931: sec_left = (sec_left) % (60);
932: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
933: return ascdiff;
934: }
935:
936: /*************** powell ************************/
937: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
938: double (*func)(double []))
939: {
940: void linmin(double p[], double xi[], int n, double *fret,
941: double (*func)(double []));
942: int i,ibig,j;
943: double del,t,*pt,*ptt,*xit;
944: double fp,fptt;
945: double *xits;
946: int niterf, itmp;
947:
948: pt=vector(1,n);
949: ptt=vector(1,n);
950: xit=vector(1,n);
951: xits=vector(1,n);
952: *fret=(*func)(p);
953: for (j=1;j<=n;j++) pt[j]=p[j];
954: for (*iter=1;;++(*iter)) {
955: fp=(*fret);
956: ibig=0;
957: del=0.0;
958: last_time=curr_time;
959: (void) gettimeofday(&curr_time,&tzp);
960: 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);
961: /* 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);
962: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
963: */
964: for (i=1;i<=n;i++) {
965: printf(" %d %.12f",i, p[i]);
966: fprintf(ficlog," %d %.12lf",i, p[i]);
967: fprintf(ficrespow," %.12lf", p[i]);
968: }
969: printf("\n");
970: fprintf(ficlog,"\n");
971: fprintf(ficrespow,"\n");fflush(ficrespow);
972: if(*iter <=3){
973: tm = *localtime(&curr_time.tv_sec);
974: strcpy(strcurr,asctime(&tm));
975: /* asctime_r(&tm,strcurr); */
976: forecast_time=curr_time;
977: itmp = strlen(strcurr);
978: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
979: strcurr[itmp-1]='\0';
980: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
981: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
982: for(niterf=10;niterf<=30;niterf+=10){
983: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
984: tmf = *localtime(&forecast_time.tv_sec);
985: /* asctime_r(&tmf,strfor); */
986: strcpy(strfor,asctime(&tmf));
987: itmp = strlen(strfor);
988: if(strfor[itmp-1]=='\n')
989: strfor[itmp-1]='\0';
990: 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);
991: 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);
992: }
993: }
994: for (i=1;i<=n;i++) {
995: for (j=1;j<=n;j++) xit[j]=xi[j][i];
996: fptt=(*fret);
997: #ifdef DEBUG
998: printf("fret=%lf \n",*fret);
999: fprintf(ficlog,"fret=%lf \n",*fret);
1000: #endif
1001: printf("%d",i);fflush(stdout);
1002: fprintf(ficlog,"%d",i);fflush(ficlog);
1003: linmin(p,xit,n,fret,func);
1004: if (fabs(fptt-(*fret)) > del) {
1005: del=fabs(fptt-(*fret));
1006: ibig=i;
1007: }
1008: #ifdef DEBUG
1009: printf("%d %.12e",i,(*fret));
1010: fprintf(ficlog,"%d %.12e",i,(*fret));
1011: for (j=1;j<=n;j++) {
1012: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1013: printf(" x(%d)=%.12e",j,xit[j]);
1014: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1015: }
1016: for(j=1;j<=n;j++) {
1017: printf(" p=%.12e",p[j]);
1018: fprintf(ficlog," p=%.12e",p[j]);
1019: }
1020: printf("\n");
1021: fprintf(ficlog,"\n");
1022: #endif
1023: }
1024: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1025: #ifdef DEBUG
1026: int k[2],l;
1027: k[0]=1;
1028: k[1]=-1;
1029: printf("Max: %.12e",(*func)(p));
1030: fprintf(ficlog,"Max: %.12e",(*func)(p));
1031: for (j=1;j<=n;j++) {
1032: printf(" %.12e",p[j]);
1033: fprintf(ficlog," %.12e",p[j]);
1034: }
1035: printf("\n");
1036: fprintf(ficlog,"\n");
1037: for(l=0;l<=1;l++) {
1038: for (j=1;j<=n;j++) {
1039: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1040: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1041: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1042: }
1043: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1044: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1045: }
1046: #endif
1047:
1048:
1049: free_vector(xit,1,n);
1050: free_vector(xits,1,n);
1051: free_vector(ptt,1,n);
1052: free_vector(pt,1,n);
1053: return;
1054: }
1055: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1056: for (j=1;j<=n;j++) {
1057: ptt[j]=2.0*p[j]-pt[j];
1058: xit[j]=p[j]-pt[j];
1059: pt[j]=p[j];
1060: }
1061: fptt=(*func)(ptt);
1062: if (fptt < fp) {
1063: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1064: if (t < 0.0) {
1065: linmin(p,xit,n,fret,func);
1066: for (j=1;j<=n;j++) {
1067: xi[j][ibig]=xi[j][n];
1068: xi[j][n]=xit[j];
1069: }
1070: #ifdef DEBUG
1071: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1072: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1073: for(j=1;j<=n;j++){
1074: printf(" %.12e",xit[j]);
1075: fprintf(ficlog," %.12e",xit[j]);
1076: }
1077: printf("\n");
1078: fprintf(ficlog,"\n");
1079: #endif
1080: }
1081: }
1082: }
1083: }
1084:
1085: /**** Prevalence limit (stable or period prevalence) ****************/
1086:
1087: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1088: {
1089: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1090: matrix by transitions matrix until convergence is reached */
1091:
1092: int i, ii,j,k;
1093: double min, max, maxmin, maxmax,sumnew=0.;
1094: double **matprod2();
1095: double **out, cov[NCOVMAX], **pmij();
1096: double **newm;
1097: double agefin, delaymax=50 ; /* Max number of years to converge */
1098:
1099: for (ii=1;ii<=nlstate+ndeath;ii++)
1100: for (j=1;j<=nlstate+ndeath;j++){
1101: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1102: }
1103:
1104: cov[1]=1.;
1105:
1106: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1107: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1108: newm=savm;
1109: /* Covariates have to be included here again */
1110: cov[2]=agefin;
1111:
1112: for (k=1; k<=cptcovn;k++) {
1113: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1114: /* 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]]);*/
1115: }
1116: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1117: for (k=1; k<=cptcovprod;k++)
1118: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1119:
1120: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1121: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1122: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1123: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1124:
1125: savm=oldm;
1126: oldm=newm;
1127: maxmax=0.;
1128: for(j=1;j<=nlstate;j++){
1129: min=1.;
1130: max=0.;
1131: for(i=1; i<=nlstate; i++) {
1132: sumnew=0;
1133: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1134: prlim[i][j]= newm[i][j]/(1-sumnew);
1135: max=FMAX(max,prlim[i][j]);
1136: min=FMIN(min,prlim[i][j]);
1137: }
1138: maxmin=max-min;
1139: maxmax=FMAX(maxmax,maxmin);
1140: }
1141: if(maxmax < ftolpl){
1142: return prlim;
1143: }
1144: }
1145: }
1146:
1147: /*************** transition probabilities ***************/
1148:
1149: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1150: {
1151: double s1, s2;
1152: /*double t34;*/
1153: int i,j,j1, nc, ii, jj;
1154:
1155: for(i=1; i<= nlstate; i++){
1156: for(j=1; j<i;j++){
1157: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1158: /*s2 += param[i][j][nc]*cov[nc];*/
1159: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1160: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1161: }
1162: ps[i][j]=s2;
1163: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1164: }
1165: for(j=i+1; j<=nlstate+ndeath;j++){
1166: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1167: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1168: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1169: }
1170: ps[i][j]=s2;
1171: }
1172: }
1173: /*ps[3][2]=1;*/
1174:
1175: for(i=1; i<= nlstate; i++){
1176: s1=0;
1177: for(j=1; j<i; j++)
1178: s1+=exp(ps[i][j]);
1179: for(j=i+1; j<=nlstate+ndeath; j++)
1180: s1+=exp(ps[i][j]);
1181: ps[i][i]=1./(s1+1.);
1182: for(j=1; j<i; j++)
1183: ps[i][j]= exp(ps[i][j])*ps[i][i];
1184: for(j=i+1; j<=nlstate+ndeath; j++)
1185: ps[i][j]= exp(ps[i][j])*ps[i][i];
1186: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1187: } /* end i */
1188:
1189: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1190: for(jj=1; jj<= nlstate+ndeath; jj++){
1191: ps[ii][jj]=0;
1192: ps[ii][ii]=1;
1193: }
1194: }
1195:
1196:
1197: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1198: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1199: /* printf("ddd %lf ",ps[ii][jj]); */
1200: /* } */
1201: /* printf("\n "); */
1202: /* } */
1203: /* printf("\n ");printf("%lf ",cov[2]); */
1204: /*
1205: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1206: goto end;*/
1207: return ps;
1208: }
1209:
1210: /**************** Product of 2 matrices ******************/
1211:
1212: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1213: {
1214: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1215: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1216: /* in, b, out are matrice of pointers which should have been initialized
1217: before: only the contents of out is modified. The function returns
1218: a pointer to pointers identical to out */
1219: long i, j, k;
1220: for(i=nrl; i<= nrh; i++)
1221: for(k=ncolol; k<=ncoloh; k++)
1222: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1223: out[i][k] +=in[i][j]*b[j][k];
1224:
1225: return out;
1226: }
1227:
1228:
1229: /************* Higher Matrix Product ***************/
1230:
1231: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1232: {
1233: /* Computes the transition matrix starting at age 'age' over
1234: 'nhstepm*hstepm*stepm' months (i.e. until
1235: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1236: nhstepm*hstepm matrices.
1237: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1238: (typically every 2 years instead of every month which is too big
1239: for the memory).
1240: Model is determined by parameters x and covariates have to be
1241: included manually here.
1242:
1243: */
1244:
1245: int i, j, d, h, k;
1246: double **out, cov[NCOVMAX];
1247: double **newm;
1248:
1249: /* Hstepm could be zero and should return the unit matrix */
1250: for (i=1;i<=nlstate+ndeath;i++)
1251: for (j=1;j<=nlstate+ndeath;j++){
1252: oldm[i][j]=(i==j ? 1.0 : 0.0);
1253: po[i][j][0]=(i==j ? 1.0 : 0.0);
1254: }
1255: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1256: for(h=1; h <=nhstepm; h++){
1257: for(d=1; d <=hstepm; d++){
1258: newm=savm;
1259: /* Covariates have to be included here again */
1260: cov[1]=1.;
1261: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1262: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1263: for (k=1; k<=cptcovage;k++)
1264: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1265: for (k=1; k<=cptcovprod;k++)
1266: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1267:
1268:
1269: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1270: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1271: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1272: pmij(pmmij,cov,ncovmodel,x,nlstate));
1273: savm=oldm;
1274: oldm=newm;
1275: }
1276: for(i=1; i<=nlstate+ndeath; i++)
1277: for(j=1;j<=nlstate+ndeath;j++) {
1278: po[i][j][h]=newm[i][j];
1279: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1280: */
1281: }
1282: } /* end h */
1283: return po;
1284: }
1285:
1286:
1287: /*************** log-likelihood *************/
1288: double func( double *x)
1289: {
1290: int i, ii, j, k, mi, d, kk;
1291: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1292: double **out;
1293: double sw; /* Sum of weights */
1294: double lli; /* Individual log likelihood */
1295: int s1, s2;
1296: double bbh, survp;
1297: long ipmx;
1298: /*extern weight */
1299: /* We are differentiating ll according to initial status */
1300: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1301: /*for(i=1;i<imx;i++)
1302: printf(" %d\n",s[4][i]);
1303: */
1304: cov[1]=1.;
1305:
1306: for(k=1; k<=nlstate; k++) ll[k]=0.;
1307:
1308: if(mle==1){
1309: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1310: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1311: for(mi=1; mi<= wav[i]-1; mi++){
1312: for (ii=1;ii<=nlstate+ndeath;ii++)
1313: for (j=1;j<=nlstate+ndeath;j++){
1314: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1315: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1316: }
1317: for(d=0; d<dh[mi][i]; d++){
1318: newm=savm;
1319: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1320: for (kk=1; kk<=cptcovage;kk++) {
1321: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1322: }
1323: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1324: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1325: savm=oldm;
1326: oldm=newm;
1327: } /* end mult */
1328:
1329: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1330: /* But now since version 0.9 we anticipate for bias at large stepm.
1331: * If stepm is larger than one month (smallest stepm) and if the exact delay
1332: * (in months) between two waves is not a multiple of stepm, we rounded to
1333: * the nearest (and in case of equal distance, to the lowest) interval but now
1334: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1335: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1336: * probability in order to take into account the bias as a fraction of the way
1337: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1338: * -stepm/2 to stepm/2 .
1339: * For stepm=1 the results are the same as for previous versions of Imach.
1340: * For stepm > 1 the results are less biased than in previous versions.
1341: */
1342: s1=s[mw[mi][i]][i];
1343: s2=s[mw[mi+1][i]][i];
1344: bbh=(double)bh[mi][i]/(double)stepm;
1345: /* bias bh is positive if real duration
1346: * is higher than the multiple of stepm and negative otherwise.
1347: */
1348: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1349: if( s2 > nlstate){
1350: /* i.e. if s2 is a death state and if the date of death is known
1351: then the contribution to the likelihood is the probability to
1352: die between last step unit time and current step unit time,
1353: which is also equal to probability to die before dh
1354: minus probability to die before dh-stepm .
1355: In version up to 0.92 likelihood was computed
1356: as if date of death was unknown. Death was treated as any other
1357: health state: the date of the interview describes the actual state
1358: and not the date of a change in health state. The former idea was
1359: to consider that at each interview the state was recorded
1360: (healthy, disable or death) and IMaCh was corrected; but when we
1361: introduced the exact date of death then we should have modified
1362: the contribution of an exact death to the likelihood. This new
1363: contribution is smaller and very dependent of the step unit
1364: stepm. It is no more the probability to die between last interview
1365: and month of death but the probability to survive from last
1366: interview up to one month before death multiplied by the
1367: probability to die within a month. Thanks to Chris
1368: Jackson for correcting this bug. Former versions increased
1369: mortality artificially. The bad side is that we add another loop
1370: which slows down the processing. The difference can be up to 10%
1371: lower mortality.
1372: */
1373: lli=log(out[s1][s2] - savm[s1][s2]);
1374:
1375:
1376: } else if (s2==-2) {
1377: for (j=1,survp=0. ; j<=nlstate; j++)
1378: survp += out[s1][j];
1379: lli= survp;
1380: }
1381:
1382: else if (s2==-4) {
1383: for (j=3,survp=0. ; j<=nlstate; j++)
1384: survp += out[s1][j];
1385: lli= survp;
1386: }
1387:
1388: else if (s2==-5) {
1389: for (j=1,survp=0. ; j<=2; j++)
1390: survp += out[s1][j];
1391: lli= survp;
1392: }
1393:
1394:
1395: else{
1396: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1397: /* 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 */
1398: }
1399: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1400: /*if(lli ==000.0)*/
1401: /*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); */
1402: ipmx +=1;
1403: sw += weight[i];
1404: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1405: } /* end of wave */
1406: } /* end of individual */
1407: } else if(mle==2){
1408: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1409: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1410: for(mi=1; mi<= wav[i]-1; mi++){
1411: for (ii=1;ii<=nlstate+ndeath;ii++)
1412: for (j=1;j<=nlstate+ndeath;j++){
1413: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1414: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1415: }
1416: for(d=0; d<=dh[mi][i]; d++){
1417: newm=savm;
1418: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1419: for (kk=1; kk<=cptcovage;kk++) {
1420: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1421: }
1422: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1423: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1424: savm=oldm;
1425: oldm=newm;
1426: } /* end mult */
1427:
1428: s1=s[mw[mi][i]][i];
1429: s2=s[mw[mi+1][i]][i];
1430: bbh=(double)bh[mi][i]/(double)stepm;
1431: 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 */
1432: ipmx +=1;
1433: sw += weight[i];
1434: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1435: } /* end of wave */
1436: } /* end of individual */
1437: } else if(mle==3){ /* exponential inter-extrapolation */
1438: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1439: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1440: for(mi=1; mi<= wav[i]-1; mi++){
1441: for (ii=1;ii<=nlstate+ndeath;ii++)
1442: for (j=1;j<=nlstate+ndeath;j++){
1443: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1444: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1445: }
1446: for(d=0; d<dh[mi][i]; d++){
1447: newm=savm;
1448: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1449: for (kk=1; kk<=cptcovage;kk++) {
1450: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1451: }
1452: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1453: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1454: savm=oldm;
1455: oldm=newm;
1456: } /* end mult */
1457:
1458: s1=s[mw[mi][i]][i];
1459: s2=s[mw[mi+1][i]][i];
1460: bbh=(double)bh[mi][i]/(double)stepm;
1461: 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 */
1462: ipmx +=1;
1463: sw += weight[i];
1464: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1465: } /* end of wave */
1466: } /* end of individual */
1467: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1468: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1469: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1470: for(mi=1; mi<= wav[i]-1; mi++){
1471: for (ii=1;ii<=nlstate+ndeath;ii++)
1472: for (j=1;j<=nlstate+ndeath;j++){
1473: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1474: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1475: }
1476: for(d=0; d<dh[mi][i]; d++){
1477: newm=savm;
1478: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1479: for (kk=1; kk<=cptcovage;kk++) {
1480: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1481: }
1482:
1483: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1484: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1485: savm=oldm;
1486: oldm=newm;
1487: } /* end mult */
1488:
1489: s1=s[mw[mi][i]][i];
1490: s2=s[mw[mi+1][i]][i];
1491: if( s2 > nlstate){
1492: lli=log(out[s1][s2] - savm[s1][s2]);
1493: }else{
1494: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1495: }
1496: ipmx +=1;
1497: sw += weight[i];
1498: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1499: /* 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]); */
1500: } /* end of wave */
1501: } /* end of individual */
1502: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1503: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1504: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1505: for(mi=1; mi<= wav[i]-1; mi++){
1506: for (ii=1;ii<=nlstate+ndeath;ii++)
1507: for (j=1;j<=nlstate+ndeath;j++){
1508: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1509: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1510: }
1511: for(d=0; d<dh[mi][i]; d++){
1512: newm=savm;
1513: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1514: for (kk=1; kk<=cptcovage;kk++) {
1515: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1516: }
1517:
1518: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1519: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1520: savm=oldm;
1521: oldm=newm;
1522: } /* end mult */
1523:
1524: s1=s[mw[mi][i]][i];
1525: s2=s[mw[mi+1][i]][i];
1526: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1527: ipmx +=1;
1528: sw += weight[i];
1529: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1530: /*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]);*/
1531: } /* end of wave */
1532: } /* end of individual */
1533: } /* End of if */
1534: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1535: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1536: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1537: return -l;
1538: }
1539:
1540: /*************** log-likelihood *************/
1541: double funcone( double *x)
1542: {
1543: /* Same as likeli but slower because of a lot of printf and if */
1544: int i, ii, j, k, mi, d, kk;
1545: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1546: double **out;
1547: double lli; /* Individual log likelihood */
1548: double llt;
1549: int s1, s2;
1550: double bbh, survp;
1551: /*extern weight */
1552: /* We are differentiating ll according to initial status */
1553: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1554: /*for(i=1;i<imx;i++)
1555: printf(" %d\n",s[4][i]);
1556: */
1557: cov[1]=1.;
1558:
1559: for(k=1; k<=nlstate; k++) ll[k]=0.;
1560:
1561: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1562: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1563: for(mi=1; mi<= wav[i]-1; mi++){
1564: for (ii=1;ii<=nlstate+ndeath;ii++)
1565: for (j=1;j<=nlstate+ndeath;j++){
1566: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1567: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1568: }
1569: for(d=0; d<dh[mi][i]; d++){
1570: newm=savm;
1571: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1572: for (kk=1; kk<=cptcovage;kk++) {
1573: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1574: }
1575: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1576: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1577: savm=oldm;
1578: oldm=newm;
1579: } /* end mult */
1580:
1581: s1=s[mw[mi][i]][i];
1582: s2=s[mw[mi+1][i]][i];
1583: bbh=(double)bh[mi][i]/(double)stepm;
1584: /* bias is positive if real duration
1585: * is higher than the multiple of stepm and negative otherwise.
1586: */
1587: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1588: lli=log(out[s1][s2] - savm[s1][s2]);
1589: } else if (mle==1){
1590: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1591: } else if(mle==2){
1592: 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 */
1593: } else if(mle==3){ /* exponential inter-extrapolation */
1594: 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 */
1595: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1596: lli=log(out[s1][s2]); /* Original formula */
1597: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1598: lli=log(out[s1][s2]); /* Original formula */
1599: } /* End of if */
1600: ipmx +=1;
1601: sw += weight[i];
1602: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1603: /* 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]); */
1604: if(globpr){
1605: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1606: %10.6f %10.6f %10.6f ", \
1607: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1608: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1609: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1610: llt +=ll[k]*gipmx/gsw;
1611: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1612: }
1613: fprintf(ficresilk," %10.6f\n", -llt);
1614: }
1615: } /* end of wave */
1616: } /* end of individual */
1617: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1618: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1619: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1620: if(globpr==0){ /* First time we count the contributions and weights */
1621: gipmx=ipmx;
1622: gsw=sw;
1623: }
1624: return -l;
1625: }
1626:
1627:
1628: /*************** function likelione ***********/
1629: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1630: {
1631: /* This routine should help understanding what is done with
1632: the selection of individuals/waves and
1633: to check the exact contribution to the likelihood.
1634: Plotting could be done.
1635: */
1636: int k;
1637:
1638: if(*globpri !=0){ /* Just counts and sums, no printings */
1639: strcpy(fileresilk,"ilk");
1640: strcat(fileresilk,fileres);
1641: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1642: printf("Problem with resultfile: %s\n", fileresilk);
1643: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1644: }
1645: 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");
1646: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1647: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1648: for(k=1; k<=nlstate; k++)
1649: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1650: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1651: }
1652:
1653: *fretone=(*funcone)(p);
1654: if(*globpri !=0){
1655: fclose(ficresilk);
1656: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1657: fflush(fichtm);
1658: }
1659: return;
1660: }
1661:
1662:
1663: /*********** Maximum Likelihood Estimation ***************/
1664:
1665: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1666: {
1667: int i,j, iter;
1668: double **xi;
1669: double fret;
1670: double fretone; /* Only one call to likelihood */
1671: /* char filerespow[FILENAMELENGTH];*/
1672: xi=matrix(1,npar,1,npar);
1673: for (i=1;i<=npar;i++)
1674: for (j=1;j<=npar;j++)
1675: xi[i][j]=(i==j ? 1.0 : 0.0);
1676: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1677: strcpy(filerespow,"pow");
1678: strcat(filerespow,fileres);
1679: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1680: printf("Problem with resultfile: %s\n", filerespow);
1681: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1682: }
1683: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1684: for (i=1;i<=nlstate;i++)
1685: for(j=1;j<=nlstate+ndeath;j++)
1686: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1687: fprintf(ficrespow,"\n");
1688:
1689: powell(p,xi,npar,ftol,&iter,&fret,func);
1690:
1691: free_matrix(xi,1,npar,1,npar);
1692: fclose(ficrespow);
1693: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1694: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1695: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1696:
1697: }
1698:
1699: /**** Computes Hessian and covariance matrix ***/
1700: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1701: {
1702: double **a,**y,*x,pd;
1703: double **hess;
1704: int i, j,jk;
1705: int *indx;
1706:
1707: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1708: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1709: void lubksb(double **a, int npar, int *indx, double b[]) ;
1710: void ludcmp(double **a, int npar, int *indx, double *d) ;
1711: double gompertz(double p[]);
1712: hess=matrix(1,npar,1,npar);
1713:
1714: printf("\nCalculation of the hessian matrix. Wait...\n");
1715: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1716: for (i=1;i<=npar;i++){
1717: printf("%d",i);fflush(stdout);
1718: fprintf(ficlog,"%d",i);fflush(ficlog);
1719:
1720: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1721:
1722: /* printf(" %f ",p[i]);
1723: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1724: }
1725:
1726: for (i=1;i<=npar;i++) {
1727: for (j=1;j<=npar;j++) {
1728: if (j>i) {
1729: printf(".%d%d",i,j);fflush(stdout);
1730: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1731: hess[i][j]=hessij(p,delti,i,j,func,npar);
1732:
1733: hess[j][i]=hess[i][j];
1734: /*printf(" %lf ",hess[i][j]);*/
1735: }
1736: }
1737: }
1738: printf("\n");
1739: fprintf(ficlog,"\n");
1740:
1741: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1742: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1743:
1744: a=matrix(1,npar,1,npar);
1745: y=matrix(1,npar,1,npar);
1746: x=vector(1,npar);
1747: indx=ivector(1,npar);
1748: for (i=1;i<=npar;i++)
1749: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1750: ludcmp(a,npar,indx,&pd);
1751:
1752: for (j=1;j<=npar;j++) {
1753: for (i=1;i<=npar;i++) x[i]=0;
1754: x[j]=1;
1755: lubksb(a,npar,indx,x);
1756: for (i=1;i<=npar;i++){
1757: matcov[i][j]=x[i];
1758: }
1759: }
1760:
1761: printf("\n#Hessian matrix#\n");
1762: fprintf(ficlog,"\n#Hessian matrix#\n");
1763: for (i=1;i<=npar;i++) {
1764: for (j=1;j<=npar;j++) {
1765: printf("%.3e ",hess[i][j]);
1766: fprintf(ficlog,"%.3e ",hess[i][j]);
1767: }
1768: printf("\n");
1769: fprintf(ficlog,"\n");
1770: }
1771:
1772: /* Recompute Inverse */
1773: for (i=1;i<=npar;i++)
1774: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1775: ludcmp(a,npar,indx,&pd);
1776:
1777: /* printf("\n#Hessian matrix recomputed#\n");
1778:
1779: for (j=1;j<=npar;j++) {
1780: for (i=1;i<=npar;i++) x[i]=0;
1781: x[j]=1;
1782: lubksb(a,npar,indx,x);
1783: for (i=1;i<=npar;i++){
1784: y[i][j]=x[i];
1785: printf("%.3e ",y[i][j]);
1786: fprintf(ficlog,"%.3e ",y[i][j]);
1787: }
1788: printf("\n");
1789: fprintf(ficlog,"\n");
1790: }
1791: */
1792:
1793: free_matrix(a,1,npar,1,npar);
1794: free_matrix(y,1,npar,1,npar);
1795: free_vector(x,1,npar);
1796: free_ivector(indx,1,npar);
1797: free_matrix(hess,1,npar,1,npar);
1798:
1799:
1800: }
1801:
1802: /*************** hessian matrix ****************/
1803: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1804: {
1805: int i;
1806: int l=1, lmax=20;
1807: double k1,k2;
1808: double p2[NPARMAX+1];
1809: double res;
1810: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1811: double fx;
1812: int k=0,kmax=10;
1813: double l1;
1814:
1815: fx=func(x);
1816: for (i=1;i<=npar;i++) p2[i]=x[i];
1817: for(l=0 ; l <=lmax; l++){
1818: l1=pow(10,l);
1819: delts=delt;
1820: for(k=1 ; k <kmax; k=k+1){
1821: delt = delta*(l1*k);
1822: p2[theta]=x[theta] +delt;
1823: k1=func(p2)-fx;
1824: p2[theta]=x[theta]-delt;
1825: k2=func(p2)-fx;
1826: /*res= (k1-2.0*fx+k2)/delt/delt; */
1827: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1828:
1829: #ifdef DEBUG
1830: 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);
1831: 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);
1832: #endif
1833: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1834: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1835: k=kmax;
1836: }
1837: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1838: k=kmax; l=lmax*10.;
1839: }
1840: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1841: delts=delt;
1842: }
1843: }
1844: }
1845: delti[theta]=delts;
1846: return res;
1847:
1848: }
1849:
1850: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1851: {
1852: int i;
1853: int l=1, l1, lmax=20;
1854: double k1,k2,k3,k4,res,fx;
1855: double p2[NPARMAX+1];
1856: int k;
1857:
1858: fx=func(x);
1859: for (k=1; k<=2; k++) {
1860: for (i=1;i<=npar;i++) p2[i]=x[i];
1861: p2[thetai]=x[thetai]+delti[thetai]/k;
1862: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1863: k1=func(p2)-fx;
1864:
1865: p2[thetai]=x[thetai]+delti[thetai]/k;
1866: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1867: k2=func(p2)-fx;
1868:
1869: p2[thetai]=x[thetai]-delti[thetai]/k;
1870: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1871: k3=func(p2)-fx;
1872:
1873: p2[thetai]=x[thetai]-delti[thetai]/k;
1874: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1875: k4=func(p2)-fx;
1876: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1877: #ifdef DEBUG
1878: 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);
1879: 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);
1880: #endif
1881: }
1882: return res;
1883: }
1884:
1885: /************** Inverse of matrix **************/
1886: void ludcmp(double **a, int n, int *indx, double *d)
1887: {
1888: int i,imax,j,k;
1889: double big,dum,sum,temp;
1890: double *vv;
1891:
1892: vv=vector(1,n);
1893: *d=1.0;
1894: for (i=1;i<=n;i++) {
1895: big=0.0;
1896: for (j=1;j<=n;j++)
1897: if ((temp=fabs(a[i][j])) > big) big=temp;
1898: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1899: vv[i]=1.0/big;
1900: }
1901: for (j=1;j<=n;j++) {
1902: for (i=1;i<j;i++) {
1903: sum=a[i][j];
1904: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1905: a[i][j]=sum;
1906: }
1907: big=0.0;
1908: for (i=j;i<=n;i++) {
1909: sum=a[i][j];
1910: for (k=1;k<j;k++)
1911: sum -= a[i][k]*a[k][j];
1912: a[i][j]=sum;
1913: if ( (dum=vv[i]*fabs(sum)) >= big) {
1914: big=dum;
1915: imax=i;
1916: }
1917: }
1918: if (j != imax) {
1919: for (k=1;k<=n;k++) {
1920: dum=a[imax][k];
1921: a[imax][k]=a[j][k];
1922: a[j][k]=dum;
1923: }
1924: *d = -(*d);
1925: vv[imax]=vv[j];
1926: }
1927: indx[j]=imax;
1928: if (a[j][j] == 0.0) a[j][j]=TINY;
1929: if (j != n) {
1930: dum=1.0/(a[j][j]);
1931: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1932: }
1933: }
1934: free_vector(vv,1,n); /* Doesn't work */
1935: ;
1936: }
1937:
1938: void lubksb(double **a, int n, int *indx, double b[])
1939: {
1940: int i,ii=0,ip,j;
1941: double sum;
1942:
1943: for (i=1;i<=n;i++) {
1944: ip=indx[i];
1945: sum=b[ip];
1946: b[ip]=b[i];
1947: if (ii)
1948: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1949: else if (sum) ii=i;
1950: b[i]=sum;
1951: }
1952: for (i=n;i>=1;i--) {
1953: sum=b[i];
1954: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1955: b[i]=sum/a[i][i];
1956: }
1957: }
1958:
1959: void pstamp(FILE *fichier)
1960: {
1961: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1962: }
1963:
1964: /************ Frequencies ********************/
1965: 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[])
1966: { /* Some frequencies */
1967:
1968: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1969: int first;
1970: double ***freq; /* Frequencies */
1971: double *pp, **prop;
1972: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1973: char fileresp[FILENAMELENGTH];
1974:
1975: pp=vector(1,nlstate);
1976: prop=matrix(1,nlstate,iagemin,iagemax+3);
1977: strcpy(fileresp,"p");
1978: strcat(fileresp,fileres);
1979: if((ficresp=fopen(fileresp,"w"))==NULL) {
1980: printf("Problem with prevalence resultfile: %s\n", fileresp);
1981: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1982: exit(0);
1983: }
1984: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1985: j1=0;
1986:
1987: j=cptcoveff;
1988: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1989:
1990: first=1;
1991:
1992: for(k1=1; k1<=j;k1++){
1993: for(i1=1; i1<=ncodemax[k1];i1++){
1994: j1++;
1995: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1996: scanf("%d", i);*/
1997: for (i=-5; i<=nlstate+ndeath; i++)
1998: for (jk=-5; jk<=nlstate+ndeath; jk++)
1999: for(m=iagemin; m <= iagemax+3; m++)
2000: freq[i][jk][m]=0;
2001:
2002: for (i=1; i<=nlstate; i++)
2003: for(m=iagemin; m <= iagemax+3; m++)
2004: prop[i][m]=0;
2005:
2006: dateintsum=0;
2007: k2cpt=0;
2008: for (i=1; i<=imx; i++) {
2009: bool=1;
2010: if (cptcovn>0) {
2011: for (z1=1; z1<=cptcoveff; z1++)
2012: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2013: bool=0;
2014: }
2015: if (bool==1){
2016: for(m=firstpass; m<=lastpass; m++){
2017: k2=anint[m][i]+(mint[m][i]/12.);
2018: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2019: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2020: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2021: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2022: if (m<lastpass) {
2023: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2024: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2025: }
2026:
2027: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2028: dateintsum=dateintsum+k2;
2029: k2cpt++;
2030: }
2031: /*}*/
2032: }
2033: }
2034: }
2035:
2036: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2037: pstamp(ficresp);
2038: if (cptcovn>0) {
2039: fprintf(ficresp, "\n#********** Variable ");
2040: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2041: fprintf(ficresp, "**********\n#");
2042: }
2043: for(i=1; i<=nlstate;i++)
2044: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2045: fprintf(ficresp, "\n");
2046:
2047: for(i=iagemin; i <= iagemax+3; i++){
2048: if(i==iagemax+3){
2049: fprintf(ficlog,"Total");
2050: }else{
2051: if(first==1){
2052: first=0;
2053: printf("See log file for details...\n");
2054: }
2055: fprintf(ficlog,"Age %d", i);
2056: }
2057: for(jk=1; jk <=nlstate ; jk++){
2058: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2059: pp[jk] += freq[jk][m][i];
2060: }
2061: for(jk=1; jk <=nlstate ; jk++){
2062: for(m=-1, pos=0; m <=0 ; m++)
2063: pos += freq[jk][m][i];
2064: if(pp[jk]>=1.e-10){
2065: if(first==1){
2066: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2067: }
2068: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2069: }else{
2070: if(first==1)
2071: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2072: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2073: }
2074: }
2075:
2076: for(jk=1; jk <=nlstate ; jk++){
2077: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2078: pp[jk] += freq[jk][m][i];
2079: }
2080: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2081: pos += pp[jk];
2082: posprop += prop[jk][i];
2083: }
2084: for(jk=1; jk <=nlstate ; jk++){
2085: if(pos>=1.e-5){
2086: if(first==1)
2087: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2088: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2089: }else{
2090: if(first==1)
2091: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2092: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2093: }
2094: if( i <= iagemax){
2095: if(pos>=1.e-5){
2096: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2097: /*probs[i][jk][j1]= pp[jk]/pos;*/
2098: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2099: }
2100: else
2101: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2102: }
2103: }
2104:
2105: for(jk=-1; jk <=nlstate+ndeath; jk++)
2106: for(m=-1; m <=nlstate+ndeath; m++)
2107: if(freq[jk][m][i] !=0 ) {
2108: if(first==1)
2109: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2110: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2111: }
2112: if(i <= iagemax)
2113: fprintf(ficresp,"\n");
2114: if(first==1)
2115: printf("Others in log...\n");
2116: fprintf(ficlog,"\n");
2117: }
2118: }
2119: }
2120: dateintmean=dateintsum/k2cpt;
2121:
2122: fclose(ficresp);
2123: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2124: free_vector(pp,1,nlstate);
2125: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2126: /* End of Freq */
2127: }
2128:
2129: /************ Prevalence ********************/
2130: 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)
2131: {
2132: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2133: in each health status at the date of interview (if between dateprev1 and dateprev2).
2134: We still use firstpass and lastpass as another selection.
2135: */
2136:
2137: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2138: double ***freq; /* Frequencies */
2139: double *pp, **prop;
2140: double pos,posprop;
2141: double y2; /* in fractional years */
2142: int iagemin, iagemax;
2143:
2144: iagemin= (int) agemin;
2145: iagemax= (int) agemax;
2146: /*pp=vector(1,nlstate);*/
2147: prop=matrix(1,nlstate,iagemin,iagemax+3);
2148: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2149: j1=0;
2150:
2151: j=cptcoveff;
2152: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2153:
2154: for(k1=1; k1<=j;k1++){
2155: for(i1=1; i1<=ncodemax[k1];i1++){
2156: j1++;
2157:
2158: for (i=1; i<=nlstate; i++)
2159: for(m=iagemin; m <= iagemax+3; m++)
2160: prop[i][m]=0.0;
2161:
2162: for (i=1; i<=imx; i++) { /* Each individual */
2163: bool=1;
2164: if (cptcovn>0) {
2165: for (z1=1; z1<=cptcoveff; z1++)
2166: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2167: bool=0;
2168: }
2169: if (bool==1) {
2170: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2171: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2172: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2173: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2174: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2175: 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);
2176: if (s[m][i]>0 && s[m][i]<=nlstate) {
2177: /*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]]);*/
2178: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2179: prop[s[m][i]][iagemax+3] += weight[i];
2180: }
2181: }
2182: } /* end selection of waves */
2183: }
2184: }
2185: for(i=iagemin; i <= iagemax+3; i++){
2186:
2187: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2188: posprop += prop[jk][i];
2189: }
2190:
2191: for(jk=1; jk <=nlstate ; jk++){
2192: if( i <= iagemax){
2193: if(posprop>=1.e-5){
2194: probs[i][jk][j1]= prop[jk][i]/posprop;
2195: }
2196: }
2197: }/* end jk */
2198: }/* end i */
2199: } /* end i1 */
2200: } /* end k1 */
2201:
2202: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2203: /*free_vector(pp,1,nlstate);*/
2204: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2205: } /* End of prevalence */
2206:
2207: /************* Waves Concatenation ***************/
2208:
2209: 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)
2210: {
2211: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2212: Death is a valid wave (if date is known).
2213: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2214: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2215: and mw[mi+1][i]. dh depends on stepm.
2216: */
2217:
2218: int i, mi, m;
2219: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2220: double sum=0., jmean=0.;*/
2221: int first;
2222: int j, k=0,jk, ju, jl;
2223: double sum=0.;
2224: first=0;
2225: jmin=1e+5;
2226: jmax=-1;
2227: jmean=0.;
2228: for(i=1; i<=imx; i++){
2229: mi=0;
2230: m=firstpass;
2231: while(s[m][i] <= nlstate){
2232: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2233: mw[++mi][i]=m;
2234: if(m >=lastpass)
2235: break;
2236: else
2237: m++;
2238: }/* end while */
2239: if (s[m][i] > nlstate){
2240: mi++; /* Death is another wave */
2241: /* if(mi==0) never been interviewed correctly before death */
2242: /* Only death is a correct wave */
2243: mw[mi][i]=m;
2244: }
2245:
2246: wav[i]=mi;
2247: if(mi==0){
2248: nbwarn++;
2249: if(first==0){
2250: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2251: first=1;
2252: }
2253: if(first==1){
2254: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2255: }
2256: } /* end mi==0 */
2257: } /* End individuals */
2258:
2259: for(i=1; i<=imx; i++){
2260: for(mi=1; mi<wav[i];mi++){
2261: if (stepm <=0)
2262: dh[mi][i]=1;
2263: else{
2264: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2265: if (agedc[i] < 2*AGESUP) {
2266: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2267: if(j==0) j=1; /* Survives at least one month after exam */
2268: else if(j<0){
2269: nberr++;
2270: 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]);
2271: j=1; /* Temporary Dangerous patch */
2272: 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);
2273: 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]);
2274: 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);
2275: }
2276: k=k+1;
2277: if (j >= jmax){
2278: jmax=j;
2279: ijmax=i;
2280: }
2281: if (j <= jmin){
2282: jmin=j;
2283: ijmin=i;
2284: }
2285: sum=sum+j;
2286: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2287: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2288: }
2289: }
2290: else{
2291: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2292: /* 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]); */
2293:
2294: k=k+1;
2295: if (j >= jmax) {
2296: jmax=j;
2297: ijmax=i;
2298: }
2299: else if (j <= jmin){
2300: jmin=j;
2301: ijmin=i;
2302: }
2303: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2304: /*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]);*/
2305: if(j<0){
2306: nberr++;
2307: 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]);
2308: 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]);
2309: }
2310: sum=sum+j;
2311: }
2312: jk= j/stepm;
2313: jl= j -jk*stepm;
2314: ju= j -(jk+1)*stepm;
2315: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2316: if(jl==0){
2317: dh[mi][i]=jk;
2318: bh[mi][i]=0;
2319: }else{ /* We want a negative bias in order to only have interpolation ie
2320: * at the price of an extra matrix product in likelihood */
2321: dh[mi][i]=jk+1;
2322: bh[mi][i]=ju;
2323: }
2324: }else{
2325: if(jl <= -ju){
2326: dh[mi][i]=jk;
2327: bh[mi][i]=jl; /* bias is positive if real duration
2328: * is higher than the multiple of stepm and negative otherwise.
2329: */
2330: }
2331: else{
2332: dh[mi][i]=jk+1;
2333: bh[mi][i]=ju;
2334: }
2335: if(dh[mi][i]==0){
2336: dh[mi][i]=1; /* At least one step */
2337: bh[mi][i]=ju; /* At least one step */
2338: /* 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);*/
2339: }
2340: } /* end if mle */
2341: }
2342: } /* end wave */
2343: }
2344: jmean=sum/k;
2345: 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);
2346: 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);
2347: }
2348:
2349: /*********** Tricode ****************************/
2350: void tricode(int *Tvar, int **nbcode, int imx)
2351: {
2352:
2353: int Ndum[20],ij=1, k, j, i, maxncov=19;
2354: int cptcode=0;
2355: cptcoveff=0;
2356:
2357: for (k=0; k<maxncov; k++) Ndum[k]=0;
2358: for (k=1; k<=7; k++) ncodemax[k]=0;
2359:
2360: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2361: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2362: modality*/
2363: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2364: Ndum[ij]++; /*store the modality */
2365: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2366: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2367: Tvar[j]. If V=sex and male is 0 and
2368: female is 1, then cptcode=1.*/
2369: }
2370:
2371: for (i=0; i<=cptcode; i++) {
2372: 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 */
2373: }
2374:
2375: ij=1;
2376: for (i=1; i<=ncodemax[j]; i++) {
2377: for (k=0; k<= maxncov; k++) {
2378: if (Ndum[k] != 0) {
2379: nbcode[Tvar[j]][ij]=k;
2380: /* 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; */
2381:
2382: ij++;
2383: }
2384: if (ij > ncodemax[j]) break;
2385: }
2386: }
2387: }
2388:
2389: for (k=0; k< maxncov; k++) Ndum[k]=0;
2390:
2391: for (i=1; i<=ncovmodel-2; i++) {
2392: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2393: ij=Tvar[i];
2394: Ndum[ij]++;
2395: }
2396:
2397: ij=1;
2398: for (i=1; i<= maxncov; i++) {
2399: if((Ndum[i]!=0) && (i<=ncovcol)){
2400: Tvaraff[ij]=i; /*For printing */
2401: ij++;
2402: }
2403: }
2404:
2405: cptcoveff=ij-1; /*Number of simple covariates*/
2406: }
2407:
2408: /*********** Health Expectancies ****************/
2409:
2410: 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[] )
2411:
2412: {
2413: /* Health expectancies, no variances */
2414: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2415: double age, agelim, hf;
2416: double ***p3mat;
2417: double eip;
2418:
2419: pstamp(ficreseij);
2420: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2421: fprintf(ficreseij,"# Age");
2422: for(i=1; i<=nlstate;i++){
2423: for(j=1; j<=nlstate;j++){
2424: fprintf(ficreseij," e%1d%1d ",i,j);
2425: }
2426: fprintf(ficreseij," e%1d. ",i);
2427: }
2428: fprintf(ficreseij,"\n");
2429:
2430:
2431: if(estepm < stepm){
2432: printf ("Problem %d lower than %d\n",estepm, stepm);
2433: }
2434: else hstepm=estepm;
2435: /* We compute the life expectancy from trapezoids spaced every estepm months
2436: * This is mainly to measure the difference between two models: for example
2437: * if stepm=24 months pijx are given only every 2 years and by summing them
2438: * we are calculating an estimate of the Life Expectancy assuming a linear
2439: * progression in between and thus overestimating or underestimating according
2440: * to the curvature of the survival function. If, for the same date, we
2441: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2442: * to compare the new estimate of Life expectancy with the same linear
2443: * hypothesis. A more precise result, taking into account a more precise
2444: * curvature will be obtained if estepm is as small as stepm. */
2445:
2446: /* For example we decided to compute the life expectancy with the smallest unit */
2447: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2448: nhstepm is the number of hstepm from age to agelim
2449: nstepm is the number of stepm from age to agelin.
2450: Look at hpijx to understand the reason of that which relies in memory size
2451: and note for a fixed period like estepm months */
2452: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2453: survival function given by stepm (the optimization length). Unfortunately it
2454: means that if the survival funtion is printed only each two years of age and if
2455: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2456: results. So we changed our mind and took the option of the best precision.
2457: */
2458: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2459:
2460: agelim=AGESUP;
2461: /* nhstepm age range expressed in number of stepm */
2462: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2463: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2464: /* if (stepm >= YEARM) hstepm=1;*/
2465: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2466: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2467:
2468: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2469: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2470: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2471:
2472: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2473:
2474: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2475:
2476: /* Computing Variances of health expectancies */
2477: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2478: decrease memory allocation */
2479: printf("%d|",(int)age);fflush(stdout);
2480: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2481: /* Computing expectancies */
2482: for(i=1; i<=nlstate;i++)
2483: for(j=1; j<=nlstate;j++)
2484: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2485: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2486:
2487: /* 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]);*/
2488:
2489: }
2490:
2491: fprintf(ficreseij,"%3.0f",age );
2492: for(i=1; i<=nlstate;i++){
2493: eip=0;
2494: for(j=1; j<=nlstate;j++){
2495: eip +=eij[i][j][(int)age];
2496: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2497: }
2498: fprintf(ficreseij,"%9.4f", eip );
2499: }
2500: fprintf(ficreseij,"\n");
2501:
2502: }
2503: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2504: printf("\n");
2505: fprintf(ficlog,"\n");
2506:
2507: }
2508:
2509: 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[] )
2510:
2511: {
2512: /* Covariances of health expectancies eij and of total life expectancies according
2513: to initial status i, ei. .
2514: */
2515: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2516: double age, agelim, hf;
2517: double ***p3matp, ***p3matm, ***varhe;
2518: double **dnewm,**doldm;
2519: double *xp, *xm;
2520: double **gp, **gm;
2521: double ***gradg, ***trgradg;
2522: int theta;
2523:
2524: double eip, vip;
2525:
2526: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2527: xp=vector(1,npar);
2528: xm=vector(1,npar);
2529: dnewm=matrix(1,nlstate*nlstate,1,npar);
2530: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2531:
2532: pstamp(ficresstdeij);
2533: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2534: fprintf(ficresstdeij,"# Age");
2535: for(i=1; i<=nlstate;i++){
2536: for(j=1; j<=nlstate;j++)
2537: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2538: fprintf(ficresstdeij," e%1d. ",i);
2539: }
2540: fprintf(ficresstdeij,"\n");
2541:
2542: pstamp(ficrescveij);
2543: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2544: fprintf(ficrescveij,"# Age");
2545: for(i=1; i<=nlstate;i++)
2546: for(j=1; j<=nlstate;j++){
2547: cptj= (j-1)*nlstate+i;
2548: for(i2=1; i2<=nlstate;i2++)
2549: for(j2=1; j2<=nlstate;j2++){
2550: cptj2= (j2-1)*nlstate+i2;
2551: if(cptj2 <= cptj)
2552: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2553: }
2554: }
2555: fprintf(ficrescveij,"\n");
2556:
2557: if(estepm < stepm){
2558: printf ("Problem %d lower than %d\n",estepm, stepm);
2559: }
2560: else hstepm=estepm;
2561: /* We compute the life expectancy from trapezoids spaced every estepm months
2562: * This is mainly to measure the difference between two models: for example
2563: * if stepm=24 months pijx are given only every 2 years and by summing them
2564: * we are calculating an estimate of the Life Expectancy assuming a linear
2565: * progression in between and thus overestimating or underestimating according
2566: * to the curvature of the survival function. If, for the same date, we
2567: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2568: * to compare the new estimate of Life expectancy with the same linear
2569: * hypothesis. A more precise result, taking into account a more precise
2570: * curvature will be obtained if estepm is as small as stepm. */
2571:
2572: /* For example we decided to compute the life expectancy with the smallest unit */
2573: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2574: nhstepm is the number of hstepm from age to agelim
2575: nstepm is the number of stepm from age to agelin.
2576: Look at hpijx to understand the reason of that which relies in memory size
2577: and note for a fixed period like estepm months */
2578: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2579: survival function given by stepm (the optimization length). Unfortunately it
2580: means that if the survival funtion is printed only each two years of age and if
2581: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2582: results. So we changed our mind and took the option of the best precision.
2583: */
2584: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2585:
2586: /* If stepm=6 months */
2587: /* nhstepm age range expressed in number of stepm */
2588: agelim=AGESUP;
2589: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2590: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2591: /* if (stepm >= YEARM) hstepm=1;*/
2592: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2593:
2594: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2595: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2596: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2597: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2598: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2599: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2600:
2601: for (age=bage; age<=fage; age ++){
2602:
2603: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2604: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2605:
2606: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2607:
2608: /* Computing Variances of health expectancies */
2609: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2610: decrease memory allocation */
2611: for(theta=1; theta <=npar; theta++){
2612: for(i=1; i<=npar; i++){
2613: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2614: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2615: }
2616: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2617: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2618:
2619: for(j=1; j<= nlstate; j++){
2620: for(i=1; i<=nlstate; i++){
2621: for(h=0; h<=nhstepm-1; h++){
2622: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2623: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2624: }
2625: }
2626: }
2627:
2628: for(ij=1; ij<= nlstate*nlstate; ij++)
2629: for(h=0; h<=nhstepm-1; h++){
2630: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2631: }
2632: }/* End theta */
2633:
2634:
2635: for(h=0; h<=nhstepm-1; h++)
2636: for(j=1; j<=nlstate*nlstate;j++)
2637: for(theta=1; theta <=npar; theta++)
2638: trgradg[h][j][theta]=gradg[h][theta][j];
2639:
2640:
2641: for(ij=1;ij<=nlstate*nlstate;ij++)
2642: for(ji=1;ji<=nlstate*nlstate;ji++)
2643: varhe[ij][ji][(int)age] =0.;
2644:
2645: printf("%d|",(int)age);fflush(stdout);
2646: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2647: for(h=0;h<=nhstepm-1;h++){
2648: for(k=0;k<=nhstepm-1;k++){
2649: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2650: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2651: for(ij=1;ij<=nlstate*nlstate;ij++)
2652: for(ji=1;ji<=nlstate*nlstate;ji++)
2653: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2654: }
2655: }
2656: /* Computing expectancies */
2657: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2658: for(i=1; i<=nlstate;i++)
2659: for(j=1; j<=nlstate;j++)
2660: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2661: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2662:
2663: /* 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]);*/
2664:
2665: }
2666:
2667: fprintf(ficresstdeij,"%3.0f",age );
2668: for(i=1; i<=nlstate;i++){
2669: eip=0.;
2670: vip=0.;
2671: for(j=1; j<=nlstate;j++){
2672: eip += eij[i][j][(int)age];
2673: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2674: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2675: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2676: }
2677: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2678: }
2679: fprintf(ficresstdeij,"\n");
2680:
2681: fprintf(ficrescveij,"%3.0f",age );
2682: for(i=1; i<=nlstate;i++)
2683: for(j=1; j<=nlstate;j++){
2684: cptj= (j-1)*nlstate+i;
2685: for(i2=1; i2<=nlstate;i2++)
2686: for(j2=1; j2<=nlstate;j2++){
2687: cptj2= (j2-1)*nlstate+i2;
2688: if(cptj2 <= cptj)
2689: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2690: }
2691: }
2692: fprintf(ficrescveij,"\n");
2693:
2694: }
2695: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2696: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2697: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2698: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2699: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2700: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2701: printf("\n");
2702: fprintf(ficlog,"\n");
2703:
2704: free_vector(xm,1,npar);
2705: free_vector(xp,1,npar);
2706: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2707: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2708: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2709: }
2710:
2711: /************ Variance ******************/
2712: 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[])
2713: {
2714: /* Variance of health expectancies */
2715: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2716: /* double **newm;*/
2717: double **dnewm,**doldm;
2718: double **dnewmp,**doldmp;
2719: int i, j, nhstepm, hstepm, h, nstepm ;
2720: int k, cptcode;
2721: double *xp;
2722: double **gp, **gm; /* for var eij */
2723: double ***gradg, ***trgradg; /*for var eij */
2724: double **gradgp, **trgradgp; /* for var p point j */
2725: double *gpp, *gmp; /* for var p point j */
2726: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2727: double ***p3mat;
2728: double age,agelim, hf;
2729: double ***mobaverage;
2730: int theta;
2731: char digit[4];
2732: char digitp[25];
2733:
2734: char fileresprobmorprev[FILENAMELENGTH];
2735:
2736: if(popbased==1){
2737: if(mobilav!=0)
2738: strcpy(digitp,"-populbased-mobilav-");
2739: else strcpy(digitp,"-populbased-nomobil-");
2740: }
2741: else
2742: strcpy(digitp,"-stablbased-");
2743:
2744: if (mobilav!=0) {
2745: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2746: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2747: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2748: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2749: }
2750: }
2751:
2752: strcpy(fileresprobmorprev,"prmorprev");
2753: sprintf(digit,"%-d",ij);
2754: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2755: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2756: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2757: strcat(fileresprobmorprev,fileres);
2758: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2759: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2760: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2761: }
2762: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2763:
2764: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2765: pstamp(ficresprobmorprev);
2766: 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);
2767: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2768: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2769: fprintf(ficresprobmorprev," p.%-d SE",j);
2770: for(i=1; i<=nlstate;i++)
2771: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2772: }
2773: fprintf(ficresprobmorprev,"\n");
2774: fprintf(ficgp,"\n# Routine varevsij");
2775: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2776: 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");
2777: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2778: /* } */
2779: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2780: pstamp(ficresvij);
2781: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2782: if(popbased==1)
2783: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2784: else
2785: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2786: fprintf(ficresvij,"# Age");
2787: for(i=1; i<=nlstate;i++)
2788: for(j=1; j<=nlstate;j++)
2789: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2790: fprintf(ficresvij,"\n");
2791:
2792: xp=vector(1,npar);
2793: dnewm=matrix(1,nlstate,1,npar);
2794: doldm=matrix(1,nlstate,1,nlstate);
2795: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2796: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2797:
2798: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2799: gpp=vector(nlstate+1,nlstate+ndeath);
2800: gmp=vector(nlstate+1,nlstate+ndeath);
2801: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2802:
2803: if(estepm < stepm){
2804: printf ("Problem %d lower than %d\n",estepm, stepm);
2805: }
2806: else hstepm=estepm;
2807: /* For example we decided to compute the life expectancy with the smallest unit */
2808: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2809: nhstepm is the number of hstepm from age to agelim
2810: nstepm is the number of stepm from age to agelin.
2811: Look at hpijx to understand the reason of that which relies in memory size
2812: and note for a fixed period like k years */
2813: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2814: survival function given by stepm (the optimization length). Unfortunately it
2815: means that if the survival funtion is printed every two years of age and if
2816: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2817: results. So we changed our mind and took the option of the best precision.
2818: */
2819: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2820: agelim = AGESUP;
2821: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2822: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2823: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2824: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2825: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2826: gp=matrix(0,nhstepm,1,nlstate);
2827: gm=matrix(0,nhstepm,1,nlstate);
2828:
2829:
2830: for(theta=1; theta <=npar; theta++){
2831: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2832: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2833: }
2834: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2835: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2836:
2837: if (popbased==1) {
2838: if(mobilav ==0){
2839: for(i=1; i<=nlstate;i++)
2840: prlim[i][i]=probs[(int)age][i][ij];
2841: }else{ /* mobilav */
2842: for(i=1; i<=nlstate;i++)
2843: prlim[i][i]=mobaverage[(int)age][i][ij];
2844: }
2845: }
2846:
2847: for(j=1; j<= nlstate; j++){
2848: for(h=0; h<=nhstepm; h++){
2849: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2850: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2851: }
2852: }
2853: /* This for computing probability of death (h=1 means
2854: computed over hstepm matrices product = hstepm*stepm months)
2855: as a weighted average of prlim.
2856: */
2857: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2858: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2859: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2860: }
2861: /* end probability of death */
2862:
2863: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2864: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2865: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2866: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2867:
2868: if (popbased==1) {
2869: if(mobilav ==0){
2870: for(i=1; i<=nlstate;i++)
2871: prlim[i][i]=probs[(int)age][i][ij];
2872: }else{ /* mobilav */
2873: for(i=1; i<=nlstate;i++)
2874: prlim[i][i]=mobaverage[(int)age][i][ij];
2875: }
2876: }
2877:
2878: for(j=1; j<= nlstate; j++){
2879: for(h=0; h<=nhstepm; h++){
2880: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2881: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2882: }
2883: }
2884: /* This for computing probability of death (h=1 means
2885: computed over hstepm matrices product = hstepm*stepm months)
2886: as a weighted average of prlim.
2887: */
2888: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2889: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2890: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2891: }
2892: /* end probability of death */
2893:
2894: for(j=1; j<= nlstate; j++) /* vareij */
2895: for(h=0; h<=nhstepm; h++){
2896: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2897: }
2898:
2899: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2900: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2901: }
2902:
2903: } /* End theta */
2904:
2905: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2906:
2907: for(h=0; h<=nhstepm; h++) /* veij */
2908: for(j=1; j<=nlstate;j++)
2909: for(theta=1; theta <=npar; theta++)
2910: trgradg[h][j][theta]=gradg[h][theta][j];
2911:
2912: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2913: for(theta=1; theta <=npar; theta++)
2914: trgradgp[j][theta]=gradgp[theta][j];
2915:
2916:
2917: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2918: for(i=1;i<=nlstate;i++)
2919: for(j=1;j<=nlstate;j++)
2920: vareij[i][j][(int)age] =0.;
2921:
2922: for(h=0;h<=nhstepm;h++){
2923: for(k=0;k<=nhstepm;k++){
2924: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2925: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2926: for(i=1;i<=nlstate;i++)
2927: for(j=1;j<=nlstate;j++)
2928: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2929: }
2930: }
2931:
2932: /* pptj */
2933: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2934: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2935: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2936: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2937: varppt[j][i]=doldmp[j][i];
2938: /* end ppptj */
2939: /* x centered again */
2940: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2941: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2942:
2943: if (popbased==1) {
2944: if(mobilav ==0){
2945: for(i=1; i<=nlstate;i++)
2946: prlim[i][i]=probs[(int)age][i][ij];
2947: }else{ /* mobilav */
2948: for(i=1; i<=nlstate;i++)
2949: prlim[i][i]=mobaverage[(int)age][i][ij];
2950: }
2951: }
2952:
2953: /* This for computing probability of death (h=1 means
2954: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2955: as a weighted average of prlim.
2956: */
2957: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2958: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2959: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2960: }
2961: /* end probability of death */
2962:
2963: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2964: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2965: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2966: for(i=1; i<=nlstate;i++){
2967: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2968: }
2969: }
2970: fprintf(ficresprobmorprev,"\n");
2971:
2972: fprintf(ficresvij,"%.0f ",age );
2973: for(i=1; i<=nlstate;i++)
2974: for(j=1; j<=nlstate;j++){
2975: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2976: }
2977: fprintf(ficresvij,"\n");
2978: free_matrix(gp,0,nhstepm,1,nlstate);
2979: free_matrix(gm,0,nhstepm,1,nlstate);
2980: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2981: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2982: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2983: } /* End age */
2984: free_vector(gpp,nlstate+1,nlstate+ndeath);
2985: free_vector(gmp,nlstate+1,nlstate+ndeath);
2986: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2987: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2988: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2989: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2990: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2991: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2992: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2993: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2994: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2995: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2996: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2997: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2998: 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);
2999: /* 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);
3000: */
3001: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3002: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3003:
3004: free_vector(xp,1,npar);
3005: free_matrix(doldm,1,nlstate,1,nlstate);
3006: free_matrix(dnewm,1,nlstate,1,npar);
3007: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3008: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3009: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3010: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3011: fclose(ficresprobmorprev);
3012: fflush(ficgp);
3013: fflush(fichtm);
3014: } /* end varevsij */
3015:
3016: /************ Variance of prevlim ******************/
3017: 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[])
3018: {
3019: /* Variance of prevalence limit */
3020: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3021: double **newm;
3022: double **dnewm,**doldm;
3023: int i, j, nhstepm, hstepm;
3024: int k, cptcode;
3025: double *xp;
3026: double *gp, *gm;
3027: double **gradg, **trgradg;
3028: double age,agelim;
3029: int theta;
3030:
3031: pstamp(ficresvpl);
3032: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3033: fprintf(ficresvpl,"# Age");
3034: for(i=1; i<=nlstate;i++)
3035: fprintf(ficresvpl," %1d-%1d",i,i);
3036: fprintf(ficresvpl,"\n");
3037:
3038: xp=vector(1,npar);
3039: dnewm=matrix(1,nlstate,1,npar);
3040: doldm=matrix(1,nlstate,1,nlstate);
3041:
3042: hstepm=1*YEARM; /* Every year of age */
3043: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3044: agelim = AGESUP;
3045: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3046: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3047: if (stepm >= YEARM) hstepm=1;
3048: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3049: gradg=matrix(1,npar,1,nlstate);
3050: gp=vector(1,nlstate);
3051: gm=vector(1,nlstate);
3052:
3053: for(theta=1; theta <=npar; theta++){
3054: for(i=1; i<=npar; i++){ /* Computes gradient */
3055: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3056: }
3057: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3058: for(i=1;i<=nlstate;i++)
3059: gp[i] = prlim[i][i];
3060:
3061: for(i=1; i<=npar; i++) /* Computes gradient */
3062: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3063: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3064: for(i=1;i<=nlstate;i++)
3065: gm[i] = prlim[i][i];
3066:
3067: for(i=1;i<=nlstate;i++)
3068: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3069: } /* End theta */
3070:
3071: trgradg =matrix(1,nlstate,1,npar);
3072:
3073: for(j=1; j<=nlstate;j++)
3074: for(theta=1; theta <=npar; theta++)
3075: trgradg[j][theta]=gradg[theta][j];
3076:
3077: for(i=1;i<=nlstate;i++)
3078: varpl[i][(int)age] =0.;
3079: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3080: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3081: for(i=1;i<=nlstate;i++)
3082: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3083:
3084: fprintf(ficresvpl,"%.0f ",age );
3085: for(i=1; i<=nlstate;i++)
3086: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3087: fprintf(ficresvpl,"\n");
3088: free_vector(gp,1,nlstate);
3089: free_vector(gm,1,nlstate);
3090: free_matrix(gradg,1,npar,1,nlstate);
3091: free_matrix(trgradg,1,nlstate,1,npar);
3092: } /* End age */
3093:
3094: free_vector(xp,1,npar);
3095: free_matrix(doldm,1,nlstate,1,npar);
3096: free_matrix(dnewm,1,nlstate,1,nlstate);
3097:
3098: }
3099:
3100: /************ Variance of one-step probabilities ******************/
3101: 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[])
3102: {
3103: int i, j=0, i1, k1, l1, t, tj;
3104: int k2, l2, j1, z1;
3105: int k=0,l, cptcode;
3106: int first=1, first1;
3107: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3108: double **dnewm,**doldm;
3109: double *xp;
3110: double *gp, *gm;
3111: double **gradg, **trgradg;
3112: double **mu;
3113: double age,agelim, cov[NCOVMAX];
3114: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3115: int theta;
3116: char fileresprob[FILENAMELENGTH];
3117: char fileresprobcov[FILENAMELENGTH];
3118: char fileresprobcor[FILENAMELENGTH];
3119:
3120: double ***varpij;
3121:
3122: strcpy(fileresprob,"prob");
3123: strcat(fileresprob,fileres);
3124: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3125: printf("Problem with resultfile: %s\n", fileresprob);
3126: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3127: }
3128: strcpy(fileresprobcov,"probcov");
3129: strcat(fileresprobcov,fileres);
3130: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3131: printf("Problem with resultfile: %s\n", fileresprobcov);
3132: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3133: }
3134: strcpy(fileresprobcor,"probcor");
3135: strcat(fileresprobcor,fileres);
3136: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3137: printf("Problem with resultfile: %s\n", fileresprobcor);
3138: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3139: }
3140: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3141: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3142: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3143: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3144: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3145: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3146: pstamp(ficresprob);
3147: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3148: fprintf(ficresprob,"# Age");
3149: pstamp(ficresprobcov);
3150: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3151: fprintf(ficresprobcov,"# Age");
3152: pstamp(ficresprobcor);
3153: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3154: fprintf(ficresprobcor,"# Age");
3155:
3156:
3157: for(i=1; i<=nlstate;i++)
3158: for(j=1; j<=(nlstate+ndeath);j++){
3159: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3160: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3161: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3162: }
3163: /* fprintf(ficresprob,"\n");
3164: fprintf(ficresprobcov,"\n");
3165: fprintf(ficresprobcor,"\n");
3166: */
3167: xp=vector(1,npar);
3168: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3169: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3170: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3171: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3172: first=1;
3173: fprintf(ficgp,"\n# Routine varprob");
3174: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3175: fprintf(fichtm,"\n");
3176:
3177: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3178: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3179: file %s<br>\n",optionfilehtmcov);
3180: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3181: and drawn. It helps understanding how is the covariance between two incidences.\
3182: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3183: 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. \
3184: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3185: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3186: standard deviations wide on each axis. <br>\
3187: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3188: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3189: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3190:
3191: cov[1]=1;
3192: tj=cptcoveff;
3193: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3194: j1=0;
3195: for(t=1; t<=tj;t++){
3196: for(i1=1; i1<=ncodemax[t];i1++){
3197: j1++;
3198: if (cptcovn>0) {
3199: fprintf(ficresprob, "\n#********** Variable ");
3200: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3201: fprintf(ficresprob, "**********\n#\n");
3202: fprintf(ficresprobcov, "\n#********** Variable ");
3203: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3204: fprintf(ficresprobcov, "**********\n#\n");
3205:
3206: fprintf(ficgp, "\n#********** Variable ");
3207: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3208: fprintf(ficgp, "**********\n#\n");
3209:
3210:
3211: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3212: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3213: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3214:
3215: fprintf(ficresprobcor, "\n#********** Variable ");
3216: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3217: fprintf(ficresprobcor, "**********\n#");
3218: }
3219:
3220: for (age=bage; age<=fage; age ++){
3221: cov[2]=age;
3222: for (k=1; k<=cptcovn;k++) {
3223: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3224: }
3225: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3226: for (k=1; k<=cptcovprod;k++)
3227: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3228:
3229: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3230: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3231: gp=vector(1,(nlstate)*(nlstate+ndeath));
3232: gm=vector(1,(nlstate)*(nlstate+ndeath));
3233:
3234: for(theta=1; theta <=npar; theta++){
3235: for(i=1; i<=npar; i++)
3236: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3237:
3238: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3239:
3240: k=0;
3241: for(i=1; i<= (nlstate); i++){
3242: for(j=1; j<=(nlstate+ndeath);j++){
3243: k=k+1;
3244: gp[k]=pmmij[i][j];
3245: }
3246: }
3247:
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: k=0;
3253: for(i=1; i<=(nlstate); i++){
3254: for(j=1; j<=(nlstate+ndeath);j++){
3255: k=k+1;
3256: gm[k]=pmmij[i][j];
3257: }
3258: }
3259:
3260: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3261: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3262: }
3263:
3264: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3265: for(theta=1; theta <=npar; theta++)
3266: trgradg[j][theta]=gradg[theta][j];
3267:
3268: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3269: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3270: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3271: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3272: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3273: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3274:
3275: pmij(pmmij,cov,ncovmodel,x,nlstate);
3276:
3277: k=0;
3278: for(i=1; i<=(nlstate); i++){
3279: for(j=1; j<=(nlstate+ndeath);j++){
3280: k=k+1;
3281: mu[k][(int) age]=pmmij[i][j];
3282: }
3283: }
3284: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3285: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3286: varpij[i][j][(int)age] = doldm[i][j];
3287:
3288: /*printf("\n%d ",(int)age);
3289: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3290: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3291: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3292: }*/
3293:
3294: fprintf(ficresprob,"\n%d ",(int)age);
3295: fprintf(ficresprobcov,"\n%d ",(int)age);
3296: fprintf(ficresprobcor,"\n%d ",(int)age);
3297:
3298: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3299: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3300: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3301: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3302: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3303: }
3304: i=0;
3305: for (k=1; k<=(nlstate);k++){
3306: for (l=1; l<=(nlstate+ndeath);l++){
3307: i=i++;
3308: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3309: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3310: for (j=1; j<=i;j++){
3311: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3312: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3313: }
3314: }
3315: }/* end of loop for state */
3316: } /* end of loop for age */
3317:
3318: /* Confidence intervalle of pij */
3319: /*
3320: fprintf(ficgp,"\nset noparametric;unset label");
3321: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3322: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3323: 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);
3324: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3325: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3326: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3327: */
3328:
3329: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3330: first1=1;
3331: for (k2=1; k2<=(nlstate);k2++){
3332: for (l2=1; l2<=(nlstate+ndeath);l2++){
3333: if(l2==k2) continue;
3334: j=(k2-1)*(nlstate+ndeath)+l2;
3335: for (k1=1; k1<=(nlstate);k1++){
3336: for (l1=1; l1<=(nlstate+ndeath);l1++){
3337: if(l1==k1) continue;
3338: i=(k1-1)*(nlstate+ndeath)+l1;
3339: if(i<=j) continue;
3340: for (age=bage; age<=fage; age ++){
3341: if ((int)age %5==0){
3342: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3343: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3344: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3345: mu1=mu[i][(int) age]/stepm*YEARM ;
3346: mu2=mu[j][(int) age]/stepm*YEARM;
3347: c12=cv12/sqrt(v1*v2);
3348: /* Computing eigen value of matrix of covariance */
3349: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3350: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3351: /* Eigen vectors */
3352: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3353: /*v21=sqrt(1.-v11*v11); *//* error */
3354: v21=(lc1-v1)/cv12*v11;
3355: v12=-v21;
3356: v22=v11;
3357: tnalp=v21/v11;
3358: if(first1==1){
3359: first1=0;
3360: 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);
3361: }
3362: 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);
3363: /*printf(fignu*/
3364: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3365: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3366: if(first==1){
3367: first=0;
3368: fprintf(ficgp,"\nset parametric;unset label");
3369: 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);
3370: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3371: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3372: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3373: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3374: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3375: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3376: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3377: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3378: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3379: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3380: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3381: 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",\
3382: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3383: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3384: }else{
3385: first=0;
3386: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3387: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3388: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3389: 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",\
3390: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3391: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3392: }/* if first */
3393: } /* age mod 5 */
3394: } /* end loop age */
3395: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3396: first=1;
3397: } /*l12 */
3398: } /* k12 */
3399: } /*l1 */
3400: }/* k1 */
3401: } /* loop covariates */
3402: }
3403: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3404: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3405: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3406: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3407: free_vector(xp,1,npar);
3408: fclose(ficresprob);
3409: fclose(ficresprobcov);
3410: fclose(ficresprobcor);
3411: fflush(ficgp);
3412: fflush(fichtmcov);
3413: }
3414:
3415:
3416: /******************* Printing html file ***********/
3417: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3418: int lastpass, int stepm, int weightopt, char model[],\
3419: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3420: int popforecast, int estepm ,\
3421: double jprev1, double mprev1,double anprev1, \
3422: double jprev2, double mprev2,double anprev2){
3423: int jj1, k1, i1, cpt;
3424:
3425: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3426: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3427: </ul>");
3428: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3429: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3430: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3431: fprintf(fichtm,"\
3432: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3433: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3434: fprintf(fichtm,"\
3435: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3436: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3437: fprintf(fichtm,"\
3438: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij (estepm=%2d months): \
3439: <a href=\"%s\">%s</a> <br>\n</li>",
3440: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3441:
3442:
3443: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3444:
3445: m=cptcoveff;
3446: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3447:
3448: jj1=0;
3449: for(k1=1; k1<=m;k1++){
3450: for(i1=1; i1<=ncodemax[k1];i1++){
3451: jj1++;
3452: if (cptcovn > 0) {
3453: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3454: for (cpt=1; cpt<=cptcoveff;cpt++)
3455: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3456: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3457: }
3458: /* Pij */
3459: 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> \
3460: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3461: /* Quasi-incidences */
3462: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3463: 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> \
3464: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3465: /* Period (stable) prevalence in each health state */
3466: for(cpt=1; cpt<nlstate;cpt++){
3467: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3468: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3469: }
3470: for(cpt=1; cpt<=nlstate;cpt++) {
3471: 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> \
3472: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3473: }
3474: } /* end i1 */
3475: }/* End k1 */
3476: fprintf(fichtm,"</ul>");
3477:
3478:
3479: fprintf(fichtm,"\
3480: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3481: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3482:
3483: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3484: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3485: fprintf(fichtm,"\
3486: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3487: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3488:
3489: fprintf(fichtm,"\
3490: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3491: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3492: fprintf(fichtm,"\
3493: - 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): \
3494: <a href=\"%s\">%s</a> <br>\n</li>",
3495: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3496: fprintf(fichtm,"\
3497: - (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): \
3498: <a href=\"%s\">%s</a> <br>\n</li>",
3499: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3500: fprintf(fichtm,"\
3501: - 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",
3502: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3503: fprintf(fichtm,"\
3504: - 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",
3505: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3506: fprintf(fichtm,"\
3507: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3508: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3509:
3510: /* if(popforecast==1) fprintf(fichtm,"\n */
3511: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3512: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3513: /* <br>",fileres,fileres,fileres,fileres); */
3514: /* else */
3515: /* 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); */
3516: fflush(fichtm);
3517: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3518:
3519: m=cptcoveff;
3520: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3521:
3522: jj1=0;
3523: for(k1=1; k1<=m;k1++){
3524: for(i1=1; i1<=ncodemax[k1];i1++){
3525: jj1++;
3526: if (cptcovn > 0) {
3527: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3528: for (cpt=1; cpt<=cptcoveff;cpt++)
3529: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3530: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3531: }
3532: for(cpt=1; cpt<=nlstate;cpt++) {
3533: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3534: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3535: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3536: }
3537: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3538: health expectancies in states (1) and (2): %s%d.png<br>\
3539: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3540: } /* end i1 */
3541: }/* End k1 */
3542: fprintf(fichtm,"</ul>");
3543: fflush(fichtm);
3544: }
3545:
3546: /******************* Gnuplot file **************/
3547: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3548:
3549: char dirfileres[132],optfileres[132];
3550: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3551: int ng;
3552: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3553: /* printf("Problem with file %s",optionfilegnuplot); */
3554: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3555: /* } */
3556:
3557: /*#ifdef windows */
3558: fprintf(ficgp,"cd \"%s\" \n",pathc);
3559: /*#endif */
3560: m=pow(2,cptcoveff);
3561:
3562: strcpy(dirfileres,optionfilefiname);
3563: strcpy(optfileres,"vpl");
3564: /* 1eme*/
3565: for (cpt=1; cpt<= nlstate ; cpt ++) {
3566: for (k1=1; k1<= m ; k1 ++) {
3567: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3568: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3569: fprintf(ficgp,"set xlabel \"Age\" \n\
3570: set ylabel \"Probability\" \n\
3571: set ter png small\n\
3572: set size 0.65,0.65\n\
3573: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3574:
3575: for (i=1; i<= nlstate ; i ++) {
3576: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3577: else fprintf(ficgp," \%%*lf (\%%*lf)");
3578: }
3579: 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);
3580: for (i=1; i<= nlstate ; i ++) {
3581: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3582: else fprintf(ficgp," \%%*lf (\%%*lf)");
3583: }
3584: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3585: for (i=1; i<= nlstate ; i ++) {
3586: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3587: else fprintf(ficgp," \%%*lf (\%%*lf)");
3588: }
3589: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3590: }
3591: }
3592: /*2 eme*/
3593:
3594: for (k1=1; k1<= m ; k1 ++) {
3595: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3596: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3597:
3598: for (i=1; i<= nlstate+1 ; i ++) {
3599: k=2*i;
3600: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3601: for (j=1; j<= nlstate+1 ; j ++) {
3602: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3603: else fprintf(ficgp," \%%*lf (\%%*lf)");
3604: }
3605: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3606: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3607: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3608: for (j=1; j<= nlstate+1 ; j ++) {
3609: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3610: else fprintf(ficgp," \%%*lf (\%%*lf)");
3611: }
3612: fprintf(ficgp,"\" t\"\" w l 0,");
3613: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3614: for (j=1; j<= nlstate+1 ; j ++) {
3615: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3616: else fprintf(ficgp," \%%*lf (\%%*lf)");
3617: }
3618: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3619: else fprintf(ficgp,"\" t\"\" w l 0,");
3620: }
3621: }
3622:
3623: /*3eme*/
3624:
3625: for (k1=1; k1<= m ; k1 ++) {
3626: for (cpt=1; cpt<= nlstate ; cpt ++) {
3627: /* k=2+nlstate*(2*cpt-2); */
3628: k=2+(nlstate+1)*(cpt-1);
3629: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3630: fprintf(ficgp,"set ter png small\n\
3631: set size 0.65,0.65\n\
3632: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3633: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3634: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3635: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3636: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3637: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3638: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3639:
3640: */
3641: for (i=1; i< nlstate ; i ++) {
3642: 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);
3643: /* 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);*/
3644:
3645: }
3646: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3647: }
3648: }
3649:
3650: /* CV preval stable (period) */
3651: for (k1=1; k1<= m ; k1 ++) {
3652: for (cpt=1; cpt<=nlstate ; cpt ++) {
3653: k=3;
3654: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3655: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3656: set ter png small\nset size 0.65,0.65\n\
3657: unset log y\n\
3658: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3659:
3660: for (i=1; i< nlstate ; i ++)
3661: fprintf(ficgp,"+$%d",k+i+1);
3662: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3663:
3664: l=3+(nlstate+ndeath)*cpt;
3665: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3666: for (i=1; i< nlstate ; i ++) {
3667: l=3+(nlstate+ndeath)*cpt;
3668: fprintf(ficgp,"+$%d",l+i+1);
3669: }
3670: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3671: }
3672: }
3673:
3674: /* proba elementaires */
3675: for(i=1,jk=1; i <=nlstate; i++){
3676: for(k=1; k <=(nlstate+ndeath); k++){
3677: if (k != i) {
3678: for(j=1; j <=ncovmodel; j++){
3679: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3680: jk++;
3681: fprintf(ficgp,"\n");
3682: }
3683: }
3684: }
3685: }
3686:
3687: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3688: for(jk=1; jk <=m; jk++) {
3689: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3690: if (ng==2)
3691: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3692: else
3693: fprintf(ficgp,"\nset title \"Probability\"\n");
3694: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3695: i=1;
3696: for(k2=1; k2<=nlstate; k2++) {
3697: k3=i;
3698: for(k=1; k<=(nlstate+ndeath); k++) {
3699: if (k != k2){
3700: if(ng==2)
3701: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3702: else
3703: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3704: ij=1;
3705: for(j=3; j <=ncovmodel; j++) {
3706: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3707: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3708: ij++;
3709: }
3710: else
3711: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3712: }
3713: fprintf(ficgp,")/(1");
3714:
3715: for(k1=1; k1 <=nlstate; k1++){
3716: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+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",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3721: ij++;
3722: }
3723: else
3724: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3725: }
3726: fprintf(ficgp,")");
3727: }
3728: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3729: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3730: i=i+ncovmodel;
3731: }
3732: } /* end k */
3733: } /* end k2 */
3734: } /* end jk */
3735: } /* end ng */
3736: fflush(ficgp);
3737: } /* end gnuplot */
3738:
3739:
3740: /*************** Moving average **************/
3741: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3742:
3743: int i, cpt, cptcod;
3744: int modcovmax =1;
3745: int mobilavrange, mob;
3746: double age;
3747:
3748: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3749: a covariate has 2 modalities */
3750: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3751:
3752: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3753: if(mobilav==1) mobilavrange=5; /* default */
3754: else mobilavrange=mobilav;
3755: for (age=bage; age<=fage; age++)
3756: for (i=1; i<=nlstate;i++)
3757: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3758: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3759: /* We keep the original values on the extreme ages bage, fage and for
3760: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3761: we use a 5 terms etc. until the borders are no more concerned.
3762: */
3763: for (mob=3;mob <=mobilavrange;mob=mob+2){
3764: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3765: for (i=1; i<=nlstate;i++){
3766: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3767: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3768: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3769: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3770: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3771: }
3772: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3773: }
3774: }
3775: }/* end age */
3776: }/* end mob */
3777: }else return -1;
3778: return 0;
3779: }/* End movingaverage */
3780:
3781:
3782: /************** Forecasting ******************/
3783: 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){
3784: /* proj1, year, month, day of starting projection
3785: agemin, agemax range of age
3786: dateprev1 dateprev2 range of dates during which prevalence is computed
3787: anproj2 year of en of projection (same day and month as proj1).
3788: */
3789: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3790: int *popage;
3791: double agec; /* generic age */
3792: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3793: double *popeffectif,*popcount;
3794: double ***p3mat;
3795: double ***mobaverage;
3796: char fileresf[FILENAMELENGTH];
3797:
3798: agelim=AGESUP;
3799: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3800:
3801: strcpy(fileresf,"f");
3802: strcat(fileresf,fileres);
3803: if((ficresf=fopen(fileresf,"w"))==NULL) {
3804: printf("Problem with forecast resultfile: %s\n", fileresf);
3805: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3806: }
3807: printf("Computing forecasting: result on file '%s' \n", fileresf);
3808: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3809:
3810: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3811:
3812: if (mobilav!=0) {
3813: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3814: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3815: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3816: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3817: }
3818: }
3819:
3820: stepsize=(int) (stepm+YEARM-1)/YEARM;
3821: if (stepm<=12) stepsize=1;
3822: if(estepm < stepm){
3823: printf ("Problem %d lower than %d\n",estepm, stepm);
3824: }
3825: else hstepm=estepm;
3826:
3827: hstepm=hstepm/stepm;
3828: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3829: fractional in yp1 */
3830: anprojmean=yp;
3831: yp2=modf((yp1*12),&yp);
3832: mprojmean=yp;
3833: yp1=modf((yp2*30.5),&yp);
3834: jprojmean=yp;
3835: if(jprojmean==0) jprojmean=1;
3836: if(mprojmean==0) jprojmean=1;
3837:
3838: i1=cptcoveff;
3839: if (cptcovn < 1){i1=1;}
3840:
3841: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3842:
3843: fprintf(ficresf,"#****** Routine prevforecast **\n");
3844:
3845: /* if (h==(int)(YEARM*yearp)){ */
3846: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3847: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3848: k=k+1;
3849: fprintf(ficresf,"\n#******");
3850: for(j=1;j<=cptcoveff;j++) {
3851: 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]]);
3852: }
3853: fprintf(ficresf,"******\n");
3854: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3855: for(j=1; j<=nlstate+ndeath;j++){
3856: for(i=1; i<=nlstate;i++)
3857: fprintf(ficresf," p%d%d",i,j);
3858: fprintf(ficresf," p.%d",j);
3859: }
3860: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3861: fprintf(ficresf,"\n");
3862: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3863:
3864: for (agec=fage; agec>=(ageminpar-1); agec--){
3865: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3866: nhstepm = nhstepm/hstepm;
3867: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3868: oldm=oldms;savm=savms;
3869: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3870:
3871: for (h=0; h<=nhstepm; h++){
3872: if (h*hstepm/YEARM*stepm ==yearp) {
3873: fprintf(ficresf,"\n");
3874: for(j=1;j<=cptcoveff;j++)
3875: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3876: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3877: }
3878: for(j=1; j<=nlstate+ndeath;j++) {
3879: ppij=0.;
3880: for(i=1; i<=nlstate;i++) {
3881: if (mobilav==1)
3882: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3883: else {
3884: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3885: }
3886: if (h*hstepm/YEARM*stepm== yearp) {
3887: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3888: }
3889: } /* end i */
3890: if (h*hstepm/YEARM*stepm==yearp) {
3891: fprintf(ficresf," %.3f", ppij);
3892: }
3893: }/* end j */
3894: } /* end h */
3895: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3896: } /* end agec */
3897: } /* end yearp */
3898: } /* end cptcod */
3899: } /* end cptcov */
3900:
3901: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3902:
3903: fclose(ficresf);
3904: }
3905:
3906: /************** Forecasting *****not tested NB*************/
3907: 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){
3908:
3909: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3910: int *popage;
3911: double calagedatem, agelim, kk1, kk2;
3912: double *popeffectif,*popcount;
3913: double ***p3mat,***tabpop,***tabpopprev;
3914: double ***mobaverage;
3915: char filerespop[FILENAMELENGTH];
3916:
3917: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3918: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3919: agelim=AGESUP;
3920: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3921:
3922: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3923:
3924:
3925: strcpy(filerespop,"pop");
3926: strcat(filerespop,fileres);
3927: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3928: printf("Problem with forecast resultfile: %s\n", filerespop);
3929: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3930: }
3931: printf("Computing forecasting: result on file '%s' \n", filerespop);
3932: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3933:
3934: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3935:
3936: if (mobilav!=0) {
3937: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3938: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3939: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3940: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3941: }
3942: }
3943:
3944: stepsize=(int) (stepm+YEARM-1)/YEARM;
3945: if (stepm<=12) stepsize=1;
3946:
3947: agelim=AGESUP;
3948:
3949: hstepm=1;
3950: hstepm=hstepm/stepm;
3951:
3952: if (popforecast==1) {
3953: if((ficpop=fopen(popfile,"r"))==NULL) {
3954: printf("Problem with population file : %s\n",popfile);exit(0);
3955: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3956: }
3957: popage=ivector(0,AGESUP);
3958: popeffectif=vector(0,AGESUP);
3959: popcount=vector(0,AGESUP);
3960:
3961: i=1;
3962: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3963:
3964: imx=i;
3965: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3966: }
3967:
3968: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3969: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3970: k=k+1;
3971: fprintf(ficrespop,"\n#******");
3972: for(j=1;j<=cptcoveff;j++) {
3973: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3974: }
3975: fprintf(ficrespop,"******\n");
3976: fprintf(ficrespop,"# Age");
3977: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3978: if (popforecast==1) fprintf(ficrespop," [Population]");
3979:
3980: for (cpt=0; cpt<=0;cpt++) {
3981: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3982:
3983: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3984: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3985: nhstepm = nhstepm/hstepm;
3986:
3987: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3988: oldm=oldms;savm=savms;
3989: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3990:
3991: for (h=0; h<=nhstepm; h++){
3992: if (h==(int) (calagedatem+YEARM*cpt)) {
3993: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3994: }
3995: for(j=1; j<=nlstate+ndeath;j++) {
3996: kk1=0.;kk2=0;
3997: for(i=1; i<=nlstate;i++) {
3998: if (mobilav==1)
3999: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4000: else {
4001: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4002: }
4003: }
4004: if (h==(int)(calagedatem+12*cpt)){
4005: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4006: /*fprintf(ficrespop," %.3f", kk1);
4007: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4008: }
4009: }
4010: for(i=1; i<=nlstate;i++){
4011: kk1=0.;
4012: for(j=1; j<=nlstate;j++){
4013: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4014: }
4015: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4016: }
4017:
4018: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4019: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4020: }
4021: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4022: }
4023: }
4024:
4025: /******/
4026:
4027: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4028: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4029: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4030: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4031: nhstepm = nhstepm/hstepm;
4032:
4033: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4034: oldm=oldms;savm=savms;
4035: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4036: for (h=0; h<=nhstepm; h++){
4037: if (h==(int) (calagedatem+YEARM*cpt)) {
4038: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4039: }
4040: for(j=1; j<=nlstate+ndeath;j++) {
4041: kk1=0.;kk2=0;
4042: for(i=1; i<=nlstate;i++) {
4043: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4044: }
4045: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4046: }
4047: }
4048: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4049: }
4050: }
4051: }
4052: }
4053:
4054: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4055:
4056: if (popforecast==1) {
4057: free_ivector(popage,0,AGESUP);
4058: free_vector(popeffectif,0,AGESUP);
4059: free_vector(popcount,0,AGESUP);
4060: }
4061: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4062: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4063: fclose(ficrespop);
4064: } /* End of popforecast */
4065:
4066: int fileappend(FILE *fichier, char *optionfich)
4067: {
4068: if((fichier=fopen(optionfich,"a"))==NULL) {
4069: printf("Problem with file: %s\n", optionfich);
4070: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4071: return (0);
4072: }
4073: fflush(fichier);
4074: return (1);
4075: }
4076:
4077:
4078: /**************** function prwizard **********************/
4079: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4080: {
4081:
4082: /* Wizard to print covariance matrix template */
4083:
4084: char ca[32], cb[32], cc[32];
4085: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4086: int numlinepar;
4087:
4088: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4089: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4090: for(i=1; i <=nlstate; i++){
4091: jj=0;
4092: for(j=1; j <=nlstate+ndeath; j++){
4093: if(j==i) continue;
4094: jj++;
4095: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4096: printf("%1d%1d",i,j);
4097: fprintf(ficparo,"%1d%1d",i,j);
4098: for(k=1; k<=ncovmodel;k++){
4099: /* printf(" %lf",param[i][j][k]); */
4100: /* fprintf(ficparo," %lf",param[i][j][k]); */
4101: printf(" 0.");
4102: fprintf(ficparo," 0.");
4103: }
4104: printf("\n");
4105: fprintf(ficparo,"\n");
4106: }
4107: }
4108: printf("# Scales (for hessian or gradient estimation)\n");
4109: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4110: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4111: for(i=1; i <=nlstate; i++){
4112: jj=0;
4113: for(j=1; j <=nlstate+ndeath; j++){
4114: if(j==i) continue;
4115: jj++;
4116: fprintf(ficparo,"%1d%1d",i,j);
4117: printf("%1d%1d",i,j);
4118: fflush(stdout);
4119: for(k=1; k<=ncovmodel;k++){
4120: /* printf(" %le",delti3[i][j][k]); */
4121: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4122: printf(" 0.");
4123: fprintf(ficparo," 0.");
4124: }
4125: numlinepar++;
4126: printf("\n");
4127: fprintf(ficparo,"\n");
4128: }
4129: }
4130: printf("# Covariance matrix\n");
4131: /* # 121 Var(a12)\n\ */
4132: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4133: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4134: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4135: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4136: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4137: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4138: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4139: fflush(stdout);
4140: fprintf(ficparo,"# Covariance matrix\n");
4141: /* # 121 Var(a12)\n\ */
4142: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4143: /* # ...\n\ */
4144: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4145:
4146: for(itimes=1;itimes<=2;itimes++){
4147: jj=0;
4148: for(i=1; i <=nlstate; i++){
4149: for(j=1; j <=nlstate+ndeath; j++){
4150: if(j==i) continue;
4151: for(k=1; k<=ncovmodel;k++){
4152: jj++;
4153: ca[0]= k+'a'-1;ca[1]='\0';
4154: if(itimes==1){
4155: printf("#%1d%1d%d",i,j,k);
4156: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4157: }else{
4158: printf("%1d%1d%d",i,j,k);
4159: fprintf(ficparo,"%1d%1d%d",i,j,k);
4160: /* printf(" %.5le",matcov[i][j]); */
4161: }
4162: ll=0;
4163: for(li=1;li <=nlstate; li++){
4164: for(lj=1;lj <=nlstate+ndeath; lj++){
4165: if(lj==li) continue;
4166: for(lk=1;lk<=ncovmodel;lk++){
4167: ll++;
4168: if(ll<=jj){
4169: cb[0]= lk +'a'-1;cb[1]='\0';
4170: if(ll<jj){
4171: if(itimes==1){
4172: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4173: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4174: }else{
4175: printf(" 0.");
4176: fprintf(ficparo," 0.");
4177: }
4178: }else{
4179: if(itimes==1){
4180: printf(" Var(%s%1d%1d)",ca,i,j);
4181: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4182: }else{
4183: printf(" 0.");
4184: fprintf(ficparo," 0.");
4185: }
4186: }
4187: }
4188: } /* end lk */
4189: } /* end lj */
4190: } /* end li */
4191: printf("\n");
4192: fprintf(ficparo,"\n");
4193: numlinepar++;
4194: } /* end k*/
4195: } /*end j */
4196: } /* end i */
4197: } /* end itimes */
4198:
4199: } /* end of prwizard */
4200: /******************* Gompertz Likelihood ******************************/
4201: double gompertz(double x[])
4202: {
4203: double A,B,L=0.0,sump=0.,num=0.;
4204: int i,n=0; /* n is the size of the sample */
4205:
4206: for (i=0;i<=imx-1 ; i++) {
4207: sump=sump+weight[i];
4208: /* sump=sump+1;*/
4209: num=num+1;
4210: }
4211:
4212:
4213: /* for (i=0; i<=imx; i++)
4214: 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]);*/
4215:
4216: for (i=1;i<=imx ; i++)
4217: {
4218: if (cens[i] == 1 && wav[i]>1)
4219: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4220:
4221: if (cens[i] == 0 && wav[i]>1)
4222: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4223: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4224:
4225: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4226: if (wav[i] > 1 ) { /* ??? */
4227: L=L+A*weight[i];
4228: /* 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]);*/
4229: }
4230: }
4231:
4232: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4233:
4234: return -2*L*num/sump;
4235: }
4236:
4237: /******************* Printing html file ***********/
4238: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4239: int lastpass, int stepm, int weightopt, char model[],\
4240: int imx, double p[],double **matcov,double agemortsup){
4241: int i,k;
4242:
4243: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4244: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4245: for (i=1;i<=2;i++)
4246: 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]));
4247: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4248: fprintf(fichtm,"</ul>");
4249:
4250: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4251:
4252: 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>");
4253:
4254: for (k=agegomp;k<(agemortsup-2);k++)
4255: 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]);
4256:
4257:
4258: fflush(fichtm);
4259: }
4260:
4261: /******************* Gnuplot file **************/
4262: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4263:
4264: char dirfileres[132],optfileres[132];
4265: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4266: int ng;
4267:
4268:
4269: /*#ifdef windows */
4270: fprintf(ficgp,"cd \"%s\" \n",pathc);
4271: /*#endif */
4272:
4273:
4274: strcpy(dirfileres,optionfilefiname);
4275: strcpy(optfileres,"vpl");
4276: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4277: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4278: fprintf(ficgp, "set ter png small\n set log y\n");
4279: fprintf(ficgp, "set size 0.65,0.65\n");
4280: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4281:
4282: }
4283:
4284:
4285:
4286:
4287:
4288: /***********************************************/
4289: /**************** Main Program *****************/
4290: /***********************************************/
4291:
4292: int main(int argc, char *argv[])
4293: {
4294: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4295: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4296: int linei, month, year,iout;
4297: int jj, ll, li, lj, lk, imk;
4298: int numlinepar=0; /* Current linenumber of parameter file */
4299: int itimes;
4300: int NDIM=2;
4301:
4302: char ca[32], cb[32], cc[32];
4303: char dummy[]=" ";
4304: /* FILE *fichtm; *//* Html File */
4305: /* FILE *ficgp;*/ /*Gnuplot File */
4306: struct stat info;
4307: double agedeb, agefin,hf;
4308: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4309:
4310: double fret;
4311: double **xi,tmp,delta;
4312:
4313: double dum; /* Dummy variable */
4314: double ***p3mat;
4315: double ***mobaverage;
4316: int *indx;
4317: char line[MAXLINE], linepar[MAXLINE];
4318: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4319: char pathr[MAXLINE], pathimach[MAXLINE];
4320: char **bp, *tok, *val; /* pathtot */
4321: int firstobs=1, lastobs=10;
4322: int sdeb, sfin; /* Status at beginning and end */
4323: int c, h , cpt,l;
4324: int ju,jl, mi;
4325: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4326: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4327: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4328: int mobilav=0,popforecast=0;
4329: int hstepm, nhstepm;
4330: int agemortsup;
4331: float sumlpop=0.;
4332: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4333: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4334:
4335: double bage, fage, age, agelim, agebase;
4336: double ftolpl=FTOL;
4337: double **prlim;
4338: double *severity;
4339: double ***param; /* Matrix of parameters */
4340: double *p;
4341: double **matcov; /* Matrix of covariance */
4342: double ***delti3; /* Scale */
4343: double *delti; /* Scale */
4344: double ***eij, ***vareij;
4345: double **varpl; /* Variances of prevalence limits by age */
4346: double *epj, vepp;
4347: double kk1, kk2;
4348: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4349: double **ximort;
4350: char *alph[]={"a","a","b","c","d","e"}, str[4];
4351: int *dcwave;
4352:
4353: char z[1]="c", occ;
4354:
4355: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4356: char *strt, strtend[80];
4357: char *stratrunc;
4358: int lstra;
4359:
4360: long total_usecs;
4361:
4362: /* setlocale (LC_ALL, ""); */
4363: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4364: /* textdomain (PACKAGE); */
4365: /* setlocale (LC_CTYPE, ""); */
4366: /* setlocale (LC_MESSAGES, ""); */
4367:
4368: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4369: (void) gettimeofday(&start_time,&tzp);
4370: curr_time=start_time;
4371: tm = *localtime(&start_time.tv_sec);
4372: tmg = *gmtime(&start_time.tv_sec);
4373: strcpy(strstart,asctime(&tm));
4374:
4375: /* printf("Localtime (at start)=%s",strstart); */
4376: /* tp.tv_sec = tp.tv_sec +86400; */
4377: /* tm = *localtime(&start_time.tv_sec); */
4378: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4379: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4380: /* tmg.tm_hour=tmg.tm_hour + 1; */
4381: /* tp.tv_sec = mktime(&tmg); */
4382: /* strt=asctime(&tmg); */
4383: /* printf("Time(after) =%s",strstart); */
4384: /* (void) time (&time_value);
4385: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4386: * tm = *localtime(&time_value);
4387: * strstart=asctime(&tm);
4388: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4389: */
4390:
4391: nberr=0; /* Number of errors and warnings */
4392: nbwarn=0;
4393: getcwd(pathcd, size);
4394:
4395: printf("\n%s\n%s",version,fullversion);
4396: if(argc <=1){
4397: printf("\nEnter the parameter file name: ");
4398: fgets(pathr,FILENAMELENGTH,stdin);
4399: i=strlen(pathr);
4400: if(pathr[i-1]=='\n')
4401: pathr[i-1]='\0';
4402: for (tok = pathr; tok != NULL; ){
4403: printf("Pathr |%s|\n",pathr);
4404: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4405: printf("val= |%s| pathr=%s\n",val,pathr);
4406: strcpy (pathtot, val);
4407: if(pathr[0] == '\0') break; /* Un peu sale */
4408: }
4409: }
4410: else{
4411: strcpy(pathtot,argv[1]);
4412: }
4413: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4414: /*cygwin_split_path(pathtot,path,optionfile);
4415: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4416: /* cutv(path,optionfile,pathtot,'\\');*/
4417:
4418: /* Split argv[0], imach program to get pathimach */
4419: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4420: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4421: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4422: /* strcpy(pathimach,argv[0]); */
4423: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4424: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4425: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4426: chdir(path);
4427: strcpy(command,"mkdir ");
4428: strcat(command,optionfilefiname);
4429: if((outcmd=system(command)) != 0){
4430: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4431: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4432: /* fclose(ficlog); */
4433: /* exit(1); */
4434: }
4435: /* if((imk=mkdir(optionfilefiname))<0){ */
4436: /* perror("mkdir"); */
4437: /* } */
4438:
4439: /*-------- arguments in the command line --------*/
4440:
4441: /* Log file */
4442: strcat(filelog, optionfilefiname);
4443: strcat(filelog,".log"); /* */
4444: if((ficlog=fopen(filelog,"w"))==NULL) {
4445: printf("Problem with logfile %s\n",filelog);
4446: goto end;
4447: }
4448: fprintf(ficlog,"Log filename:%s\n",filelog);
4449: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4450: fprintf(ficlog,"\nEnter the parameter file name: \n");
4451: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4452: path=%s \n\
4453: optionfile=%s\n\
4454: optionfilext=%s\n\
4455: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4456:
4457: printf("Local time (at start):%s",strstart);
4458: fprintf(ficlog,"Local time (at start): %s",strstart);
4459: fflush(ficlog);
4460: /* (void) gettimeofday(&curr_time,&tzp); */
4461: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4462:
4463: /* */
4464: strcpy(fileres,"r");
4465: strcat(fileres, optionfilefiname);
4466: strcat(fileres,".txt"); /* Other files have txt extension */
4467:
4468: /*---------arguments file --------*/
4469:
4470: if((ficpar=fopen(optionfile,"r"))==NULL) {
4471: printf("Problem with optionfile %s\n",optionfile);
4472: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4473: fflush(ficlog);
4474: goto end;
4475: }
4476:
4477:
4478:
4479: strcpy(filereso,"o");
4480: strcat(filereso,fileres);
4481: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4482: printf("Problem with Output resultfile: %s\n", filereso);
4483: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4484: fflush(ficlog);
4485: goto end;
4486: }
4487:
4488: /* Reads comments: lines beginning with '#' */
4489: numlinepar=0;
4490: while((c=getc(ficpar))=='#' && c!= EOF){
4491: ungetc(c,ficpar);
4492: fgets(line, MAXLINE, ficpar);
4493: numlinepar++;
4494: puts(line);
4495: fputs(line,ficparo);
4496: fputs(line,ficlog);
4497: }
4498: ungetc(c,ficpar);
4499:
4500: 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);
4501: numlinepar++;
4502: 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);
4503: 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);
4504: 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);
4505: fflush(ficlog);
4506: while((c=getc(ficpar))=='#' && c!= EOF){
4507: ungetc(c,ficpar);
4508: fgets(line, MAXLINE, ficpar);
4509: numlinepar++;
4510: puts(line);
4511: fputs(line,ficparo);
4512: fputs(line,ficlog);
4513: }
4514: ungetc(c,ficpar);
4515:
4516:
4517: covar=matrix(0,NCOVMAX,1,n);
4518: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4519: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4520:
4521: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4522: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4523: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4524:
4525: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4526: delti=delti3[1][1];
4527: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4528: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4529: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4530: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4531: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4532: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4533: fclose (ficparo);
4534: fclose (ficlog);
4535: exit(0);
4536: }
4537: else if(mle==-3) {
4538: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4539: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4540: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4541: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4542: matcov=matrix(1,npar,1,npar);
4543: }
4544: else{
4545: /* Read guess parameters */
4546: /* Reads comments: lines beginning with '#' */
4547: while((c=getc(ficpar))=='#' && c!= EOF){
4548: ungetc(c,ficpar);
4549: fgets(line, MAXLINE, ficpar);
4550: numlinepar++;
4551: puts(line);
4552: fputs(line,ficparo);
4553: fputs(line,ficlog);
4554: }
4555: ungetc(c,ficpar);
4556:
4557: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4558: for(i=1; i <=nlstate; i++){
4559: j=0;
4560: for(jj=1; jj <=nlstate+ndeath; jj++){
4561: if(jj==i) continue;
4562: j++;
4563: fscanf(ficpar,"%1d%1d",&i1,&j1);
4564: if ((i1 != i) && (j1 != j)){
4565: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4566: exit(1);
4567: }
4568: fprintf(ficparo,"%1d%1d",i1,j1);
4569: if(mle==1)
4570: printf("%1d%1d",i,j);
4571: fprintf(ficlog,"%1d%1d",i,j);
4572: for(k=1; k<=ncovmodel;k++){
4573: fscanf(ficpar," %lf",¶m[i][j][k]);
4574: if(mle==1){
4575: printf(" %lf",param[i][j][k]);
4576: fprintf(ficlog," %lf",param[i][j][k]);
4577: }
4578: else
4579: fprintf(ficlog," %lf",param[i][j][k]);
4580: fprintf(ficparo," %lf",param[i][j][k]);
4581: }
4582: fscanf(ficpar,"\n");
4583: numlinepar++;
4584: if(mle==1)
4585: printf("\n");
4586: fprintf(ficlog,"\n");
4587: fprintf(ficparo,"\n");
4588: }
4589: }
4590: fflush(ficlog);
4591:
4592: p=param[1][1];
4593:
4594: /* Reads comments: lines beginning with '#' */
4595: while((c=getc(ficpar))=='#' && c!= EOF){
4596: ungetc(c,ficpar);
4597: fgets(line, MAXLINE, ficpar);
4598: numlinepar++;
4599: puts(line);
4600: fputs(line,ficparo);
4601: fputs(line,ficlog);
4602: }
4603: ungetc(c,ficpar);
4604:
4605: for(i=1; i <=nlstate; i++){
4606: for(j=1; j <=nlstate+ndeath-1; j++){
4607: fscanf(ficpar,"%1d%1d",&i1,&j1);
4608: if ((i1-i)*(j1-j)!=0){
4609: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4610: exit(1);
4611: }
4612: printf("%1d%1d",i,j);
4613: fprintf(ficparo,"%1d%1d",i1,j1);
4614: fprintf(ficlog,"%1d%1d",i1,j1);
4615: for(k=1; k<=ncovmodel;k++){
4616: fscanf(ficpar,"%le",&delti3[i][j][k]);
4617: printf(" %le",delti3[i][j][k]);
4618: fprintf(ficparo," %le",delti3[i][j][k]);
4619: fprintf(ficlog," %le",delti3[i][j][k]);
4620: }
4621: fscanf(ficpar,"\n");
4622: numlinepar++;
4623: printf("\n");
4624: fprintf(ficparo,"\n");
4625: fprintf(ficlog,"\n");
4626: }
4627: }
4628: fflush(ficlog);
4629:
4630: delti=delti3[1][1];
4631:
4632:
4633: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4634:
4635: /* Reads comments: lines beginning with '#' */
4636: while((c=getc(ficpar))=='#' && c!= EOF){
4637: ungetc(c,ficpar);
4638: fgets(line, MAXLINE, ficpar);
4639: numlinepar++;
4640: puts(line);
4641: fputs(line,ficparo);
4642: fputs(line,ficlog);
4643: }
4644: ungetc(c,ficpar);
4645:
4646: matcov=matrix(1,npar,1,npar);
4647: for(i=1; i <=npar; i++){
4648: fscanf(ficpar,"%s",&str);
4649: if(mle==1)
4650: printf("%s",str);
4651: fprintf(ficlog,"%s",str);
4652: fprintf(ficparo,"%s",str);
4653: for(j=1; j <=i; j++){
4654: fscanf(ficpar," %le",&matcov[i][j]);
4655: if(mle==1){
4656: printf(" %.5le",matcov[i][j]);
4657: }
4658: fprintf(ficlog," %.5le",matcov[i][j]);
4659: fprintf(ficparo," %.5le",matcov[i][j]);
4660: }
4661: fscanf(ficpar,"\n");
4662: numlinepar++;
4663: if(mle==1)
4664: printf("\n");
4665: fprintf(ficlog,"\n");
4666: fprintf(ficparo,"\n");
4667: }
4668: for(i=1; i <=npar; i++)
4669: for(j=i+1;j<=npar;j++)
4670: matcov[i][j]=matcov[j][i];
4671:
4672: if(mle==1)
4673: printf("\n");
4674: fprintf(ficlog,"\n");
4675:
4676: fflush(ficlog);
4677:
4678: /*-------- Rewriting parameter file ----------*/
4679: strcpy(rfileres,"r"); /* "Rparameterfile */
4680: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4681: strcat(rfileres,"."); /* */
4682: strcat(rfileres,optionfilext); /* Other files have txt extension */
4683: if((ficres =fopen(rfileres,"w"))==NULL) {
4684: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4685: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4686: }
4687: fprintf(ficres,"#%s\n",version);
4688: } /* End of mle != -3 */
4689:
4690: /*-------- data file ----------*/
4691: if((fic=fopen(datafile,"r"))==NULL) {
4692: printf("Problem with datafile: %s\n", datafile);goto end;
4693: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4694: }
4695:
4696: n= lastobs;
4697: severity = vector(1,maxwav);
4698: outcome=imatrix(1,maxwav+1,1,n);
4699: num=lvector(1,n);
4700: moisnais=vector(1,n);
4701: annais=vector(1,n);
4702: moisdc=vector(1,n);
4703: andc=vector(1,n);
4704: agedc=vector(1,n);
4705: cod=ivector(1,n);
4706: weight=vector(1,n);
4707: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4708: mint=matrix(1,maxwav,1,n);
4709: anint=matrix(1,maxwav,1,n);
4710: s=imatrix(1,maxwav+1,1,n);
4711: tab=ivector(1,NCOVMAX);
4712: ncodemax=ivector(1,8);
4713:
4714: i=1;
4715: linei=0;
4716: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4717: linei=linei+1;
4718: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4719: if(line[j] == '\t')
4720: line[j] = ' ';
4721: }
4722: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4723: ;
4724: };
4725: line[j+1]=0; /* Trims blanks at end of line */
4726: if(line[0]=='#'){
4727: fprintf(ficlog,"Comment line\n%s\n",line);
4728: printf("Comment line\n%s\n",line);
4729: continue;
4730: }
4731:
4732: for (j=maxwav;j>=1;j--){
4733: cutv(stra, strb,line,' ');
4734: errno=0;
4735: lval=strtol(strb,&endptr,10);
4736: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4737: if( strb[0]=='\0' || (*endptr != '\0')){
4738: 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);
4739: exit(1);
4740: }
4741: s[j][i]=lval;
4742:
4743: strcpy(line,stra);
4744: cutv(stra, strb,line,' ');
4745: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4746: }
4747: else if(iout=sscanf(strb,"%s.") != 0){
4748: month=99;
4749: year=9999;
4750: }else{
4751: 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);
4752: exit(1);
4753: }
4754: anint[j][i]= (double) year;
4755: mint[j][i]= (double)month;
4756: strcpy(line,stra);
4757: } /* ENd Waves */
4758:
4759: cutv(stra, strb,line,' ');
4760: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4761: }
4762: else if(iout=sscanf(strb,"%s.",dummy) != 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 death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4767: exit(1);
4768: }
4769: andc[i]=(double) year;
4770: moisdc[i]=(double) month;
4771: strcpy(line,stra);
4772:
4773: cutv(stra, strb,line,' ');
4774: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4775: }
4776: else if(iout=sscanf(strb,"%s.") != 0){
4777: month=99;
4778: year=9999;
4779: }else{
4780: 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);
4781: exit(1);
4782: }
4783: annais[i]=(double)(year);
4784: moisnais[i]=(double)(month);
4785: strcpy(line,stra);
4786:
4787: cutv(stra, strb,line,' ');
4788: errno=0;
4789: lval=strtol(strb,&endptr,10);
4790: if( strb[0]=='\0' || (*endptr != '\0')){
4791: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4792: exit(1);
4793: }
4794: weight[i]=(double)(lval);
4795: strcpy(line,stra);
4796:
4797: for (j=ncovcol;j>=1;j--){
4798: cutv(stra, strb,line,' ');
4799: errno=0;
4800: lval=strtol(strb,&endptr,10);
4801: if( strb[0]=='\0' || (*endptr != '\0')){
4802: 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);
4803: exit(1);
4804: }
4805: if(lval <-1 || lval >1){
4806: 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);
4807: exit(1);
4808: }
4809: covar[j][i]=(double)(lval);
4810: strcpy(line,stra);
4811: }
4812: lstra=strlen(stra);
4813:
4814: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4815: stratrunc = &(stra[lstra-9]);
4816: num[i]=atol(stratrunc);
4817: }
4818: else
4819: num[i]=atol(stra);
4820: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4821: 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;}*/
4822:
4823: i=i+1;
4824: } /* End loop reading data */
4825: fclose(fic);
4826: /* printf("ii=%d", ij);
4827: scanf("%d",i);*/
4828: imx=i-1; /* Number of individuals */
4829:
4830: /* for (i=1; i<=imx; i++){
4831: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4832: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4833: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4834: }*/
4835: /* for (i=1; i<=imx; i++){
4836: if (s[4][i]==9) s[4][i]=-1;
4837: 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]));}*/
4838:
4839: /* for (i=1; i<=imx; i++) */
4840:
4841: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4842: else weight[i]=1;*/
4843:
4844: /* Calculation of the number of parameters from char model */
4845: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4846: Tprod=ivector(1,15);
4847: Tvaraff=ivector(1,15);
4848: Tvard=imatrix(1,15,1,2);
4849: Tage=ivector(1,15);
4850:
4851: if (strlen(model) >1){ /* If there is at least 1 covariate */
4852: j=0, j1=0, k1=1, k2=1;
4853: j=nbocc(model,'+'); /* j=Number of '+' */
4854: j1=nbocc(model,'*'); /* j1=Number of '*' */
4855: cptcovn=j+1;
4856: cptcovprod=j1; /*Number of products */
4857:
4858: strcpy(modelsav,model);
4859: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4860: printf("Error. Non available option model=%s ",model);
4861: fprintf(ficlog,"Error. Non available option model=%s ",model);
4862: goto end;
4863: }
4864:
4865: /* This loop fills the array Tvar from the string 'model'.*/
4866:
4867: for(i=(j+1); i>=1;i--){
4868: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4869: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4870: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4871: /*scanf("%d",i);*/
4872: if (strchr(strb,'*')) { /* Model includes a product */
4873: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4874: if (strcmp(strc,"age")==0) { /* Vn*age */
4875: cptcovprod--;
4876: cutv(strb,stre,strd,'V');
4877: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4878: cptcovage++;
4879: Tage[cptcovage]=i;
4880: /*printf("stre=%s ", stre);*/
4881: }
4882: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4883: cptcovprod--;
4884: cutv(strb,stre,strc,'V');
4885: Tvar[i]=atoi(stre);
4886: cptcovage++;
4887: Tage[cptcovage]=i;
4888: }
4889: else { /* Age is not in the model */
4890: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4891: Tvar[i]=ncovcol+k1;
4892: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4893: Tprod[k1]=i;
4894: Tvard[k1][1]=atoi(strc); /* m*/
4895: Tvard[k1][2]=atoi(stre); /* n */
4896: Tvar[cptcovn+k2]=Tvard[k1][1];
4897: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4898: for (k=1; k<=lastobs;k++)
4899: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4900: k1++;
4901: k2=k2+2;
4902: }
4903: }
4904: else { /* no more sum */
4905: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4906: /* scanf("%d",i);*/
4907: cutv(strd,strc,strb,'V');
4908: Tvar[i]=atoi(strc);
4909: }
4910: strcpy(modelsav,stra);
4911: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4912: scanf("%d",i);*/
4913: } /* end of loop + */
4914: } /* end model */
4915:
4916: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4917: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4918:
4919: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4920: printf("cptcovprod=%d ", cptcovprod);
4921: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4922:
4923: scanf("%d ",i);*/
4924:
4925: /* if(mle==1){*/
4926: if (weightopt != 1) { /* Maximisation without weights*/
4927: for(i=1;i<=n;i++) weight[i]=1.0;
4928: }
4929: /*-calculation of age at interview from date of interview and age at death -*/
4930: agev=matrix(1,maxwav,1,imx);
4931:
4932: for (i=1; i<=imx; i++) {
4933: for(m=2; (m<= maxwav); m++) {
4934: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4935: anint[m][i]=9999;
4936: s[m][i]=-1;
4937: }
4938: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4939: nberr++;
4940: 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);
4941: 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);
4942: s[m][i]=-1;
4943: }
4944: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4945: nberr++;
4946: 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]);
4947: 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]);
4948: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4949: }
4950: }
4951: }
4952:
4953: for (i=1; i<=imx; i++) {
4954: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4955: for(m=firstpass; (m<= lastpass); m++){
4956: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4957: if (s[m][i] >= nlstate+1) {
4958: if(agedc[i]>0)
4959: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4960: agev[m][i]=agedc[i];
4961: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4962: else {
4963: if ((int)andc[i]!=9999){
4964: nbwarn++;
4965: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4966: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4967: agev[m][i]=-1;
4968: }
4969: }
4970: }
4971: else if(s[m][i] !=9){ /* Standard case, age in fractional
4972: years but with the precision of a month */
4973: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4974: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4975: agev[m][i]=1;
4976: else if(agev[m][i] <agemin){
4977: agemin=agev[m][i];
4978: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4979: }
4980: else if(agev[m][i] >agemax){
4981: agemax=agev[m][i];
4982: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4983: }
4984: /*agev[m][i]=anint[m][i]-annais[i];*/
4985: /* agev[m][i] = age[i]+2*m;*/
4986: }
4987: else { /* =9 */
4988: agev[m][i]=1;
4989: s[m][i]=-1;
4990: }
4991: }
4992: else /*= 0 Unknown */
4993: agev[m][i]=1;
4994: }
4995:
4996: }
4997: for (i=1; i<=imx; i++) {
4998: for(m=firstpass; (m<=lastpass); m++){
4999: if (s[m][i] > (nlstate+ndeath)) {
5000: nberr++;
5001: 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);
5002: 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);
5003: goto end;
5004: }
5005: }
5006: }
5007:
5008: /*for (i=1; i<=imx; i++){
5009: for (m=firstpass; (m<lastpass); m++){
5010: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5011: }
5012:
5013: }*/
5014:
5015:
5016: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5017: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5018:
5019: agegomp=(int)agemin;
5020: free_vector(severity,1,maxwav);
5021: free_imatrix(outcome,1,maxwav+1,1,n);
5022: free_vector(moisnais,1,n);
5023: free_vector(annais,1,n);
5024: /* free_matrix(mint,1,maxwav,1,n);
5025: free_matrix(anint,1,maxwav,1,n);*/
5026: free_vector(moisdc,1,n);
5027: free_vector(andc,1,n);
5028:
5029:
5030: wav=ivector(1,imx);
5031: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5032: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5033: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5034:
5035: /* Concatenates waves */
5036: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5037:
5038: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5039:
5040: Tcode=ivector(1,100);
5041: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5042: ncodemax[1]=1;
5043: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5044:
5045: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5046: the estimations*/
5047: h=0;
5048: m=pow(2,cptcoveff);
5049:
5050: for(k=1;k<=cptcoveff; k++){
5051: for(i=1; i <=(m/pow(2,k));i++){
5052: for(j=1; j <= ncodemax[k]; j++){
5053: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5054: h++;
5055: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5056: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5057: }
5058: }
5059: }
5060: }
5061: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5062: codtab[1][2]=1;codtab[2][2]=2; */
5063: /* for(i=1; i <=m ;i++){
5064: for(k=1; k <=cptcovn; k++){
5065: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5066: }
5067: printf("\n");
5068: }
5069: scanf("%d",i);*/
5070:
5071: /*------------ gnuplot -------------*/
5072: strcpy(optionfilegnuplot,optionfilefiname);
5073: if(mle==-3)
5074: strcat(optionfilegnuplot,"-mort");
5075: strcat(optionfilegnuplot,".gp");
5076:
5077: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5078: printf("Problem with file %s",optionfilegnuplot);
5079: }
5080: else{
5081: fprintf(ficgp,"\n# %s\n", version);
5082: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5083: fprintf(ficgp,"set missing 'NaNq'\n");
5084: }
5085: /* fclose(ficgp);*/
5086: /*--------- index.htm --------*/
5087:
5088: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5089: if(mle==-3)
5090: strcat(optionfilehtm,"-mort");
5091: strcat(optionfilehtm,".htm");
5092: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5093: printf("Problem with %s \n",optionfilehtm), exit(0);
5094: }
5095:
5096: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5097: strcat(optionfilehtmcov,"-cov.htm");
5098: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5099: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5100: }
5101: else{
5102: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5103: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5104: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5105: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5106: }
5107:
5108: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
5109: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5110: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5111: \n\
5112: <hr size=\"2\" color=\"#EC5E5E\">\
5113: <ul><li><h4>Parameter files</h4>\n\
5114: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5115: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5116: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5117: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5118: - Date and time at start: %s</ul>\n",\
5119: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5120: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5121: fileres,fileres,\
5122: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5123: fflush(fichtm);
5124:
5125: strcpy(pathr,path);
5126: strcat(pathr,optionfilefiname);
5127: chdir(optionfilefiname); /* Move to directory named optionfile */
5128:
5129: /* Calculates basic frequencies. Computes observed prevalence at single age
5130: and prints on file fileres'p'. */
5131: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5132:
5133: fprintf(fichtm,"\n");
5134: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5135: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5136: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5137: imx,agemin,agemax,jmin,jmax,jmean);
5138: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5139: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5140: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5141: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5142: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5143:
5144:
5145: /* For Powell, parameters are in a vector p[] starting at p[1]
5146: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5147: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5148:
5149: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5150:
5151: if (mle==-3){
5152: ximort=matrix(1,NDIM,1,NDIM);
5153: cens=ivector(1,n);
5154: ageexmed=vector(1,n);
5155: agecens=vector(1,n);
5156: dcwave=ivector(1,n);
5157:
5158: for (i=1; i<=imx; i++){
5159: dcwave[i]=-1;
5160: for (m=firstpass; m<=lastpass; m++)
5161: if (s[m][i]>nlstate) {
5162: dcwave[i]=m;
5163: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5164: break;
5165: }
5166: }
5167:
5168: for (i=1; i<=imx; i++) {
5169: if (wav[i]>0){
5170: ageexmed[i]=agev[mw[1][i]][i];
5171: j=wav[i];
5172: agecens[i]=1.;
5173:
5174: if (ageexmed[i]> 1 && wav[i] > 0){
5175: agecens[i]=agev[mw[j][i]][i];
5176: cens[i]= 1;
5177: }else if (ageexmed[i]< 1)
5178: cens[i]= -1;
5179: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5180: cens[i]=0 ;
5181: }
5182: else cens[i]=-1;
5183: }
5184:
5185: for (i=1;i<=NDIM;i++) {
5186: for (j=1;j<=NDIM;j++)
5187: ximort[i][j]=(i == j ? 1.0 : 0.0);
5188: }
5189:
5190: p[1]=0.0268; p[NDIM]=0.083;
5191: /*printf("%lf %lf", p[1], p[2]);*/
5192:
5193:
5194: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5195: strcpy(filerespow,"pow-mort");
5196: strcat(filerespow,fileres);
5197: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5198: printf("Problem with resultfile: %s\n", filerespow);
5199: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5200: }
5201: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5202: /* for (i=1;i<=nlstate;i++)
5203: for(j=1;j<=nlstate+ndeath;j++)
5204: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5205: */
5206: fprintf(ficrespow,"\n");
5207:
5208: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5209: fclose(ficrespow);
5210:
5211: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5212:
5213: for(i=1; i <=NDIM; i++)
5214: for(j=i+1;j<=NDIM;j++)
5215: matcov[i][j]=matcov[j][i];
5216:
5217: printf("\nCovariance matrix\n ");
5218: for(i=1; i <=NDIM; i++) {
5219: for(j=1;j<=NDIM;j++){
5220: printf("%f ",matcov[i][j]);
5221: }
5222: printf("\n ");
5223: }
5224:
5225: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5226: for (i=1;i<=NDIM;i++)
5227: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5228:
5229: lsurv=vector(1,AGESUP);
5230: lpop=vector(1,AGESUP);
5231: tpop=vector(1,AGESUP);
5232: lsurv[agegomp]=100000;
5233:
5234: for (k=agegomp;k<=AGESUP;k++) {
5235: agemortsup=k;
5236: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5237: }
5238:
5239: for (k=agegomp;k<agemortsup;k++)
5240: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5241:
5242: for (k=agegomp;k<agemortsup;k++){
5243: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5244: sumlpop=sumlpop+lpop[k];
5245: }
5246:
5247: tpop[agegomp]=sumlpop;
5248: for (k=agegomp;k<(agemortsup-3);k++){
5249: /* tpop[k+1]=2;*/
5250: tpop[k+1]=tpop[k]-lpop[k];
5251: }
5252:
5253:
5254: printf("\nAge lx qx dx Lx Tx e(x)\n");
5255: for (k=agegomp;k<(agemortsup-2);k++)
5256: 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]);
5257:
5258:
5259: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5260: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5261:
5262: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5263: stepm, weightopt,\
5264: model,imx,p,matcov,agemortsup);
5265:
5266: free_vector(lsurv,1,AGESUP);
5267: free_vector(lpop,1,AGESUP);
5268: free_vector(tpop,1,AGESUP);
5269: } /* Endof if mle==-3 */
5270:
5271: else{ /* For mle >=1 */
5272:
5273: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5274: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5275: for (k=1; k<=npar;k++)
5276: printf(" %d %8.5f",k,p[k]);
5277: printf("\n");
5278: globpr=1; /* to print the contributions */
5279: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5280: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5281: for (k=1; k<=npar;k++)
5282: printf(" %d %8.5f",k,p[k]);
5283: printf("\n");
5284: if(mle>=1){ /* Could be 1 or 2 */
5285: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5286: }
5287:
5288: /*--------- results files --------------*/
5289: 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);
5290:
5291:
5292: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5293: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5294: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5295: for(i=1,jk=1; i <=nlstate; i++){
5296: for(k=1; k <=(nlstate+ndeath); k++){
5297: if (k != i) {
5298: printf("%d%d ",i,k);
5299: fprintf(ficlog,"%d%d ",i,k);
5300: fprintf(ficres,"%1d%1d ",i,k);
5301: for(j=1; j <=ncovmodel; j++){
5302: printf("%f ",p[jk]);
5303: fprintf(ficlog,"%f ",p[jk]);
5304: fprintf(ficres,"%f ",p[jk]);
5305: jk++;
5306: }
5307: printf("\n");
5308: fprintf(ficlog,"\n");
5309: fprintf(ficres,"\n");
5310: }
5311: }
5312: }
5313: if(mle!=0){
5314: /* Computing hessian and covariance matrix */
5315: ftolhess=ftol; /* Usually correct */
5316: hesscov(matcov, p, npar, delti, ftolhess, func);
5317: }
5318: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5319: printf("# Scales (for hessian or gradient estimation)\n");
5320: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5321: for(i=1,jk=1; i <=nlstate; i++){
5322: for(j=1; j <=nlstate+ndeath; j++){
5323: if (j!=i) {
5324: fprintf(ficres,"%1d%1d",i,j);
5325: printf("%1d%1d",i,j);
5326: fprintf(ficlog,"%1d%1d",i,j);
5327: for(k=1; k<=ncovmodel;k++){
5328: printf(" %.5e",delti[jk]);
5329: fprintf(ficlog," %.5e",delti[jk]);
5330: fprintf(ficres," %.5e",delti[jk]);
5331: jk++;
5332: }
5333: printf("\n");
5334: fprintf(ficlog,"\n");
5335: fprintf(ficres,"\n");
5336: }
5337: }
5338: }
5339:
5340: 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");
5341: if(mle>=1)
5342: 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");
5343: 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");
5344: /* # 121 Var(a12)\n\ */
5345: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5346: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5347: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5348: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5349: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5350: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5351: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5352:
5353:
5354: /* Just to have a covariance matrix which will be more understandable
5355: even is we still don't want to manage dictionary of variables
5356: */
5357: for(itimes=1;itimes<=2;itimes++){
5358: jj=0;
5359: for(i=1; i <=nlstate; i++){
5360: for(j=1; j <=nlstate+ndeath; j++){
5361: if(j==i) continue;
5362: for(k=1; k<=ncovmodel;k++){
5363: jj++;
5364: ca[0]= k+'a'-1;ca[1]='\0';
5365: if(itimes==1){
5366: if(mle>=1)
5367: printf("#%1d%1d%d",i,j,k);
5368: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5369: fprintf(ficres,"#%1d%1d%d",i,j,k);
5370: }else{
5371: if(mle>=1)
5372: printf("%1d%1d%d",i,j,k);
5373: fprintf(ficlog,"%1d%1d%d",i,j,k);
5374: fprintf(ficres,"%1d%1d%d",i,j,k);
5375: }
5376: ll=0;
5377: for(li=1;li <=nlstate; li++){
5378: for(lj=1;lj <=nlstate+ndeath; lj++){
5379: if(lj==li) continue;
5380: for(lk=1;lk<=ncovmodel;lk++){
5381: ll++;
5382: if(ll<=jj){
5383: cb[0]= lk +'a'-1;cb[1]='\0';
5384: if(ll<jj){
5385: if(itimes==1){
5386: if(mle>=1)
5387: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5388: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5389: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5390: }else{
5391: if(mle>=1)
5392: printf(" %.5e",matcov[jj][ll]);
5393: fprintf(ficlog," %.5e",matcov[jj][ll]);
5394: fprintf(ficres," %.5e",matcov[jj][ll]);
5395: }
5396: }else{
5397: if(itimes==1){
5398: if(mle>=1)
5399: printf(" Var(%s%1d%1d)",ca,i,j);
5400: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5401: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5402: }else{
5403: if(mle>=1)
5404: printf(" %.5e",matcov[jj][ll]);
5405: fprintf(ficlog," %.5e",matcov[jj][ll]);
5406: fprintf(ficres," %.5e",matcov[jj][ll]);
5407: }
5408: }
5409: }
5410: } /* end lk */
5411: } /* end lj */
5412: } /* end li */
5413: if(mle>=1)
5414: printf("\n");
5415: fprintf(ficlog,"\n");
5416: fprintf(ficres,"\n");
5417: numlinepar++;
5418: } /* end k*/
5419: } /*end j */
5420: } /* end i */
5421: } /* end itimes */
5422:
5423: fflush(ficlog);
5424: fflush(ficres);
5425:
5426: while((c=getc(ficpar))=='#' && c!= EOF){
5427: ungetc(c,ficpar);
5428: fgets(line, MAXLINE, ficpar);
5429: puts(line);
5430: fputs(line,ficparo);
5431: }
5432: ungetc(c,ficpar);
5433:
5434: estepm=0;
5435: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5436: if (estepm==0 || estepm < stepm) estepm=stepm;
5437: if (fage <= 2) {
5438: bage = ageminpar;
5439: fage = agemaxpar;
5440: }
5441:
5442: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5443: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5444: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5445:
5446: while((c=getc(ficpar))=='#' && c!= EOF){
5447: ungetc(c,ficpar);
5448: fgets(line, MAXLINE, ficpar);
5449: puts(line);
5450: fputs(line,ficparo);
5451: }
5452: ungetc(c,ficpar);
5453:
5454: 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);
5455: 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);
5456: 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);
5457: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5458: 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);
5459:
5460: while((c=getc(ficpar))=='#' && c!= EOF){
5461: ungetc(c,ficpar);
5462: fgets(line, MAXLINE, ficpar);
5463: puts(line);
5464: fputs(line,ficparo);
5465: }
5466: ungetc(c,ficpar);
5467:
5468:
5469: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5470: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5471:
5472: fscanf(ficpar,"pop_based=%d\n",&popbased);
5473: fprintf(ficparo,"pop_based=%d\n",popbased);
5474: fprintf(ficres,"pop_based=%d\n",popbased);
5475:
5476: while((c=getc(ficpar))=='#' && c!= EOF){
5477: ungetc(c,ficpar);
5478: fgets(line, MAXLINE, ficpar);
5479: puts(line);
5480: fputs(line,ficparo);
5481: }
5482: ungetc(c,ficpar);
5483:
5484: 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);
5485: 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);
5486: 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);
5487: 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);
5488: 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);
5489: /* day and month of proj2 are not used but only year anproj2.*/
5490:
5491:
5492:
5493: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5494: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5495:
5496: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5497: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5498:
5499: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5500: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5501: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5502:
5503: /*------------ free_vector -------------*/
5504: /* chdir(path); */
5505:
5506: free_ivector(wav,1,imx);
5507: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5508: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5509: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5510: free_lvector(num,1,n);
5511: free_vector(agedc,1,n);
5512: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5513: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5514: fclose(ficparo);
5515: fclose(ficres);
5516:
5517:
5518: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5519:
5520: strcpy(filerespl,"pl");
5521: strcat(filerespl,fileres);
5522: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5523: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5524: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5525: }
5526: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5527: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5528: pstamp(ficrespl);
5529: fprintf(ficrespl,"# Period (stable) prevalence \n");
5530: fprintf(ficrespl,"#Age ");
5531: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5532: fprintf(ficrespl,"\n");
5533:
5534: prlim=matrix(1,nlstate,1,nlstate);
5535:
5536: agebase=ageminpar;
5537: agelim=agemaxpar;
5538: ftolpl=1.e-10;
5539: i1=cptcoveff;
5540: if (cptcovn < 1){i1=1;}
5541:
5542: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5543: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5544: k=k+1;
5545: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5546: fprintf(ficrespl,"\n#******");
5547: printf("\n#******");
5548: fprintf(ficlog,"\n#******");
5549: for(j=1;j<=cptcoveff;j++) {
5550: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5551: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5552: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5553: }
5554: fprintf(ficrespl,"******\n");
5555: printf("******\n");
5556: fprintf(ficlog,"******\n");
5557:
5558: for (age=agebase; age<=agelim; age++){
5559: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5560: fprintf(ficrespl,"%.0f ",age );
5561: for(j=1;j<=cptcoveff;j++)
5562: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5563: for(i=1; i<=nlstate;i++)
5564: fprintf(ficrespl," %.5f", prlim[i][i]);
5565: fprintf(ficrespl,"\n");
5566: }
5567: }
5568: }
5569: fclose(ficrespl);
5570:
5571: /*------------- h Pij x at various ages ------------*/
5572:
5573: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5574: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5575: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5576: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5577: }
5578: printf("Computing pij: result on file '%s' \n", filerespij);
5579: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5580:
5581: stepsize=(int) (stepm+YEARM-1)/YEARM;
5582: /*if (stepm<=24) stepsize=2;*/
5583:
5584: agelim=AGESUP;
5585: hstepm=stepsize*YEARM; /* Every year of age */
5586: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5587:
5588: /* hstepm=1; aff par mois*/
5589: pstamp(ficrespij);
5590: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5591: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5592: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5593: k=k+1;
5594: fprintf(ficrespij,"\n#****** ");
5595: for(j=1;j<=cptcoveff;j++)
5596: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5597: fprintf(ficrespij,"******\n");
5598:
5599: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5600: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5601: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5602:
5603: /* nhstepm=nhstepm*YEARM; aff par mois*/
5604:
5605: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5606: oldm=oldms;savm=savms;
5607: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5608: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5609: for(i=1; i<=nlstate;i++)
5610: for(j=1; j<=nlstate+ndeath;j++)
5611: fprintf(ficrespij," %1d-%1d",i,j);
5612: fprintf(ficrespij,"\n");
5613: for (h=0; h<=nhstepm; h++){
5614: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5615: for(i=1; i<=nlstate;i++)
5616: for(j=1; j<=nlstate+ndeath;j++)
5617: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5618: fprintf(ficrespij,"\n");
5619: }
5620: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5621: fprintf(ficrespij,"\n");
5622: }
5623: }
5624: }
5625:
5626: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5627:
5628: fclose(ficrespij);
5629:
5630: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5631: for(i=1;i<=AGESUP;i++)
5632: for(j=1;j<=NCOVMAX;j++)
5633: for(k=1;k<=NCOVMAX;k++)
5634: probs[i][j][k]=0.;
5635:
5636: /*---------- Forecasting ------------------*/
5637: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5638: if(prevfcast==1){
5639: /* if(stepm ==1){*/
5640: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5641: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5642: /* } */
5643: /* else{ */
5644: /* erreur=108; */
5645: /* 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); */
5646: /* 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); */
5647: /* } */
5648: }
5649:
5650:
5651: /*---------- Health expectancies and variances ------------*/
5652:
5653: strcpy(filerest,"t");
5654: strcat(filerest,fileres);
5655: if((ficrest=fopen(filerest,"w"))==NULL) {
5656: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5657: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5658: }
5659: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5660: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5661:
5662:
5663: strcpy(filerese,"e");
5664: strcat(filerese,fileres);
5665: if((ficreseij=fopen(filerese,"w"))==NULL) {
5666: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5667: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5668: }
5669: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5670: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5671:
5672: strcpy(fileresstde,"stde");
5673: strcat(fileresstde,fileres);
5674: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5675: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5676: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5677: }
5678: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5679: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5680:
5681: strcpy(filerescve,"cve");
5682: strcat(filerescve,fileres);
5683: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5684: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5685: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5686: }
5687: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5688: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5689:
5690: strcpy(fileresv,"v");
5691: strcat(fileresv,fileres);
5692: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5693: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5694: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5695: }
5696: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5697: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5698:
5699: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5700: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5701: /* 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",\
5702: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5703: */
5704:
5705: if (mobilav!=0) {
5706: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5707: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5708: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5709: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5710: }
5711: }
5712:
5713: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5714: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5715: k=k+1;
5716: fprintf(ficrest,"\n#****** ");
5717: for(j=1;j<=cptcoveff;j++)
5718: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5719: fprintf(ficrest,"******\n");
5720:
5721: fprintf(ficreseij,"\n#****** ");
5722: fprintf(ficresstdeij,"\n#****** ");
5723: fprintf(ficrescveij,"\n#****** ");
5724: for(j=1;j<=cptcoveff;j++) {
5725: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5726: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5727: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5728: }
5729: fprintf(ficreseij,"******\n");
5730: fprintf(ficresstdeij,"******\n");
5731: fprintf(ficrescveij,"******\n");
5732:
5733: fprintf(ficresvij,"\n#****** ");
5734: for(j=1;j<=cptcoveff;j++)
5735: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5736: fprintf(ficresvij,"******\n");
5737:
5738: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5739: oldm=oldms;savm=savms;
5740: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5741: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5742:
5743: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5744: oldm=oldms;savm=savms;
5745: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5746: if(popbased==1){
5747: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5748: }
5749:
5750: pstamp(ficrest);
5751: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state ( e.. (std) ");
5752: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5753: fprintf(ficrest,"\n");
5754:
5755: epj=vector(1,nlstate+1);
5756: for(age=bage; age <=fage ;age++){
5757: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5758: if (popbased==1) {
5759: if(mobilav ==0){
5760: for(i=1; i<=nlstate;i++)
5761: prlim[i][i]=probs[(int)age][i][k];
5762: }else{ /* mobilav */
5763: for(i=1; i<=nlstate;i++)
5764: prlim[i][i]=mobaverage[(int)age][i][k];
5765: }
5766: }
5767:
5768: fprintf(ficrest," %4.0f",age);
5769: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5770: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5771: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5772: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5773: }
5774: epj[nlstate+1] +=epj[j];
5775: }
5776:
5777: for(i=1, vepp=0.;i <=nlstate;i++)
5778: for(j=1;j <=nlstate;j++)
5779: vepp += vareij[i][j][(int)age];
5780: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5781: for(j=1;j <=nlstate;j++){
5782: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5783: }
5784: fprintf(ficrest,"\n");
5785: }
5786: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5787: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5788: free_vector(epj,1,nlstate+1);
5789: }
5790: }
5791: free_vector(weight,1,n);
5792: free_imatrix(Tvard,1,15,1,2);
5793: free_imatrix(s,1,maxwav+1,1,n);
5794: free_matrix(anint,1,maxwav,1,n);
5795: free_matrix(mint,1,maxwav,1,n);
5796: free_ivector(cod,1,n);
5797: free_ivector(tab,1,NCOVMAX);
5798: fclose(ficreseij);
5799: fclose(ficresstdeij);
5800: fclose(ficrescveij);
5801: fclose(ficresvij);
5802: fclose(ficrest);
5803: fclose(ficpar);
5804:
5805: /*------- Variance of period (stable) prevalence------*/
5806:
5807: strcpy(fileresvpl,"vpl");
5808: strcat(fileresvpl,fileres);
5809: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5810: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5811: exit(0);
5812: }
5813: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5814:
5815: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5816: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5817: k=k+1;
5818: fprintf(ficresvpl,"\n#****** ");
5819: for(j=1;j<=cptcoveff;j++)
5820: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5821: fprintf(ficresvpl,"******\n");
5822:
5823: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5824: oldm=oldms;savm=savms;
5825: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5826: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5827: }
5828: }
5829:
5830: fclose(ficresvpl);
5831:
5832: /*---------- End : free ----------------*/
5833: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5834: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5835:
5836: } /* mle==-3 arrives here for freeing */
5837: free_matrix(prlim,1,nlstate,1,nlstate);
5838: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5839: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5840: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5841: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5842: free_matrix(covar,0,NCOVMAX,1,n);
5843: free_matrix(matcov,1,npar,1,npar);
5844: /*free_vector(delti,1,npar);*/
5845: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5846: free_matrix(agev,1,maxwav,1,imx);
5847: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5848:
5849: free_ivector(ncodemax,1,8);
5850: free_ivector(Tvar,1,15);
5851: free_ivector(Tprod,1,15);
5852: free_ivector(Tvaraff,1,15);
5853: free_ivector(Tage,1,15);
5854: free_ivector(Tcode,1,100);
5855:
5856: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5857: free_imatrix(codtab,1,100,1,10);
5858: fflush(fichtm);
5859: fflush(ficgp);
5860:
5861:
5862: if((nberr >0) || (nbwarn>0)){
5863: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5864: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5865: }else{
5866: printf("End of Imach\n");
5867: fprintf(ficlog,"End of Imach\n");
5868: }
5869: printf("See log file on %s\n",filelog);
5870: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5871: (void) gettimeofday(&end_time,&tzp);
5872: tm = *localtime(&end_time.tv_sec);
5873: tmg = *gmtime(&end_time.tv_sec);
5874: strcpy(strtend,asctime(&tm));
5875: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5876: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5877: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5878:
5879: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5880: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5881: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5882: /* printf("Total time was %d uSec.\n", total_usecs);*/
5883: /* if(fileappend(fichtm,optionfilehtm)){ */
5884: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5885: fclose(fichtm);
5886: fclose(fichtmcov);
5887: fclose(ficgp);
5888: fclose(ficlog);
5889: /*------ End -----------*/
5890:
5891: chdir(path);
5892: /*strcat(plotcmd,CHARSEPARATOR);*/
5893: sprintf(plotcmd,"gnuplot");
5894: #ifndef UNIX
5895: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5896: #endif
5897: if(!stat(plotcmd,&info)){
5898: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5899: if(!stat(getenv("GNUPLOTBIN"),&info)){
5900: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5901: }else
5902: strcpy(pplotcmd,plotcmd);
5903: #ifdef UNIX
5904: strcpy(plotcmd,GNUPLOTPROGRAM);
5905: if(!stat(plotcmd,&info)){
5906: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5907: }else
5908: strcpy(pplotcmd,plotcmd);
5909: #endif
5910: }else
5911: strcpy(pplotcmd,plotcmd);
5912:
5913: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5914: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5915:
5916: if((outcmd=system(plotcmd)) != 0){
5917: printf("\n Problem with gnuplot\n");
5918: }
5919: printf(" Wait...");
5920: while (z[0] != 'q') {
5921: /* chdir(path); */
5922: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5923: scanf("%s",z);
5924: /* if (z[0] == 'c') system("./imach"); */
5925: if (z[0] == 'e') {
5926: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5927: system(optionfilehtm);
5928: }
5929: else if (z[0] == 'g') system(plotcmd);
5930: else if (z[0] == 'q') exit(0);
5931: }
5932: end:
5933: while (z[0] != 'q') {
5934: printf("\nType q for exiting: ");
5935: scanf("%s",z);
5936: }
5937: }
5938:
5939:
5940:
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