1: /* $Id: imach.c,v 1.130 2009/05/26 06:44:34 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.130 2009/05/26 06:44:34 brouard
5: (Module): Max Covariate is now set to 20 instead of 8. A
6: lot of cleaning with variables initialized to 0. Trying to make
7: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
8:
9: Revision 1.129 2007/08/31 13:49:27 lievre
10: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
11:
12: Revision 1.128 2006/06/30 13:02:05 brouard
13: (Module): Clarifications on computing e.j
14:
15: Revision 1.127 2006/04/28 18:11:50 brouard
16: (Module): Yes the sum of survivors was wrong since
17: imach-114 because nhstepm was no more computed in the age
18: loop. Now we define nhstepma in the age loop.
19: (Module): In order to speed up (in case of numerous covariates) we
20: compute health expectancies (without variances) in a first step
21: and then all the health expectancies with variances or standard
22: deviation (needs data from the Hessian matrices) which slows the
23: computation.
24: In the future we should be able to stop the program is only health
25: expectancies and graph are needed without standard deviations.
26:
27: Revision 1.126 2006/04/28 17:23:28 brouard
28: (Module): Yes the sum of survivors was wrong since
29: imach-114 because nhstepm was no more computed in the age
30: loop. Now we define nhstepma in the age loop.
31: Version 0.98h
32:
33: Revision 1.125 2006/04/04 15:20:31 lievre
34: Errors in calculation of health expectancies. Age was not initialized.
35: Forecasting file added.
36:
37: Revision 1.124 2006/03/22 17:13:53 lievre
38: Parameters are printed with %lf instead of %f (more numbers after the comma).
39: The log-likelihood is printed in the log file
40:
41: Revision 1.123 2006/03/20 10:52:43 brouard
42: * imach.c (Module): <title> changed, corresponds to .htm file
43: name. <head> headers where missing.
44:
45: * imach.c (Module): Weights can have a decimal point as for
46: English (a comma might work with a correct LC_NUMERIC environment,
47: otherwise the weight is truncated).
48: Modification of warning when the covariates values are not 0 or
49: 1.
50: Version 0.98g
51:
52: Revision 1.122 2006/03/20 09:45:41 brouard
53: (Module): Weights can have a decimal point as for
54: English (a comma might work with a correct LC_NUMERIC environment,
55: otherwise the weight is truncated).
56: Modification of warning when the covariates values are not 0 or
57: 1.
58: Version 0.98g
59:
60: Revision 1.121 2006/03/16 17:45:01 lievre
61: * imach.c (Module): Comments concerning covariates added
62:
63: * imach.c (Module): refinements in the computation of lli if
64: status=-2 in order to have more reliable computation if stepm is
65: not 1 month. Version 0.98f
66:
67: Revision 1.120 2006/03/16 15:10:38 lievre
68: (Module): refinements in the computation of lli if
69: status=-2 in order to have more reliable computation if stepm is
70: not 1 month. Version 0.98f
71:
72: Revision 1.119 2006/03/15 17:42:26 brouard
73: (Module): Bug if status = -2, the loglikelihood was
74: computed as likelihood omitting the logarithm. Version O.98e
75:
76: Revision 1.118 2006/03/14 18:20:07 brouard
77: (Module): varevsij Comments added explaining the second
78: table of variances if popbased=1 .
79: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
80: (Module): Function pstamp added
81: (Module): Version 0.98d
82:
83: Revision 1.117 2006/03/14 17:16:22 brouard
84: (Module): varevsij Comments added explaining the second
85: table of variances if popbased=1 .
86: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
87: (Module): Function pstamp added
88: (Module): Version 0.98d
89:
90: Revision 1.116 2006/03/06 10:29:27 brouard
91: (Module): Variance-covariance wrong links and
92: varian-covariance of ej. is needed (Saito).
93:
94: Revision 1.115 2006/02/27 12:17:45 brouard
95: (Module): One freematrix added in mlikeli! 0.98c
96:
97: Revision 1.114 2006/02/26 12:57:58 brouard
98: (Module): Some improvements in processing parameter
99: filename with strsep.
100:
101: Revision 1.113 2006/02/24 14:20:24 brouard
102: (Module): Memory leaks checks with valgrind and:
103: datafile was not closed, some imatrix were not freed and on matrix
104: allocation too.
105:
106: Revision 1.112 2006/01/30 09:55:26 brouard
107: (Module): Back to gnuplot.exe instead of wgnuplot.exe
108:
109: Revision 1.111 2006/01/25 20:38:18 brouard
110: (Module): Lots of cleaning and bugs added (Gompertz)
111: (Module): Comments can be added in data file. Missing date values
112: can be a simple dot '.'.
113:
114: Revision 1.110 2006/01/25 00:51:50 brouard
115: (Module): Lots of cleaning and bugs added (Gompertz)
116:
117: Revision 1.109 2006/01/24 19:37:15 brouard
118: (Module): Comments (lines starting with a #) are allowed in data.
119:
120: Revision 1.108 2006/01/19 18:05:42 lievre
121: Gnuplot problem appeared...
122: To be fixed
123:
124: Revision 1.107 2006/01/19 16:20:37 brouard
125: Test existence of gnuplot in imach path
126:
127: Revision 1.106 2006/01/19 13:24:36 brouard
128: Some cleaning and links added in html output
129:
130: Revision 1.105 2006/01/05 20:23:19 lievre
131: *** empty log message ***
132:
133: Revision 1.104 2005/09/30 16:11:43 lievre
134: (Module): sump fixed, loop imx fixed, and simplifications.
135: (Module): If the status is missing at the last wave but we know
136: that the person is alive, then we can code his/her status as -2
137: (instead of missing=-1 in earlier versions) and his/her
138: contributions to the likelihood is 1 - Prob of dying from last
139: health status (= 1-p13= p11+p12 in the easiest case of somebody in
140: the healthy state at last known wave). Version is 0.98
141:
142: Revision 1.103 2005/09/30 15:54:49 lievre
143: (Module): sump fixed, loop imx fixed, and simplifications.
144:
145: Revision 1.102 2004/09/15 17:31:30 brouard
146: Add the possibility to read data file including tab characters.
147:
148: Revision 1.101 2004/09/15 10:38:38 brouard
149: Fix on curr_time
150:
151: Revision 1.100 2004/07/12 18:29:06 brouard
152: Add version for Mac OS X. Just define UNIX in Makefile
153:
154: Revision 1.99 2004/06/05 08:57:40 brouard
155: *** empty log message ***
156:
157: Revision 1.98 2004/05/16 15:05:56 brouard
158: New version 0.97 . First attempt to estimate force of mortality
159: directly from the data i.e. without the need of knowing the health
160: state at each age, but using a Gompertz model: log u =a + b*age .
161: This is the basic analysis of mortality and should be done before any
162: other analysis, in order to test if the mortality estimated from the
163: cross-longitudinal survey is different from the mortality estimated
164: from other sources like vital statistic data.
165:
166: The same imach parameter file can be used but the option for mle should be -3.
167:
168: Agnès, who wrote this part of the code, tried to keep most of the
169: former routines in order to include the new code within the former code.
170:
171: The output is very simple: only an estimate of the intercept and of
172: the slope with 95% confident intervals.
173:
174: Current limitations:
175: A) Even if you enter covariates, i.e. with the
176: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
177: B) There is no computation of Life Expectancy nor Life Table.
178:
179: Revision 1.97 2004/02/20 13:25:42 lievre
180: Version 0.96d. Population forecasting command line is (temporarily)
181: suppressed.
182:
183: Revision 1.96 2003/07/15 15:38:55 brouard
184: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
185: rewritten within the same printf. Workaround: many printfs.
186:
187: Revision 1.95 2003/07/08 07:54:34 brouard
188: * imach.c (Repository):
189: (Repository): Using imachwizard code to output a more meaningful covariance
190: matrix (cov(a12,c31) instead of numbers.
191:
192: Revision 1.94 2003/06/27 13:00:02 brouard
193: Just cleaning
194:
195: Revision 1.93 2003/06/25 16:33:55 brouard
196: (Module): On windows (cygwin) function asctime_r doesn't
197: exist so I changed back to asctime which exists.
198: (Module): Version 0.96b
199:
200: Revision 1.92 2003/06/25 16:30:45 brouard
201: (Module): On windows (cygwin) function asctime_r doesn't
202: exist so I changed back to asctime which exists.
203:
204: Revision 1.91 2003/06/25 15:30:29 brouard
205: * imach.c (Repository): Duplicated warning errors corrected.
206: (Repository): Elapsed time after each iteration is now output. It
207: helps to forecast when convergence will be reached. Elapsed time
208: is stamped in powell. We created a new html file for the graphs
209: concerning matrix of covariance. It has extension -cov.htm.
210:
211: Revision 1.90 2003/06/24 12:34:15 brouard
212: (Module): Some bugs corrected for windows. Also, when
213: mle=-1 a template is output in file "or"mypar.txt with the design
214: of the covariance matrix to be input.
215:
216: Revision 1.89 2003/06/24 12:30:52 brouard
217: (Module): Some bugs corrected for windows. Also, when
218: mle=-1 a template is output in file "or"mypar.txt with the design
219: of the covariance matrix to be input.
220:
221: Revision 1.88 2003/06/23 17:54:56 brouard
222: * 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.
223:
224: Revision 1.87 2003/06/18 12:26:01 brouard
225: Version 0.96
226:
227: Revision 1.86 2003/06/17 20:04:08 brouard
228: (Module): Change position of html and gnuplot routines and added
229: routine fileappend.
230:
231: Revision 1.85 2003/06/17 13:12:43 brouard
232: * imach.c (Repository): Check when date of death was earlier that
233: current date of interview. It may happen when the death was just
234: prior to the death. In this case, dh was negative and likelihood
235: was wrong (infinity). We still send an "Error" but patch by
236: assuming that the date of death was just one stepm after the
237: interview.
238: (Repository): Because some people have very long ID (first column)
239: we changed int to long in num[] and we added a new lvector for
240: memory allocation. But we also truncated to 8 characters (left
241: truncation)
242: (Repository): No more line truncation errors.
243:
244: Revision 1.84 2003/06/13 21:44:43 brouard
245: * imach.c (Repository): Replace "freqsummary" at a correct
246: place. It differs from routine "prevalence" which may be called
247: many times. Probs is memory consuming and must be used with
248: parcimony.
249: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
250:
251: Revision 1.83 2003/06/10 13:39:11 lievre
252: *** empty log message ***
253:
254: Revision 1.82 2003/06/05 15:57:20 brouard
255: Add log in imach.c and fullversion number is now printed.
256:
257: */
258: /*
259: Interpolated Markov Chain
260:
261: Short summary of the programme:
262:
263: This program computes Healthy Life Expectancies from
264: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
265: first survey ("cross") where individuals from different ages are
266: interviewed on their health status or degree of disability (in the
267: case of a health survey which is our main interest) -2- at least a
268: second wave of interviews ("longitudinal") which measure each change
269: (if any) in individual health status. Health expectancies are
270: computed from the time spent in each health state according to a
271: model. More health states you consider, more time is necessary to reach the
272: Maximum Likelihood of the parameters involved in the model. The
273: simplest model is the multinomial logistic model where pij is the
274: probability to be observed in state j at the second wave
275: conditional to be observed in state i at the first wave. Therefore
276: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
277: 'age' is age and 'sex' is a covariate. If you want to have a more
278: complex model than "constant and age", you should modify the program
279: where the markup *Covariates have to be included here again* invites
280: you to do it. More covariates you add, slower the
281: convergence.
282:
283: The advantage of this computer programme, compared to a simple
284: multinomial logistic model, is clear when the delay between waves is not
285: identical for each individual. Also, if a individual missed an
286: intermediate interview, the information is lost, but taken into
287: account using an interpolation or extrapolation.
288:
289: hPijx is the probability to be observed in state i at age x+h
290: conditional to the observed state i at age x. The delay 'h' can be
291: split into an exact number (nh*stepm) of unobserved intermediate
292: states. This elementary transition (by month, quarter,
293: semester or year) is modelled as a multinomial logistic. The hPx
294: matrix is simply the matrix product of nh*stepm elementary matrices
295: and the contribution of each individual to the likelihood is simply
296: hPijx.
297:
298: Also this programme outputs the covariance matrix of the parameters but also
299: of the life expectancies. It also computes the period (stable) prevalence.
300:
301: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
302: Institut national d'études démographiques, Paris.
303: This software have been partly granted by Euro-REVES, a concerted action
304: from the European Union.
305: It is copyrighted identically to a GNU software product, ie programme and
306: software can be distributed freely for non commercial use. Latest version
307: can be accessed at http://euroreves.ined.fr/imach .
308:
309: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
310: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
311:
312: **********************************************************************/
313: /*
314: main
315: read parameterfile
316: read datafile
317: concatwav
318: freqsummary
319: if (mle >= 1)
320: mlikeli
321: print results files
322: if mle==1
323: computes hessian
324: read end of parameter file: agemin, agemax, bage, fage, estepm
325: begin-prev-date,...
326: open gnuplot file
327: open html file
328: period (stable) prevalence
329: for age prevalim()
330: h Pij x
331: variance of p varprob
332: forecasting if prevfcast==1 prevforecast call prevalence()
333: health expectancies
334: Variance-covariance of DFLE
335: prevalence()
336: movingaverage()
337: varevsij()
338: if popbased==1 varevsij(,popbased)
339: total life expectancies
340: Variance of period (stable) prevalence
341: end
342: */
343:
344:
345:
346:
347: #include <math.h>
348: #include <stdio.h>
349: #include <stdlib.h>
350: #include <string.h>
351: #include <unistd.h>
352:
353: #include <limits.h>
354: #include <sys/types.h>
355: #include <sys/stat.h>
356: #include <errno.h>
357: extern int errno;
358:
359: /* #include <sys/time.h> */
360: #include <time.h>
361: #include "timeval.h"
362:
363: /* #include <libintl.h> */
364: /* #define _(String) gettext (String) */
365:
366: #define MAXLINE 256
367:
368: #define GNUPLOTPROGRAM "gnuplot"
369: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
370: #define FILENAMELENGTH 132
371:
372: #define GLOCK_ERROR_NOPATH -1 /* empty path */
373: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
374:
375: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
376: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
377:
378: #define NINTERVMAX 8
379: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
380: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
381: #define NCOVMAX 20 /* Maximum number of covariates */
382: #define MAXN 20000
383: #define YEARM 12. /* Number of months per year */
384: #define AGESUP 130
385: #define AGEBASE 40
386: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
387: #ifdef UNIX
388: #define DIRSEPARATOR '/'
389: #define CHARSEPARATOR "/"
390: #define ODIRSEPARATOR '\\'
391: #else
392: #define DIRSEPARATOR '\\'
393: #define CHARSEPARATOR "\\"
394: #define ODIRSEPARATOR '/'
395: #endif
396:
397: /* $Id: imach.c,v 1.130 2009/05/26 06:44:34 brouard Exp $ */
398: /* $State: Exp $ */
399:
400: char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
401: char fullversion[]="$Revision: 1.130 $ $Date: 2009/05/26 06:44:34 $";
402: char strstart[80];
403: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
404: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
405: int nvar=0;
406: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
407: int npar=NPARMAX;
408: int nlstate=2; /* Number of live states */
409: int ndeath=1; /* Number of dead states */
410: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
411: int popbased=0;
412:
413: int *wav; /* Number of waves for this individuual 0 is possible */
414: int maxwav=0; /* Maxim number of waves */
415: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
416: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
417: int gipmx=0, gsw=0; /* Global variables on the number of contributions
418: to the likelihood and the sum of weights (done by funcone)*/
419: int mle=1, weightopt=0;
420: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
421: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
422: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
423: * wave mi and wave mi+1 is not an exact multiple of stepm. */
424: double jmean=1; /* Mean space between 2 waves */
425: double **oldm, **newm, **savm; /* Working pointers to matrices */
426: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
427: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
428: FILE *ficlog, *ficrespow;
429: int globpr=0; /* Global variable for printing or not */
430: double fretone; /* Only one call to likelihood */
431: long ipmx=0; /* Number of contributions */
432: double sw; /* Sum of weights */
433: char filerespow[FILENAMELENGTH];
434: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
435: FILE *ficresilk;
436: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
437: FILE *ficresprobmorprev;
438: FILE *fichtm, *fichtmcov; /* Html File */
439: FILE *ficreseij;
440: char filerese[FILENAMELENGTH];
441: FILE *ficresstdeij;
442: char fileresstde[FILENAMELENGTH];
443: FILE *ficrescveij;
444: char filerescve[FILENAMELENGTH];
445: FILE *ficresvij;
446: char fileresv[FILENAMELENGTH];
447: FILE *ficresvpl;
448: char fileresvpl[FILENAMELENGTH];
449: char title[MAXLINE];
450: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
451: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
452: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
453: char command[FILENAMELENGTH];
454: int outcmd=0;
455:
456: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
457:
458: char filelog[FILENAMELENGTH]; /* Log file */
459: char filerest[FILENAMELENGTH];
460: char fileregp[FILENAMELENGTH];
461: char popfile[FILENAMELENGTH];
462:
463: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
464:
465: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
466: struct timezone tzp;
467: extern int gettimeofday();
468: struct tm tmg, tm, tmf, *gmtime(), *localtime();
469: long time_value;
470: extern long time();
471: char strcurr[80], strfor[80];
472:
473: char *endptr;
474: long lval;
475: double dval;
476:
477: #define NR_END 1
478: #define FREE_ARG char*
479: #define FTOL 1.0e-10
480:
481: #define NRANSI
482: #define ITMAX 200
483:
484: #define TOL 2.0e-4
485:
486: #define CGOLD 0.3819660
487: #define ZEPS 1.0e-10
488: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
489:
490: #define GOLD 1.618034
491: #define GLIMIT 100.0
492: #define TINY 1.0e-20
493:
494: static double maxarg1,maxarg2;
495: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
496: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
497:
498: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
499: #define rint(a) floor(a+0.5)
500:
501: static double sqrarg;
502: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
503: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
504: int agegomp= AGEGOMP;
505:
506: int imx;
507: int stepm=1;
508: /* Stepm, step in month: minimum step interpolation*/
509:
510: int estepm;
511: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
512:
513: int m,nb;
514: long *num;
515: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
516: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
517: double **pmmij, ***probs;
518: double *ageexmed,*agecens;
519: double dateintmean=0;
520:
521: double *weight;
522: int **s; /* Status */
523: double *agedc, **covar, idx;
524: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
525: double *lsurv, *lpop, *tpop;
526:
527: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
528: double ftolhess; /* Tolerance for computing hessian */
529:
530: /**************** split *************************/
531: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
532: {
533: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
534: the name of the file (name), its extension only (ext) and its first part of the name (finame)
535: */
536: char *ss; /* pointer */
537: int l1, l2; /* length counters */
538:
539: l1 = strlen(path ); /* length of path */
540: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
541: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
542: if ( ss == NULL ) { /* no directory, so determine current directory */
543: strcpy( name, path ); /* we got the fullname name because no directory */
544: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
545: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
546: /* get current working directory */
547: /* extern char* getcwd ( char *buf , int len);*/
548: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
549: return( GLOCK_ERROR_GETCWD );
550: }
551: /* got dirc from getcwd*/
552: printf(" DIRC = %s \n",dirc);
553: } else { /* strip direcotry from path */
554: ss++; /* after this, the filename */
555: l2 = strlen( ss ); /* length of filename */
556: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
557: strcpy( name, ss ); /* save file name */
558: strncpy( dirc, path, l1 - l2 ); /* now the directory */
559: dirc[l1-l2] = 0; /* add zero */
560: printf(" DIRC2 = %s \n",dirc);
561: }
562: /* We add a separator at the end of dirc if not exists */
563: l1 = strlen( dirc ); /* length of directory */
564: if( dirc[l1-1] != DIRSEPARATOR ){
565: dirc[l1] = DIRSEPARATOR;
566: dirc[l1+1] = 0;
567: printf(" DIRC3 = %s \n",dirc);
568: }
569: ss = strrchr( name, '.' ); /* find last / */
570: if (ss >0){
571: ss++;
572: strcpy(ext,ss); /* save extension */
573: l1= strlen( name);
574: l2= strlen(ss)+1;
575: strncpy( finame, name, l1-l2);
576: finame[l1-l2]= 0;
577: }
578:
579: return( 0 ); /* we're done */
580: }
581:
582:
583: /******************************************/
584:
585: void replace_back_to_slash(char *s, char*t)
586: {
587: int i;
588: int lg=0;
589: i=0;
590: lg=strlen(t);
591: for(i=0; i<= lg; i++) {
592: (s[i] = t[i]);
593: if (t[i]== '\\') s[i]='/';
594: }
595: }
596:
597: int nbocc(char *s, char occ)
598: {
599: int i,j=0;
600: int lg=20;
601: i=0;
602: lg=strlen(s);
603: for(i=0; i<= lg; i++) {
604: if (s[i] == occ ) j++;
605: }
606: return j;
607: }
608:
609: void cutv(char *u,char *v, char*t, char occ)
610: {
611: /* cuts string t into u and v where u ends before first occurence of char 'occ'
612: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
613: gives u="abcedf" and v="ghi2j" */
614: int i,lg,j,p=0;
615: i=0;
616: for(j=0; j<=strlen(t)-1; j++) {
617: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
618: }
619:
620: lg=strlen(t);
621: for(j=0; j<p; j++) {
622: (u[j] = t[j]);
623: }
624: u[p]='\0';
625:
626: for(j=0; j<= lg; j++) {
627: if (j>=(p+1))(v[j-p-1] = t[j]);
628: }
629: }
630:
631: /********************** nrerror ********************/
632:
633: void nrerror(char error_text[])
634: {
635: fprintf(stderr,"ERREUR ...\n");
636: fprintf(stderr,"%s\n",error_text);
637: exit(EXIT_FAILURE);
638: }
639: /*********************** vector *******************/
640: double *vector(int nl, int nh)
641: {
642: double *v;
643: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
644: if (!v) nrerror("allocation failure in vector");
645: return v-nl+NR_END;
646: }
647:
648: /************************ free vector ******************/
649: void free_vector(double*v, int nl, int nh)
650: {
651: free((FREE_ARG)(v+nl-NR_END));
652: }
653:
654: /************************ivector *******************************/
655: int *ivector(long nl,long nh)
656: {
657: int *v;
658: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
659: if (!v) nrerror("allocation failure in ivector");
660: return v-nl+NR_END;
661: }
662:
663: /******************free ivector **************************/
664: void free_ivector(int *v, long nl, long nh)
665: {
666: free((FREE_ARG)(v+nl-NR_END));
667: }
668:
669: /************************lvector *******************************/
670: long *lvector(long nl,long nh)
671: {
672: long *v;
673: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
674: if (!v) nrerror("allocation failure in ivector");
675: return v-nl+NR_END;
676: }
677:
678: /******************free lvector **************************/
679: void free_lvector(long *v, long nl, long nh)
680: {
681: free((FREE_ARG)(v+nl-NR_END));
682: }
683:
684: /******************* imatrix *******************************/
685: int **imatrix(long nrl, long nrh, long ncl, long nch)
686: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
687: {
688: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
689: int **m;
690:
691: /* allocate pointers to rows */
692: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
693: if (!m) nrerror("allocation failure 1 in matrix()");
694: m += NR_END;
695: m -= nrl;
696:
697:
698: /* allocate rows and set pointers to them */
699: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
700: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
701: m[nrl] += NR_END;
702: m[nrl] -= ncl;
703:
704: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
705:
706: /* return pointer to array of pointers to rows */
707: return m;
708: }
709:
710: /****************** free_imatrix *************************/
711: void free_imatrix(m,nrl,nrh,ncl,nch)
712: int **m;
713: long nch,ncl,nrh,nrl;
714: /* free an int matrix allocated by imatrix() */
715: {
716: free((FREE_ARG) (m[nrl]+ncl-NR_END));
717: free((FREE_ARG) (m+nrl-NR_END));
718: }
719:
720: /******************* matrix *******************************/
721: double **matrix(long nrl, long nrh, long ncl, long nch)
722: {
723: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
724: double **m;
725:
726: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
727: if (!m) nrerror("allocation failure 1 in matrix()");
728: m += NR_END;
729: m -= nrl;
730:
731: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
732: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
733: m[nrl] += NR_END;
734: m[nrl] -= ncl;
735:
736: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
737: return m;
738: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
739: */
740: }
741:
742: /*************************free matrix ************************/
743: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
744: {
745: free((FREE_ARG)(m[nrl]+ncl-NR_END));
746: free((FREE_ARG)(m+nrl-NR_END));
747: }
748:
749: /******************* ma3x *******************************/
750: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
751: {
752: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
753: double ***m;
754:
755: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
756: if (!m) nrerror("allocation failure 1 in matrix()");
757: m += NR_END;
758: m -= nrl;
759:
760: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
761: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
762: m[nrl] += NR_END;
763: m[nrl] -= ncl;
764:
765: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
766:
767: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
768: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
769: m[nrl][ncl] += NR_END;
770: m[nrl][ncl] -= nll;
771: for (j=ncl+1; j<=nch; j++)
772: m[nrl][j]=m[nrl][j-1]+nlay;
773:
774: for (i=nrl+1; i<=nrh; i++) {
775: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
776: for (j=ncl+1; j<=nch; j++)
777: m[i][j]=m[i][j-1]+nlay;
778: }
779: return m;
780: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
781: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
782: */
783: }
784:
785: /*************************free ma3x ************************/
786: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
787: {
788: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
789: free((FREE_ARG)(m[nrl]+ncl-NR_END));
790: free((FREE_ARG)(m+nrl-NR_END));
791: }
792:
793: /*************** function subdirf ***********/
794: char *subdirf(char fileres[])
795: {
796: /* Caution optionfilefiname is hidden */
797: strcpy(tmpout,optionfilefiname);
798: strcat(tmpout,"/"); /* Add to the right */
799: strcat(tmpout,fileres);
800: return tmpout;
801: }
802:
803: /*************** function subdirf2 ***********/
804: char *subdirf2(char fileres[], char *preop)
805: {
806:
807: /* Caution optionfilefiname is hidden */
808: strcpy(tmpout,optionfilefiname);
809: strcat(tmpout,"/");
810: strcat(tmpout,preop);
811: strcat(tmpout,fileres);
812: return tmpout;
813: }
814:
815: /*************** function subdirf3 ***********/
816: char *subdirf3(char fileres[], char *preop, char *preop2)
817: {
818:
819: /* Caution optionfilefiname is hidden */
820: strcpy(tmpout,optionfilefiname);
821: strcat(tmpout,"/");
822: strcat(tmpout,preop);
823: strcat(tmpout,preop2);
824: strcat(tmpout,fileres);
825: return tmpout;
826: }
827:
828: /***************** f1dim *************************/
829: extern int ncom;
830: extern double *pcom,*xicom;
831: extern double (*nrfunc)(double []);
832:
833: double f1dim(double x)
834: {
835: int j;
836: double f;
837: double *xt;
838:
839: xt=vector(1,ncom);
840: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
841: f=(*nrfunc)(xt);
842: free_vector(xt,1,ncom);
843: return f;
844: }
845:
846: /*****************brent *************************/
847: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
848: {
849: int iter;
850: double a,b,d,etemp;
851: double fu,fv,fw,fx;
852: double ftemp;
853: double p,q,r,tol1,tol2,u,v,w,x,xm;
854: double e=0.0;
855:
856: a=(ax < cx ? ax : cx);
857: b=(ax > cx ? ax : cx);
858: x=w=v=bx;
859: fw=fv=fx=(*f)(x);
860: for (iter=1;iter<=ITMAX;iter++) {
861: xm=0.5*(a+b);
862: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
863: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
864: printf(".");fflush(stdout);
865: fprintf(ficlog,".");fflush(ficlog);
866: #ifdef DEBUG
867: 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);
868: 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);
869: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
870: #endif
871: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
872: *xmin=x;
873: return fx;
874: }
875: ftemp=fu;
876: if (fabs(e) > tol1) {
877: r=(x-w)*(fx-fv);
878: q=(x-v)*(fx-fw);
879: p=(x-v)*q-(x-w)*r;
880: q=2.0*(q-r);
881: if (q > 0.0) p = -p;
882: q=fabs(q);
883: etemp=e;
884: e=d;
885: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
886: d=CGOLD*(e=(x >= xm ? a-x : b-x));
887: else {
888: d=p/q;
889: u=x+d;
890: if (u-a < tol2 || b-u < tol2)
891: d=SIGN(tol1,xm-x);
892: }
893: } else {
894: d=CGOLD*(e=(x >= xm ? a-x : b-x));
895: }
896: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
897: fu=(*f)(u);
898: if (fu <= fx) {
899: if (u >= x) a=x; else b=x;
900: SHFT(v,w,x,u)
901: SHFT(fv,fw,fx,fu)
902: } else {
903: if (u < x) a=u; else b=u;
904: if (fu <= fw || w == x) {
905: v=w;
906: w=u;
907: fv=fw;
908: fw=fu;
909: } else if (fu <= fv || v == x || v == w) {
910: v=u;
911: fv=fu;
912: }
913: }
914: }
915: nrerror("Too many iterations in brent");
916: *xmin=x;
917: return fx;
918: }
919:
920: /****************** mnbrak ***********************/
921:
922: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
923: double (*func)(double))
924: {
925: double ulim,u,r,q, dum;
926: double fu;
927:
928: *fa=(*func)(*ax);
929: *fb=(*func)(*bx);
930: if (*fb > *fa) {
931: SHFT(dum,*ax,*bx,dum)
932: SHFT(dum,*fb,*fa,dum)
933: }
934: *cx=(*bx)+GOLD*(*bx-*ax);
935: *fc=(*func)(*cx);
936: while (*fb > *fc) {
937: r=(*bx-*ax)*(*fb-*fc);
938: q=(*bx-*cx)*(*fb-*fa);
939: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
940: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
941: ulim=(*bx)+GLIMIT*(*cx-*bx);
942: if ((*bx-u)*(u-*cx) > 0.0) {
943: fu=(*func)(u);
944: } else if ((*cx-u)*(u-ulim) > 0.0) {
945: fu=(*func)(u);
946: if (fu < *fc) {
947: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
948: SHFT(*fb,*fc,fu,(*func)(u))
949: }
950: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
951: u=ulim;
952: fu=(*func)(u);
953: } else {
954: u=(*cx)+GOLD*(*cx-*bx);
955: fu=(*func)(u);
956: }
957: SHFT(*ax,*bx,*cx,u)
958: SHFT(*fa,*fb,*fc,fu)
959: }
960: }
961:
962: /*************** linmin ************************/
963:
964: int ncom;
965: double *pcom,*xicom;
966: double (*nrfunc)(double []);
967:
968: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
969: {
970: double brent(double ax, double bx, double cx,
971: double (*f)(double), double tol, double *xmin);
972: double f1dim(double x);
973: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
974: double *fc, double (*func)(double));
975: int j;
976: double xx,xmin,bx,ax;
977: double fx,fb,fa;
978:
979: ncom=n;
980: pcom=vector(1,n);
981: xicom=vector(1,n);
982: nrfunc=func;
983: for (j=1;j<=n;j++) {
984: pcom[j]=p[j];
985: xicom[j]=xi[j];
986: }
987: ax=0.0;
988: xx=1.0;
989: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
990: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
991: #ifdef DEBUG
992: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
993: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
994: #endif
995: for (j=1;j<=n;j++) {
996: xi[j] *= xmin;
997: p[j] += xi[j];
998: }
999: free_vector(xicom,1,n);
1000: free_vector(pcom,1,n);
1001: }
1002:
1003: char *asc_diff_time(long time_sec, char ascdiff[])
1004: {
1005: long sec_left, days, hours, minutes;
1006: days = (time_sec) / (60*60*24);
1007: sec_left = (time_sec) % (60*60*24);
1008: hours = (sec_left) / (60*60) ;
1009: sec_left = (sec_left) %(60*60);
1010: minutes = (sec_left) /60;
1011: sec_left = (sec_left) % (60);
1012: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1013: return ascdiff;
1014: }
1015:
1016: /*************** powell ************************/
1017: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1018: double (*func)(double []))
1019: {
1020: void linmin(double p[], double xi[], int n, double *fret,
1021: double (*func)(double []));
1022: int i,ibig,j;
1023: double del,t,*pt,*ptt,*xit;
1024: double fp,fptt;
1025: double *xits;
1026: int niterf, itmp;
1027:
1028: pt=vector(1,n);
1029: ptt=vector(1,n);
1030: xit=vector(1,n);
1031: xits=vector(1,n);
1032: *fret=(*func)(p);
1033: for (j=1;j<=n;j++) pt[j]=p[j];
1034: for (*iter=1;;++(*iter)) {
1035: fp=(*fret);
1036: ibig=0;
1037: del=0.0;
1038: last_time=curr_time;
1039: (void) gettimeofday(&curr_time,&tzp);
1040: 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);
1041: 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); fflush(ficlog);
1042: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1043: for (i=1;i<=n;i++) {
1044: printf(" %d %.12f",i, p[i]);
1045: fprintf(ficlog," %d %.12lf",i, p[i]);
1046: fprintf(ficrespow," %.12lf", p[i]);
1047: }
1048: printf("\n");
1049: fprintf(ficlog,"\n");
1050: fprintf(ficrespow,"\n");fflush(ficrespow);
1051: if(*iter <=3){
1052: tm = *localtime(&curr_time.tv_sec);
1053: strcpy(strcurr,asctime(&tm));
1054: /* asctime_r(&tm,strcurr); */
1055: forecast_time=curr_time;
1056: itmp = strlen(strcurr);
1057: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1058: strcurr[itmp-1]='\0';
1059: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1060: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1061: for(niterf=10;niterf<=30;niterf+=10){
1062: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1063: tmf = *localtime(&forecast_time.tv_sec);
1064: /* asctime_r(&tmf,strfor); */
1065: strcpy(strfor,asctime(&tmf));
1066: itmp = strlen(strfor);
1067: if(strfor[itmp-1]=='\n')
1068: strfor[itmp-1]='\0';
1069: 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);
1070: 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);
1071: }
1072: }
1073: for (i=1;i<=n;i++) {
1074: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1075: fptt=(*fret);
1076: #ifdef DEBUG
1077: printf("fret=%lf \n",*fret);
1078: fprintf(ficlog,"fret=%lf \n",*fret);
1079: #endif
1080: printf("%d",i);fflush(stdout);
1081: fprintf(ficlog,"%d",i);fflush(ficlog);
1082: linmin(p,xit,n,fret,func);
1083: if (fabs(fptt-(*fret)) > del) {
1084: del=fabs(fptt-(*fret));
1085: ibig=i;
1086: }
1087: #ifdef DEBUG
1088: printf("%d %.12e",i,(*fret));
1089: fprintf(ficlog,"%d %.12e",i,(*fret));
1090: for (j=1;j<=n;j++) {
1091: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1092: printf(" x(%d)=%.12e",j,xit[j]);
1093: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1094: }
1095: for(j=1;j<=n;j++) {
1096: printf(" p=%.12e",p[j]);
1097: fprintf(ficlog," p=%.12e",p[j]);
1098: }
1099: printf("\n");
1100: fprintf(ficlog,"\n");
1101: #endif
1102: }
1103: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1104: #ifdef DEBUG
1105: int k[2],l;
1106: k[0]=1;
1107: k[1]=-1;
1108: printf("Max: %.12e",(*func)(p));
1109: fprintf(ficlog,"Max: %.12e",(*func)(p));
1110: for (j=1;j<=n;j++) {
1111: printf(" %.12e",p[j]);
1112: fprintf(ficlog," %.12e",p[j]);
1113: }
1114: printf("\n");
1115: fprintf(ficlog,"\n");
1116: for(l=0;l<=1;l++) {
1117: for (j=1;j<=n;j++) {
1118: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1119: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1120: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1121: }
1122: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1123: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1124: }
1125: #endif
1126:
1127:
1128: free_vector(xit,1,n);
1129: free_vector(xits,1,n);
1130: free_vector(ptt,1,n);
1131: free_vector(pt,1,n);
1132: return;
1133: }
1134: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1135: for (j=1;j<=n;j++) {
1136: ptt[j]=2.0*p[j]-pt[j];
1137: xit[j]=p[j]-pt[j];
1138: pt[j]=p[j];
1139: }
1140: fptt=(*func)(ptt);
1141: if (fptt < fp) {
1142: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1143: if (t < 0.0) {
1144: linmin(p,xit,n,fret,func);
1145: for (j=1;j<=n;j++) {
1146: xi[j][ibig]=xi[j][n];
1147: xi[j][n]=xit[j];
1148: }
1149: #ifdef DEBUG
1150: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1151: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1152: for(j=1;j<=n;j++){
1153: printf(" %.12e",xit[j]);
1154: fprintf(ficlog," %.12e",xit[j]);
1155: }
1156: printf("\n");
1157: fprintf(ficlog,"\n");
1158: #endif
1159: }
1160: }
1161: }
1162: }
1163:
1164: /**** Prevalence limit (stable or period prevalence) ****************/
1165:
1166: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1167: {
1168: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1169: matrix by transitions matrix until convergence is reached */
1170:
1171: int i, ii,j,k;
1172: double min, max, maxmin, maxmax,sumnew=0.;
1173: double **matprod2();
1174: double **out, cov[NCOVMAX], **pmij();
1175: double **newm;
1176: double agefin, delaymax=50 ; /* Max number of years to converge */
1177:
1178: for (ii=1;ii<=nlstate+ndeath;ii++)
1179: for (j=1;j<=nlstate+ndeath;j++){
1180: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1181: }
1182:
1183: cov[1]=1.;
1184:
1185: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1186: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1187: newm=savm;
1188: /* Covariates have to be included here again */
1189: cov[2]=agefin;
1190:
1191: for (k=1; k<=cptcovn;k++) {
1192: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1193: /* 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]]);*/
1194: }
1195: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1196: for (k=1; k<=cptcovprod;k++)
1197: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1198:
1199: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1200: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1201: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1202: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1203:
1204: savm=oldm;
1205: oldm=newm;
1206: maxmax=0.;
1207: for(j=1;j<=nlstate;j++){
1208: min=1.;
1209: max=0.;
1210: for(i=1; i<=nlstate; i++) {
1211: sumnew=0;
1212: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1213: prlim[i][j]= newm[i][j]/(1-sumnew);
1214: max=FMAX(max,prlim[i][j]);
1215: min=FMIN(min,prlim[i][j]);
1216: }
1217: maxmin=max-min;
1218: maxmax=FMAX(maxmax,maxmin);
1219: }
1220: if(maxmax < ftolpl){
1221: return prlim;
1222: }
1223: }
1224: }
1225:
1226: /*************** transition probabilities ***************/
1227:
1228: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1229: {
1230: double s1, s2;
1231: /*double t34;*/
1232: int i,j,j1, nc, ii, jj;
1233:
1234: for(i=1; i<= nlstate; i++){
1235: for(j=1; j<i;j++){
1236: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1237: /*s2 += param[i][j][nc]*cov[nc];*/
1238: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1239: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1240: }
1241: ps[i][j]=s2;
1242: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1243: }
1244: for(j=i+1; j<=nlstate+ndeath;j++){
1245: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1246: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1247: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1248: }
1249: ps[i][j]=s2;
1250: }
1251: }
1252: /*ps[3][2]=1;*/
1253:
1254: for(i=1; i<= nlstate; i++){
1255: s1=0;
1256: for(j=1; j<i; j++)
1257: s1+=exp(ps[i][j]);
1258: for(j=i+1; j<=nlstate+ndeath; j++)
1259: s1+=exp(ps[i][j]);
1260: ps[i][i]=1./(s1+1.);
1261: for(j=1; j<i; j++)
1262: ps[i][j]= exp(ps[i][j])*ps[i][i];
1263: for(j=i+1; j<=nlstate+ndeath; j++)
1264: ps[i][j]= exp(ps[i][j])*ps[i][i];
1265: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1266: } /* end i */
1267:
1268: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1269: for(jj=1; jj<= nlstate+ndeath; jj++){
1270: ps[ii][jj]=0;
1271: ps[ii][ii]=1;
1272: }
1273: }
1274:
1275:
1276: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1277: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1278: /* printf("ddd %lf ",ps[ii][jj]); */
1279: /* } */
1280: /* printf("\n "); */
1281: /* } */
1282: /* printf("\n ");printf("%lf ",cov[2]); */
1283: /*
1284: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1285: goto end;*/
1286: return ps;
1287: }
1288:
1289: /**************** Product of 2 matrices ******************/
1290:
1291: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1292: {
1293: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1294: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1295: /* in, b, out are matrice of pointers which should have been initialized
1296: before: only the contents of out is modified. The function returns
1297: a pointer to pointers identical to out */
1298: long i, j, k;
1299: for(i=nrl; i<= nrh; i++)
1300: for(k=ncolol; k<=ncoloh; k++)
1301: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1302: out[i][k] +=in[i][j]*b[j][k];
1303:
1304: return out;
1305: }
1306:
1307:
1308: /************* Higher Matrix Product ***************/
1309:
1310: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1311: {
1312: /* Computes the transition matrix starting at age 'age' over
1313: 'nhstepm*hstepm*stepm' months (i.e. until
1314: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1315: nhstepm*hstepm matrices.
1316: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1317: (typically every 2 years instead of every month which is too big
1318: for the memory).
1319: Model is determined by parameters x and covariates have to be
1320: included manually here.
1321:
1322: */
1323:
1324: int i, j, d, h, k;
1325: double **out, cov[NCOVMAX];
1326: double **newm;
1327:
1328: /* Hstepm could be zero and should return the unit matrix */
1329: for (i=1;i<=nlstate+ndeath;i++)
1330: for (j=1;j<=nlstate+ndeath;j++){
1331: oldm[i][j]=(i==j ? 1.0 : 0.0);
1332: po[i][j][0]=(i==j ? 1.0 : 0.0);
1333: }
1334: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1335: for(h=1; h <=nhstepm; h++){
1336: for(d=1; d <=hstepm; d++){
1337: newm=savm;
1338: /* Covariates have to be included here again */
1339: cov[1]=1.;
1340: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1341: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1342: for (k=1; k<=cptcovage;k++)
1343: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1344: for (k=1; k<=cptcovprod;k++)
1345: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1346:
1347:
1348: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1349: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1350: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1351: pmij(pmmij,cov,ncovmodel,x,nlstate));
1352: savm=oldm;
1353: oldm=newm;
1354: }
1355: for(i=1; i<=nlstate+ndeath; i++)
1356: for(j=1;j<=nlstate+ndeath;j++) {
1357: po[i][j][h]=newm[i][j];
1358: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1359: }
1360: /*printf("h=%d ",h);*/
1361: } /* end h */
1362: /* printf("\n H=%d \n",h); */
1363: return po;
1364: }
1365:
1366:
1367: /*************** log-likelihood *************/
1368: double func( double *x)
1369: {
1370: int i, ii, j, k, mi, d, kk;
1371: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1372: double **out;
1373: double sw; /* Sum of weights */
1374: double lli; /* Individual log likelihood */
1375: int s1, s2;
1376: double bbh, survp;
1377: long ipmx;
1378: /*extern weight */
1379: /* We are differentiating ll according to initial status */
1380: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1381: /*for(i=1;i<imx;i++)
1382: printf(" %d\n",s[4][i]);
1383: */
1384: cov[1]=1.;
1385:
1386: for(k=1; k<=nlstate; k++) ll[k]=0.;
1387:
1388: if(mle==1){
1389: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1390: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1391: for(mi=1; mi<= wav[i]-1; mi++){
1392: for (ii=1;ii<=nlstate+ndeath;ii++)
1393: for (j=1;j<=nlstate+ndeath;j++){
1394: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1395: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1396: }
1397: for(d=0; d<dh[mi][i]; d++){
1398: newm=savm;
1399: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1400: for (kk=1; kk<=cptcovage;kk++) {
1401: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1402: }
1403: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1404: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1405: savm=oldm;
1406: oldm=newm;
1407: } /* end mult */
1408:
1409: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1410: /* But now since version 0.9 we anticipate for bias at large stepm.
1411: * If stepm is larger than one month (smallest stepm) and if the exact delay
1412: * (in months) between two waves is not a multiple of stepm, we rounded to
1413: * the nearest (and in case of equal distance, to the lowest) interval but now
1414: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1415: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1416: * probability in order to take into account the bias as a fraction of the way
1417: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1418: * -stepm/2 to stepm/2 .
1419: * For stepm=1 the results are the same as for previous versions of Imach.
1420: * For stepm > 1 the results are less biased than in previous versions.
1421: */
1422: s1=s[mw[mi][i]][i];
1423: s2=s[mw[mi+1][i]][i];
1424: bbh=(double)bh[mi][i]/(double)stepm;
1425: /* bias bh is positive if real duration
1426: * is higher than the multiple of stepm and negative otherwise.
1427: */
1428: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1429: if( s2 > nlstate){
1430: /* i.e. if s2 is a death state and if the date of death is known
1431: then the contribution to the likelihood is the probability to
1432: die between last step unit time and current step unit time,
1433: which is also equal to probability to die before dh
1434: minus probability to die before dh-stepm .
1435: In version up to 0.92 likelihood was computed
1436: as if date of death was unknown. Death was treated as any other
1437: health state: the date of the interview describes the actual state
1438: and not the date of a change in health state. The former idea was
1439: to consider that at each interview the state was recorded
1440: (healthy, disable or death) and IMaCh was corrected; but when we
1441: introduced the exact date of death then we should have modified
1442: the contribution of an exact death to the likelihood. This new
1443: contribution is smaller and very dependent of the step unit
1444: stepm. It is no more the probability to die between last interview
1445: and month of death but the probability to survive from last
1446: interview up to one month before death multiplied by the
1447: probability to die within a month. Thanks to Chris
1448: Jackson for correcting this bug. Former versions increased
1449: mortality artificially. The bad side is that we add another loop
1450: which slows down the processing. The difference can be up to 10%
1451: lower mortality.
1452: */
1453: lli=log(out[s1][s2] - savm[s1][s2]);
1454:
1455:
1456: } else if (s2==-2) {
1457: for (j=1,survp=0. ; j<=nlstate; j++)
1458: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1459: /*survp += out[s1][j]; */
1460: lli= log(survp);
1461: }
1462:
1463: else if (s2==-4) {
1464: for (j=3,survp=0. ; j<=nlstate; j++)
1465: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1466: lli= log(survp);
1467: }
1468:
1469: else if (s2==-5) {
1470: for (j=1,survp=0. ; j<=2; j++)
1471: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1472: lli= log(survp);
1473: }
1474:
1475: else{
1476: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1477: /* 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 */
1478: }
1479: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1480: /*if(lli ==000.0)*/
1481: /*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); */
1482: ipmx +=1;
1483: sw += weight[i];
1484: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1485: } /* end of wave */
1486: } /* end of individual */
1487: } else if(mle==2){
1488: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1489: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1490: for(mi=1; mi<= wav[i]-1; mi++){
1491: for (ii=1;ii<=nlstate+ndeath;ii++)
1492: for (j=1;j<=nlstate+ndeath;j++){
1493: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1494: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1495: }
1496: for(d=0; d<=dh[mi][i]; d++){
1497: newm=savm;
1498: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1499: for (kk=1; kk<=cptcovage;kk++) {
1500: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1501: }
1502: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1503: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1504: savm=oldm;
1505: oldm=newm;
1506: } /* end mult */
1507:
1508: s1=s[mw[mi][i]][i];
1509: s2=s[mw[mi+1][i]][i];
1510: bbh=(double)bh[mi][i]/(double)stepm;
1511: 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 */
1512: ipmx +=1;
1513: sw += weight[i];
1514: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1515: } /* end of wave */
1516: } /* end of individual */
1517: } else if(mle==3){ /* exponential inter-extrapolation */
1518: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1519: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1520: for(mi=1; mi<= wav[i]-1; mi++){
1521: for (ii=1;ii<=nlstate+ndeath;ii++)
1522: for (j=1;j<=nlstate+ndeath;j++){
1523: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1524: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1525: }
1526: for(d=0; d<dh[mi][i]; d++){
1527: newm=savm;
1528: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1529: for (kk=1; kk<=cptcovage;kk++) {
1530: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1531: }
1532: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1533: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1534: savm=oldm;
1535: oldm=newm;
1536: } /* end mult */
1537:
1538: s1=s[mw[mi][i]][i];
1539: s2=s[mw[mi+1][i]][i];
1540: bbh=(double)bh[mi][i]/(double)stepm;
1541: 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 */
1542: ipmx +=1;
1543: sw += weight[i];
1544: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1545: } /* end of wave */
1546: } /* end of individual */
1547: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1548: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1549: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1550: for(mi=1; mi<= wav[i]-1; mi++){
1551: for (ii=1;ii<=nlstate+ndeath;ii++)
1552: for (j=1;j<=nlstate+ndeath;j++){
1553: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1554: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1555: }
1556: for(d=0; d<dh[mi][i]; d++){
1557: newm=savm;
1558: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1559: for (kk=1; kk<=cptcovage;kk++) {
1560: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1561: }
1562:
1563: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1564: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1565: savm=oldm;
1566: oldm=newm;
1567: } /* end mult */
1568:
1569: s1=s[mw[mi][i]][i];
1570: s2=s[mw[mi+1][i]][i];
1571: if( s2 > nlstate){
1572: lli=log(out[s1][s2] - savm[s1][s2]);
1573: }else{
1574: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1575: }
1576: ipmx +=1;
1577: sw += weight[i];
1578: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1579: /* 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]); */
1580: } /* end of wave */
1581: } /* end of individual */
1582: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1583: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1584: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1585: for(mi=1; mi<= wav[i]-1; mi++){
1586: for (ii=1;ii<=nlstate+ndeath;ii++)
1587: for (j=1;j<=nlstate+ndeath;j++){
1588: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1589: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1590: }
1591: for(d=0; d<dh[mi][i]; d++){
1592: newm=savm;
1593: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1594: for (kk=1; kk<=cptcovage;kk++) {
1595: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1596: }
1597:
1598: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1599: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1600: savm=oldm;
1601: oldm=newm;
1602: } /* end mult */
1603:
1604: s1=s[mw[mi][i]][i];
1605: s2=s[mw[mi+1][i]][i];
1606: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1607: ipmx +=1;
1608: sw += weight[i];
1609: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1610: /*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]);*/
1611: } /* end of wave */
1612: } /* end of individual */
1613: } /* End of if */
1614: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1615: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1616: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1617: return -l;
1618: }
1619:
1620: /*************** log-likelihood *************/
1621: double funcone( double *x)
1622: {
1623: /* Same as likeli but slower because of a lot of printf and if */
1624: int i, ii, j, k, mi, d, kk;
1625: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1626: double **out;
1627: double lli; /* Individual log likelihood */
1628: double llt;
1629: int s1, s2;
1630: double bbh, survp;
1631: /*extern weight */
1632: /* We are differentiating ll according to initial status */
1633: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1634: /*for(i=1;i<imx;i++)
1635: printf(" %d\n",s[4][i]);
1636: */
1637: cov[1]=1.;
1638:
1639: for(k=1; k<=nlstate; k++) ll[k]=0.;
1640:
1641: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1642: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1643: for(mi=1; mi<= wav[i]-1; mi++){
1644: for (ii=1;ii<=nlstate+ndeath;ii++)
1645: for (j=1;j<=nlstate+ndeath;j++){
1646: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1647: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1648: }
1649: for(d=0; d<dh[mi][i]; d++){
1650: newm=savm;
1651: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1652: for (kk=1; kk<=cptcovage;kk++) {
1653: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1654: }
1655: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1656: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1657: savm=oldm;
1658: oldm=newm;
1659: } /* end mult */
1660:
1661: s1=s[mw[mi][i]][i];
1662: s2=s[mw[mi+1][i]][i];
1663: bbh=(double)bh[mi][i]/(double)stepm;
1664: /* bias is positive if real duration
1665: * is higher than the multiple of stepm and negative otherwise.
1666: */
1667: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1668: lli=log(out[s1][s2] - savm[s1][s2]);
1669: } else if (s2==-2) {
1670: for (j=1,survp=0. ; j<=nlstate; j++)
1671: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1672: lli= log(survp);
1673: }else if (mle==1){
1674: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1675: } else if(mle==2){
1676: 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 */
1677: } else if(mle==3){ /* exponential inter-extrapolation */
1678: 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 */
1679: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1680: lli=log(out[s1][s2]); /* Original formula */
1681: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1682: lli=log(out[s1][s2]); /* Original formula */
1683: } /* End of if */
1684: ipmx +=1;
1685: sw += weight[i];
1686: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1687: /* 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]); */
1688: if(globpr){
1689: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1690: %11.6f %11.6f %11.6f ", \
1691: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1692: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1693: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1694: llt +=ll[k]*gipmx/gsw;
1695: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1696: }
1697: fprintf(ficresilk," %10.6f\n", -llt);
1698: }
1699: } /* end of wave */
1700: } /* end of individual */
1701: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1702: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1703: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1704: if(globpr==0){ /* First time we count the contributions and weights */
1705: gipmx=ipmx;
1706: gsw=sw;
1707: }
1708: return -l;
1709: }
1710:
1711:
1712: /*************** function likelione ***********/
1713: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1714: {
1715: /* This routine should help understanding what is done with
1716: the selection of individuals/waves and
1717: to check the exact contribution to the likelihood.
1718: Plotting could be done.
1719: */
1720: int k;
1721:
1722: if(*globpri !=0){ /* Just counts and sums, no printings */
1723: strcpy(fileresilk,"ilk");
1724: strcat(fileresilk,fileres);
1725: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1726: printf("Problem with resultfile: %s\n", fileresilk);
1727: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1728: }
1729: 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");
1730: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1731: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1732: for(k=1; k<=nlstate; k++)
1733: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1734: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1735: }
1736:
1737: *fretone=(*funcone)(p);
1738: if(*globpri !=0){
1739: fclose(ficresilk);
1740: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1741: fflush(fichtm);
1742: }
1743: return;
1744: }
1745:
1746:
1747: /*********** Maximum Likelihood Estimation ***************/
1748:
1749: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1750: {
1751: int i,j, iter;
1752: double **xi;
1753: double fret;
1754: double fretone; /* Only one call to likelihood */
1755: /* char filerespow[FILENAMELENGTH];*/
1756: xi=matrix(1,npar,1,npar);
1757: for (i=1;i<=npar;i++)
1758: for (j=1;j<=npar;j++)
1759: xi[i][j]=(i==j ? 1.0 : 0.0);
1760: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1761: strcpy(filerespow,"pow");
1762: strcat(filerespow,fileres);
1763: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1764: printf("Problem with resultfile: %s\n", filerespow);
1765: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1766: }
1767: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1768: for (i=1;i<=nlstate;i++)
1769: for(j=1;j<=nlstate+ndeath;j++)
1770: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1771: fprintf(ficrespow,"\n");
1772:
1773: powell(p,xi,npar,ftol,&iter,&fret,func);
1774:
1775: free_matrix(xi,1,npar,1,npar);
1776: fclose(ficrespow);
1777: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1778: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1779: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1780:
1781: }
1782:
1783: /**** Computes Hessian and covariance matrix ***/
1784: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1785: {
1786: double **a,**y,*x,pd;
1787: double **hess;
1788: int i, j,jk;
1789: int *indx;
1790:
1791: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1792: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1793: void lubksb(double **a, int npar, int *indx, double b[]) ;
1794: void ludcmp(double **a, int npar, int *indx, double *d) ;
1795: double gompertz(double p[]);
1796: hess=matrix(1,npar,1,npar);
1797:
1798: printf("\nCalculation of the hessian matrix. Wait...\n");
1799: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1800: for (i=1;i<=npar;i++){
1801: printf("%d",i);fflush(stdout);
1802: fprintf(ficlog,"%d",i);fflush(ficlog);
1803:
1804: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1805:
1806: /* printf(" %f ",p[i]);
1807: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1808: }
1809:
1810: for (i=1;i<=npar;i++) {
1811: for (j=1;j<=npar;j++) {
1812: if (j>i) {
1813: printf(".%d%d",i,j);fflush(stdout);
1814: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1815: hess[i][j]=hessij(p,delti,i,j,func,npar);
1816:
1817: hess[j][i]=hess[i][j];
1818: /*printf(" %lf ",hess[i][j]);*/
1819: }
1820: }
1821: }
1822: printf("\n");
1823: fprintf(ficlog,"\n");
1824:
1825: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1826: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1827:
1828: a=matrix(1,npar,1,npar);
1829: y=matrix(1,npar,1,npar);
1830: x=vector(1,npar);
1831: indx=ivector(1,npar);
1832: for (i=1;i<=npar;i++)
1833: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1834: ludcmp(a,npar,indx,&pd);
1835:
1836: for (j=1;j<=npar;j++) {
1837: for (i=1;i<=npar;i++) x[i]=0;
1838: x[j]=1;
1839: lubksb(a,npar,indx,x);
1840: for (i=1;i<=npar;i++){
1841: matcov[i][j]=x[i];
1842: }
1843: }
1844:
1845: printf("\n#Hessian matrix#\n");
1846: fprintf(ficlog,"\n#Hessian matrix#\n");
1847: for (i=1;i<=npar;i++) {
1848: for (j=1;j<=npar;j++) {
1849: printf("%.3e ",hess[i][j]);
1850: fprintf(ficlog,"%.3e ",hess[i][j]);
1851: }
1852: printf("\n");
1853: fprintf(ficlog,"\n");
1854: }
1855:
1856: /* Recompute Inverse */
1857: for (i=1;i<=npar;i++)
1858: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1859: ludcmp(a,npar,indx,&pd);
1860:
1861: /* printf("\n#Hessian matrix recomputed#\n");
1862:
1863: for (j=1;j<=npar;j++) {
1864: for (i=1;i<=npar;i++) x[i]=0;
1865: x[j]=1;
1866: lubksb(a,npar,indx,x);
1867: for (i=1;i<=npar;i++){
1868: y[i][j]=x[i];
1869: printf("%.3e ",y[i][j]);
1870: fprintf(ficlog,"%.3e ",y[i][j]);
1871: }
1872: printf("\n");
1873: fprintf(ficlog,"\n");
1874: }
1875: */
1876:
1877: free_matrix(a,1,npar,1,npar);
1878: free_matrix(y,1,npar,1,npar);
1879: free_vector(x,1,npar);
1880: free_ivector(indx,1,npar);
1881: free_matrix(hess,1,npar,1,npar);
1882:
1883:
1884: }
1885:
1886: /*************** hessian matrix ****************/
1887: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1888: {
1889: int i;
1890: int l=1, lmax=20;
1891: double k1,k2;
1892: double p2[NPARMAX+1];
1893: double res;
1894: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1895: double fx;
1896: int k=0,kmax=10;
1897: double l1;
1898:
1899: fx=func(x);
1900: for (i=1;i<=npar;i++) p2[i]=x[i];
1901: for(l=0 ; l <=lmax; l++){
1902: l1=pow(10,l);
1903: delts=delt;
1904: for(k=1 ; k <kmax; k=k+1){
1905: delt = delta*(l1*k);
1906: p2[theta]=x[theta] +delt;
1907: k1=func(p2)-fx;
1908: p2[theta]=x[theta]-delt;
1909: k2=func(p2)-fx;
1910: /*res= (k1-2.0*fx+k2)/delt/delt; */
1911: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1912:
1913: #ifdef DEBUG
1914: 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);
1915: 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);
1916: #endif
1917: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1918: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1919: k=kmax;
1920: }
1921: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1922: k=kmax; l=lmax*10.;
1923: }
1924: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1925: delts=delt;
1926: }
1927: }
1928: }
1929: delti[theta]=delts;
1930: return res;
1931:
1932: }
1933:
1934: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1935: {
1936: int i;
1937: int l=1, l1, lmax=20;
1938: double k1,k2,k3,k4,res,fx;
1939: double p2[NPARMAX+1];
1940: int k;
1941:
1942: fx=func(x);
1943: for (k=1; k<=2; k++) {
1944: for (i=1;i<=npar;i++) p2[i]=x[i];
1945: p2[thetai]=x[thetai]+delti[thetai]/k;
1946: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1947: k1=func(p2)-fx;
1948:
1949: p2[thetai]=x[thetai]+delti[thetai]/k;
1950: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1951: k2=func(p2)-fx;
1952:
1953: p2[thetai]=x[thetai]-delti[thetai]/k;
1954: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1955: k3=func(p2)-fx;
1956:
1957: p2[thetai]=x[thetai]-delti[thetai]/k;
1958: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1959: k4=func(p2)-fx;
1960: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1961: #ifdef DEBUG
1962: 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);
1963: 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);
1964: #endif
1965: }
1966: return res;
1967: }
1968:
1969: /************** Inverse of matrix **************/
1970: void ludcmp(double **a, int n, int *indx, double *d)
1971: {
1972: int i,imax,j,k;
1973: double big,dum,sum,temp;
1974: double *vv;
1975:
1976: vv=vector(1,n);
1977: *d=1.0;
1978: for (i=1;i<=n;i++) {
1979: big=0.0;
1980: for (j=1;j<=n;j++)
1981: if ((temp=fabs(a[i][j])) > big) big=temp;
1982: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1983: vv[i]=1.0/big;
1984: }
1985: for (j=1;j<=n;j++) {
1986: for (i=1;i<j;i++) {
1987: sum=a[i][j];
1988: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1989: a[i][j]=sum;
1990: }
1991: big=0.0;
1992: for (i=j;i<=n;i++) {
1993: sum=a[i][j];
1994: for (k=1;k<j;k++)
1995: sum -= a[i][k]*a[k][j];
1996: a[i][j]=sum;
1997: if ( (dum=vv[i]*fabs(sum)) >= big) {
1998: big=dum;
1999: imax=i;
2000: }
2001: }
2002: if (j != imax) {
2003: for (k=1;k<=n;k++) {
2004: dum=a[imax][k];
2005: a[imax][k]=a[j][k];
2006: a[j][k]=dum;
2007: }
2008: *d = -(*d);
2009: vv[imax]=vv[j];
2010: }
2011: indx[j]=imax;
2012: if (a[j][j] == 0.0) a[j][j]=TINY;
2013: if (j != n) {
2014: dum=1.0/(a[j][j]);
2015: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2016: }
2017: }
2018: free_vector(vv,1,n); /* Doesn't work */
2019: ;
2020: }
2021:
2022: void lubksb(double **a, int n, int *indx, double b[])
2023: {
2024: int i,ii=0,ip,j;
2025: double sum;
2026:
2027: for (i=1;i<=n;i++) {
2028: ip=indx[i];
2029: sum=b[ip];
2030: b[ip]=b[i];
2031: if (ii)
2032: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2033: else if (sum) ii=i;
2034: b[i]=sum;
2035: }
2036: for (i=n;i>=1;i--) {
2037: sum=b[i];
2038: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2039: b[i]=sum/a[i][i];
2040: }
2041: }
2042:
2043: void pstamp(FILE *fichier)
2044: {
2045: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2046: }
2047:
2048: /************ Frequencies ********************/
2049: 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[])
2050: { /* Some frequencies */
2051:
2052: int i, m, jk, k1,i1, j1, bool, z1,j;
2053: int first;
2054: double ***freq; /* Frequencies */
2055: double *pp, **prop;
2056: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2057: char fileresp[FILENAMELENGTH];
2058:
2059: pp=vector(1,nlstate);
2060: prop=matrix(1,nlstate,iagemin,iagemax+3);
2061: strcpy(fileresp,"p");
2062: strcat(fileresp,fileres);
2063: if((ficresp=fopen(fileresp,"w"))==NULL) {
2064: printf("Problem with prevalence resultfile: %s\n", fileresp);
2065: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2066: exit(0);
2067: }
2068: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2069: j1=0;
2070:
2071: j=cptcoveff;
2072: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2073:
2074: first=1;
2075:
2076: for(k1=1; k1<=j;k1++){
2077: for(i1=1; i1<=ncodemax[k1];i1++){
2078: j1++;
2079: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2080: scanf("%d", i);*/
2081: for (i=-5; i<=nlstate+ndeath; i++)
2082: for (jk=-5; jk<=nlstate+ndeath; jk++)
2083: for(m=iagemin; m <= iagemax+3; m++)
2084: freq[i][jk][m]=0;
2085:
2086: for (i=1; i<=nlstate; i++)
2087: for(m=iagemin; m <= iagemax+3; m++)
2088: prop[i][m]=0;
2089:
2090: dateintsum=0;
2091: k2cpt=0;
2092: for (i=1; i<=imx; i++) {
2093: bool=1;
2094: if (cptcovn>0) {
2095: for (z1=1; z1<=cptcoveff; z1++)
2096: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2097: bool=0;
2098: }
2099: if (bool==1){
2100: for(m=firstpass; m<=lastpass; m++){
2101: k2=anint[m][i]+(mint[m][i]/12.);
2102: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2103: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2104: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2105: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2106: if (m<lastpass) {
2107: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2108: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2109: }
2110:
2111: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2112: dateintsum=dateintsum+k2;
2113: k2cpt++;
2114: }
2115: /*}*/
2116: }
2117: }
2118: }
2119:
2120: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2121: pstamp(ficresp);
2122: if (cptcovn>0) {
2123: fprintf(ficresp, "\n#********** Variable ");
2124: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2125: fprintf(ficresp, "**********\n#");
2126: }
2127: for(i=1; i<=nlstate;i++)
2128: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2129: fprintf(ficresp, "\n");
2130:
2131: for(i=iagemin; i <= iagemax+3; i++){
2132: if(i==iagemax+3){
2133: fprintf(ficlog,"Total");
2134: }else{
2135: if(first==1){
2136: first=0;
2137: printf("See log file for details...\n");
2138: }
2139: fprintf(ficlog,"Age %d", i);
2140: }
2141: for(jk=1; jk <=nlstate ; jk++){
2142: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2143: pp[jk] += freq[jk][m][i];
2144: }
2145: for(jk=1; jk <=nlstate ; jk++){
2146: for(m=-1, pos=0; m <=0 ; m++)
2147: pos += freq[jk][m][i];
2148: if(pp[jk]>=1.e-10){
2149: if(first==1){
2150: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2151: }
2152: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2153: }else{
2154: if(first==1)
2155: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2156: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2157: }
2158: }
2159:
2160: for(jk=1; jk <=nlstate ; jk++){
2161: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2162: pp[jk] += freq[jk][m][i];
2163: }
2164: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2165: pos += pp[jk];
2166: posprop += prop[jk][i];
2167: }
2168: for(jk=1; jk <=nlstate ; jk++){
2169: if(pos>=1.e-5){
2170: if(first==1)
2171: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2172: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2173: }else{
2174: if(first==1)
2175: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2176: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2177: }
2178: if( i <= iagemax){
2179: if(pos>=1.e-5){
2180: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2181: /*probs[i][jk][j1]= pp[jk]/pos;*/
2182: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2183: }
2184: else
2185: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2186: }
2187: }
2188:
2189: for(jk=-1; jk <=nlstate+ndeath; jk++)
2190: for(m=-1; m <=nlstate+ndeath; m++)
2191: if(freq[jk][m][i] !=0 ) {
2192: if(first==1)
2193: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2194: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2195: }
2196: if(i <= iagemax)
2197: fprintf(ficresp,"\n");
2198: if(first==1)
2199: printf("Others in log...\n");
2200: fprintf(ficlog,"\n");
2201: }
2202: }
2203: }
2204: dateintmean=dateintsum/k2cpt;
2205:
2206: fclose(ficresp);
2207: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2208: free_vector(pp,1,nlstate);
2209: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2210: /* End of Freq */
2211: }
2212:
2213: /************ Prevalence ********************/
2214: 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)
2215: {
2216: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2217: in each health status at the date of interview (if between dateprev1 and dateprev2).
2218: We still use firstpass and lastpass as another selection.
2219: */
2220:
2221: int i, m, jk, k1, i1, j1, bool, z1,j;
2222: double ***freq; /* Frequencies */
2223: double *pp, **prop;
2224: double pos,posprop;
2225: double y2; /* in fractional years */
2226: int iagemin, iagemax;
2227:
2228: iagemin= (int) agemin;
2229: iagemax= (int) agemax;
2230: /*pp=vector(1,nlstate);*/
2231: prop=matrix(1,nlstate,iagemin,iagemax+3);
2232: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2233: j1=0;
2234:
2235: j=cptcoveff;
2236: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2237:
2238: for(k1=1; k1<=j;k1++){
2239: for(i1=1; i1<=ncodemax[k1];i1++){
2240: j1++;
2241:
2242: for (i=1; i<=nlstate; i++)
2243: for(m=iagemin; m <= iagemax+3; m++)
2244: prop[i][m]=0.0;
2245:
2246: for (i=1; i<=imx; i++) { /* Each individual */
2247: bool=1;
2248: if (cptcovn>0) {
2249: for (z1=1; z1<=cptcoveff; z1++)
2250: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2251: bool=0;
2252: }
2253: if (bool==1) {
2254: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2255: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2256: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2257: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2258: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2259: 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);
2260: if (s[m][i]>0 && s[m][i]<=nlstate) {
2261: /*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]]);*/
2262: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2263: prop[s[m][i]][iagemax+3] += weight[i];
2264: }
2265: }
2266: } /* end selection of waves */
2267: }
2268: }
2269: for(i=iagemin; i <= iagemax+3; i++){
2270:
2271: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2272: posprop += prop[jk][i];
2273: }
2274:
2275: for(jk=1; jk <=nlstate ; jk++){
2276: if( i <= iagemax){
2277: if(posprop>=1.e-5){
2278: probs[i][jk][j1]= prop[jk][i]/posprop;
2279: } else
2280: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2281: }
2282: }/* end jk */
2283: }/* end i */
2284: } /* end i1 */
2285: } /* end k1 */
2286:
2287: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2288: /*free_vector(pp,1,nlstate);*/
2289: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2290: } /* End of prevalence */
2291:
2292: /************* Waves Concatenation ***************/
2293:
2294: 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)
2295: {
2296: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2297: Death is a valid wave (if date is known).
2298: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2299: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2300: and mw[mi+1][i]. dh depends on stepm.
2301: */
2302:
2303: int i, mi, m;
2304: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2305: double sum=0., jmean=0.;*/
2306: int first;
2307: int j, k=0,jk, ju, jl;
2308: double sum=0.;
2309: first=0;
2310: jmin=1e+5;
2311: jmax=-1;
2312: jmean=0.;
2313: for(i=1; i<=imx; i++){
2314: mi=0;
2315: m=firstpass;
2316: while(s[m][i] <= nlstate){
2317: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2318: mw[++mi][i]=m;
2319: if(m >=lastpass)
2320: break;
2321: else
2322: m++;
2323: }/* end while */
2324: if (s[m][i] > nlstate){
2325: mi++; /* Death is another wave */
2326: /* if(mi==0) never been interviewed correctly before death */
2327: /* Only death is a correct wave */
2328: mw[mi][i]=m;
2329: }
2330:
2331: wav[i]=mi;
2332: if(mi==0){
2333: nbwarn++;
2334: if(first==0){
2335: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2336: first=1;
2337: }
2338: if(first==1){
2339: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2340: }
2341: } /* end mi==0 */
2342: } /* End individuals */
2343:
2344: for(i=1; i<=imx; i++){
2345: for(mi=1; mi<wav[i];mi++){
2346: if (stepm <=0)
2347: dh[mi][i]=1;
2348: else{
2349: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2350: if (agedc[i] < 2*AGESUP) {
2351: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2352: if(j==0) j=1; /* Survives at least one month after exam */
2353: else if(j<0){
2354: nberr++;
2355: 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]);
2356: j=1; /* Temporary Dangerous patch */
2357: 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);
2358: 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]);
2359: 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);
2360: }
2361: k=k+1;
2362: if (j >= jmax){
2363: jmax=j;
2364: ijmax=i;
2365: }
2366: if (j <= jmin){
2367: jmin=j;
2368: ijmin=i;
2369: }
2370: sum=sum+j;
2371: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2372: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2373: }
2374: }
2375: else{
2376: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2377: /* 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]); */
2378:
2379: k=k+1;
2380: if (j >= jmax) {
2381: jmax=j;
2382: ijmax=i;
2383: }
2384: else if (j <= jmin){
2385: jmin=j;
2386: ijmin=i;
2387: }
2388: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2389: /*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]);*/
2390: if(j<0){
2391: nberr++;
2392: 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]);
2393: 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]);
2394: }
2395: sum=sum+j;
2396: }
2397: jk= j/stepm;
2398: jl= j -jk*stepm;
2399: ju= j -(jk+1)*stepm;
2400: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2401: if(jl==0){
2402: dh[mi][i]=jk;
2403: bh[mi][i]=0;
2404: }else{ /* We want a negative bias in order to only have interpolation ie
2405: * at the price of an extra matrix product in likelihood */
2406: dh[mi][i]=jk+1;
2407: bh[mi][i]=ju;
2408: }
2409: }else{
2410: if(jl <= -ju){
2411: dh[mi][i]=jk;
2412: bh[mi][i]=jl; /* bias is positive if real duration
2413: * is higher than the multiple of stepm and negative otherwise.
2414: */
2415: }
2416: else{
2417: dh[mi][i]=jk+1;
2418: bh[mi][i]=ju;
2419: }
2420: if(dh[mi][i]==0){
2421: dh[mi][i]=1; /* At least one step */
2422: bh[mi][i]=ju; /* At least one step */
2423: /* 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);*/
2424: }
2425: } /* end if mle */
2426: }
2427: } /* end wave */
2428: }
2429: jmean=sum/k;
2430: 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);
2431: 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);
2432: }
2433:
2434: /*********** Tricode ****************************/
2435: void tricode(int *Tvar, int **nbcode, int imx)
2436: {
2437:
2438: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2439:
2440: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=19;
2441: int cptcode=0;
2442: cptcoveff=0;
2443:
2444: for (k=0; k<maxncov; k++) Ndum[k]=0;
2445: for (k=1; k<=7; k++) ncodemax[k]=0;
2446:
2447: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2448: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2449: modality*/
2450: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2451: Ndum[ij]++; /*store the modality */
2452: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2453: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2454: Tvar[j]. If V=sex and male is 0 and
2455: female is 1, then cptcode=1.*/
2456: }
2457:
2458: for (i=0; i<=cptcode; i++) {
2459: 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 */
2460: }
2461:
2462: ij=1;
2463: for (i=1; i<=ncodemax[j]; i++) {
2464: for (k=0; k<= maxncov; k++) {
2465: if (Ndum[k] != 0) {
2466: nbcode[Tvar[j]][ij]=k;
2467: /* 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; */
2468:
2469: ij++;
2470: }
2471: if (ij > ncodemax[j]) break;
2472: }
2473: }
2474: }
2475:
2476: for (k=0; k< maxncov; k++) Ndum[k]=0;
2477:
2478: for (i=1; i<=ncovmodel-2; i++) {
2479: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2480: ij=Tvar[i];
2481: Ndum[ij]++;
2482: }
2483:
2484: ij=1;
2485: for (i=1; i<= maxncov; i++) {
2486: if((Ndum[i]!=0) && (i<=ncovcol)){
2487: Tvaraff[ij]=i; /*For printing */
2488: ij++;
2489: }
2490: }
2491:
2492: cptcoveff=ij-1; /*Number of simple covariates*/
2493: }
2494:
2495: /*********** Health Expectancies ****************/
2496:
2497: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2498:
2499: {
2500: /* Health expectancies, no variances */
2501: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2502: int nhstepma, nstepma; /* Decreasing with age */
2503: double age, agelim, hf;
2504: double ***p3mat;
2505: double eip;
2506:
2507: pstamp(ficreseij);
2508: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2509: fprintf(ficreseij,"# Age");
2510: for(i=1; i<=nlstate;i++){
2511: for(j=1; j<=nlstate;j++){
2512: fprintf(ficreseij," e%1d%1d ",i,j);
2513: }
2514: fprintf(ficreseij," e%1d. ",i);
2515: }
2516: fprintf(ficreseij,"\n");
2517:
2518:
2519: if(estepm < stepm){
2520: printf ("Problem %d lower than %d\n",estepm, stepm);
2521: }
2522: else hstepm=estepm;
2523: /* We compute the life expectancy from trapezoids spaced every estepm months
2524: * This is mainly to measure the difference between two models: for example
2525: * if stepm=24 months pijx are given only every 2 years and by summing them
2526: * we are calculating an estimate of the Life Expectancy assuming a linear
2527: * progression in between and thus overestimating or underestimating according
2528: * to the curvature of the survival function. If, for the same date, we
2529: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2530: * to compare the new estimate of Life expectancy with the same linear
2531: * hypothesis. A more precise result, taking into account a more precise
2532: * curvature will be obtained if estepm is as small as stepm. */
2533:
2534: /* For example we decided to compute the life expectancy with the smallest unit */
2535: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2536: nhstepm is the number of hstepm from age to agelim
2537: nstepm is the number of stepm from age to agelin.
2538: Look at hpijx to understand the reason of that which relies in memory size
2539: and note for a fixed period like estepm months */
2540: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2541: survival function given by stepm (the optimization length). Unfortunately it
2542: means that if the survival funtion is printed only each two years of age and if
2543: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2544: results. So we changed our mind and took the option of the best precision.
2545: */
2546: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2547:
2548: agelim=AGESUP;
2549: /* If stepm=6 months */
2550: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2551: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2552:
2553: /* nhstepm age range expressed in number of stepm */
2554: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2555: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2556: /* if (stepm >= YEARM) hstepm=1;*/
2557: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2558: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2559:
2560: for (age=bage; age<=fage; age ++){
2561: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2562: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2563: /* if (stepm >= YEARM) hstepm=1;*/
2564: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2565:
2566: /* If stepm=6 months */
2567: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2568: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2569:
2570: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2571:
2572: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2573:
2574: printf("%d|",(int)age);fflush(stdout);
2575: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2576:
2577: /* Computing expectancies */
2578: for(i=1; i<=nlstate;i++)
2579: for(j=1; j<=nlstate;j++)
2580: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2581: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2582:
2583: /* 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]);*/
2584:
2585: }
2586:
2587: fprintf(ficreseij,"%3.0f",age );
2588: for(i=1; i<=nlstate;i++){
2589: eip=0;
2590: for(j=1; j<=nlstate;j++){
2591: eip +=eij[i][j][(int)age];
2592: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2593: }
2594: fprintf(ficreseij,"%9.4f", eip );
2595: }
2596: fprintf(ficreseij,"\n");
2597:
2598: }
2599: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2600: printf("\n");
2601: fprintf(ficlog,"\n");
2602:
2603: }
2604:
2605: void cvevsij(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[] )
2606:
2607: {
2608: /* Covariances of health expectancies eij and of total life expectancies according
2609: to initial status i, ei. .
2610: */
2611: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2612: int nhstepma, nstepma; /* Decreasing with age */
2613: double age, agelim, hf;
2614: double ***p3matp, ***p3matm, ***varhe;
2615: double **dnewm,**doldm;
2616: double *xp, *xm;
2617: double **gp, **gm;
2618: double ***gradg, ***trgradg;
2619: int theta;
2620:
2621: double eip, vip;
2622:
2623: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2624: xp=vector(1,npar);
2625: xm=vector(1,npar);
2626: dnewm=matrix(1,nlstate*nlstate,1,npar);
2627: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2628:
2629: pstamp(ficresstdeij);
2630: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2631: fprintf(ficresstdeij,"# Age");
2632: for(i=1; i<=nlstate;i++){
2633: for(j=1; j<=nlstate;j++)
2634: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2635: fprintf(ficresstdeij," e%1d. ",i);
2636: }
2637: fprintf(ficresstdeij,"\n");
2638:
2639: pstamp(ficrescveij);
2640: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2641: fprintf(ficrescveij,"# Age");
2642: for(i=1; i<=nlstate;i++)
2643: for(j=1; j<=nlstate;j++){
2644: cptj= (j-1)*nlstate+i;
2645: for(i2=1; i2<=nlstate;i2++)
2646: for(j2=1; j2<=nlstate;j2++){
2647: cptj2= (j2-1)*nlstate+i2;
2648: if(cptj2 <= cptj)
2649: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2650: }
2651: }
2652: fprintf(ficrescveij,"\n");
2653:
2654: if(estepm < stepm){
2655: printf ("Problem %d lower than %d\n",estepm, stepm);
2656: }
2657: else hstepm=estepm;
2658: /* We compute the life expectancy from trapezoids spaced every estepm months
2659: * This is mainly to measure the difference between two models: for example
2660: * if stepm=24 months pijx are given only every 2 years and by summing them
2661: * we are calculating an estimate of the Life Expectancy assuming a linear
2662: * progression in between and thus overestimating or underestimating according
2663: * to the curvature of the survival function. If, for the same date, we
2664: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2665: * to compare the new estimate of Life expectancy with the same linear
2666: * hypothesis. A more precise result, taking into account a more precise
2667: * curvature will be obtained if estepm is as small as stepm. */
2668:
2669: /* For example we decided to compute the life expectancy with the smallest unit */
2670: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2671: nhstepm is the number of hstepm from age to agelim
2672: nstepm is the number of stepm from age to agelin.
2673: Look at hpijx to understand the reason of that which relies in memory size
2674: and note for a fixed period like estepm months */
2675: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2676: survival function given by stepm (the optimization length). Unfortunately it
2677: means that if the survival funtion is printed only each two years of age and if
2678: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2679: results. So we changed our mind and took the option of the best precision.
2680: */
2681: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2682:
2683: /* If stepm=6 months */
2684: /* nhstepm age range expressed in number of stepm */
2685: agelim=AGESUP;
2686: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2687: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2688: /* if (stepm >= YEARM) hstepm=1;*/
2689: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2690:
2691: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2692: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2693: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2694: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2695: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2696: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2697:
2698: for (age=bage; age<=fage; age ++){
2699: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2700: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2701: /* if (stepm >= YEARM) hstepm=1;*/
2702: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2703:
2704: /* If stepm=6 months */
2705: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2706: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2707:
2708: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2709:
2710: /* Computing Variances of health expectancies */
2711: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2712: decrease memory allocation */
2713: for(theta=1; theta <=npar; theta++){
2714: for(i=1; i<=npar; i++){
2715: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2716: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2717: }
2718: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2719: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2720:
2721: for(j=1; j<= nlstate; j++){
2722: for(i=1; i<=nlstate; i++){
2723: for(h=0; h<=nhstepm-1; h++){
2724: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2725: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2726: }
2727: }
2728: }
2729:
2730: for(ij=1; ij<= nlstate*nlstate; ij++)
2731: for(h=0; h<=nhstepm-1; h++){
2732: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2733: }
2734: }/* End theta */
2735:
2736:
2737: for(h=0; h<=nhstepm-1; h++)
2738: for(j=1; j<=nlstate*nlstate;j++)
2739: for(theta=1; theta <=npar; theta++)
2740: trgradg[h][j][theta]=gradg[h][theta][j];
2741:
2742:
2743: for(ij=1;ij<=nlstate*nlstate;ij++)
2744: for(ji=1;ji<=nlstate*nlstate;ji++)
2745: varhe[ij][ji][(int)age] =0.;
2746:
2747: printf("%d|",(int)age);fflush(stdout);
2748: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2749: for(h=0;h<=nhstepm-1;h++){
2750: for(k=0;k<=nhstepm-1;k++){
2751: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2752: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2753: for(ij=1;ij<=nlstate*nlstate;ij++)
2754: for(ji=1;ji<=nlstate*nlstate;ji++)
2755: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2756: }
2757: }
2758:
2759: /* Computing expectancies */
2760: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2761: for(i=1; i<=nlstate;i++)
2762: for(j=1; j<=nlstate;j++)
2763: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2764: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2765:
2766: /* 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]);*/
2767:
2768: }
2769:
2770: fprintf(ficresstdeij,"%3.0f",age );
2771: for(i=1; i<=nlstate;i++){
2772: eip=0.;
2773: vip=0.;
2774: for(j=1; j<=nlstate;j++){
2775: eip += eij[i][j][(int)age];
2776: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2777: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2778: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2779: }
2780: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2781: }
2782: fprintf(ficresstdeij,"\n");
2783:
2784: fprintf(ficrescveij,"%3.0f",age );
2785: for(i=1; i<=nlstate;i++)
2786: for(j=1; j<=nlstate;j++){
2787: cptj= (j-1)*nlstate+i;
2788: for(i2=1; i2<=nlstate;i2++)
2789: for(j2=1; j2<=nlstate;j2++){
2790: cptj2= (j2-1)*nlstate+i2;
2791: if(cptj2 <= cptj)
2792: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2793: }
2794: }
2795: fprintf(ficrescveij,"\n");
2796:
2797: }
2798: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2799: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2800: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2801: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2802: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2803: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2804: printf("\n");
2805: fprintf(ficlog,"\n");
2806:
2807: free_vector(xm,1,npar);
2808: free_vector(xp,1,npar);
2809: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2810: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2811: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2812: }
2813:
2814: /************ Variance ******************/
2815: 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[])
2816: {
2817: /* Variance of health expectancies */
2818: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2819: /* double **newm;*/
2820: double **dnewm,**doldm;
2821: double **dnewmp,**doldmp;
2822: int i, j, nhstepm, hstepm, h, nstepm ;
2823: int k, cptcode;
2824: double *xp;
2825: double **gp, **gm; /* for var eij */
2826: double ***gradg, ***trgradg; /*for var eij */
2827: double **gradgp, **trgradgp; /* for var p point j */
2828: double *gpp, *gmp; /* for var p point j */
2829: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2830: double ***p3mat;
2831: double age,agelim, hf;
2832: double ***mobaverage;
2833: int theta;
2834: char digit[4];
2835: char digitp[25];
2836:
2837: char fileresprobmorprev[FILENAMELENGTH];
2838:
2839: if(popbased==1){
2840: if(mobilav!=0)
2841: strcpy(digitp,"-populbased-mobilav-");
2842: else strcpy(digitp,"-populbased-nomobil-");
2843: }
2844: else
2845: strcpy(digitp,"-stablbased-");
2846:
2847: if (mobilav!=0) {
2848: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2849: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2850: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2851: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2852: }
2853: }
2854:
2855: strcpy(fileresprobmorprev,"prmorprev");
2856: sprintf(digit,"%-d",ij);
2857: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2858: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2859: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2860: strcat(fileresprobmorprev,fileres);
2861: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2862: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2863: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2864: }
2865: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2866:
2867: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2868: pstamp(ficresprobmorprev);
2869: 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);
2870: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2871: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2872: fprintf(ficresprobmorprev," p.%-d SE",j);
2873: for(i=1; i<=nlstate;i++)
2874: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2875: }
2876: fprintf(ficresprobmorprev,"\n");
2877: fprintf(ficgp,"\n# Routine varevsij");
2878: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2879: 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");
2880: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2881: /* } */
2882: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2883: pstamp(ficresvij);
2884: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2885: if(popbased==1)
2886: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
2887: else
2888: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2889: fprintf(ficresvij,"# Age");
2890: for(i=1; i<=nlstate;i++)
2891: for(j=1; j<=nlstate;j++)
2892: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2893: fprintf(ficresvij,"\n");
2894:
2895: xp=vector(1,npar);
2896: dnewm=matrix(1,nlstate,1,npar);
2897: doldm=matrix(1,nlstate,1,nlstate);
2898: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2899: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2900:
2901: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2902: gpp=vector(nlstate+1,nlstate+ndeath);
2903: gmp=vector(nlstate+1,nlstate+ndeath);
2904: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2905:
2906: if(estepm < stepm){
2907: printf ("Problem %d lower than %d\n",estepm, stepm);
2908: }
2909: else hstepm=estepm;
2910: /* For example we decided to compute the life expectancy with the smallest unit */
2911: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2912: nhstepm is the number of hstepm from age to agelim
2913: nstepm is the number of stepm from age to agelin.
2914: Look at function hpijx to understand why (it is linked to memory size questions) */
2915: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2916: survival function given by stepm (the optimization length). Unfortunately it
2917: means that if the survival funtion is printed every two years of age and if
2918: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2919: results. So we changed our mind and took the option of the best precision.
2920: */
2921: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2922: agelim = AGESUP;
2923: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2924: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2925: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2926: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2927: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2928: gp=matrix(0,nhstepm,1,nlstate);
2929: gm=matrix(0,nhstepm,1,nlstate);
2930:
2931:
2932: for(theta=1; theta <=npar; theta++){
2933: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2934: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2935: }
2936: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2937: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2938:
2939: if (popbased==1) {
2940: if(mobilav ==0){
2941: for(i=1; i<=nlstate;i++)
2942: prlim[i][i]=probs[(int)age][i][ij];
2943: }else{ /* mobilav */
2944: for(i=1; i<=nlstate;i++)
2945: prlim[i][i]=mobaverage[(int)age][i][ij];
2946: }
2947: }
2948:
2949: for(j=1; j<= nlstate; j++){
2950: for(h=0; h<=nhstepm; h++){
2951: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2952: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2953: }
2954: }
2955: /* This for computing probability of death (h=1 means
2956: computed over hstepm matrices product = hstepm*stepm months)
2957: as a weighted average of prlim.
2958: */
2959: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2960: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2961: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2962: }
2963: /* end probability of death */
2964:
2965: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2966: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2967: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2968: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2969:
2970: if (popbased==1) {
2971: if(mobilav ==0){
2972: for(i=1; i<=nlstate;i++)
2973: prlim[i][i]=probs[(int)age][i][ij];
2974: }else{ /* mobilav */
2975: for(i=1; i<=nlstate;i++)
2976: prlim[i][i]=mobaverage[(int)age][i][ij];
2977: }
2978: }
2979:
2980: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
2981: for(h=0; h<=nhstepm; h++){
2982: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2983: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2984: }
2985: }
2986: /* This for computing probability of death (h=1 means
2987: computed over hstepm matrices product = hstepm*stepm months)
2988: as a weighted average of prlim.
2989: */
2990: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2991: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2992: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2993: }
2994: /* end probability of death */
2995:
2996: for(j=1; j<= nlstate; j++) /* vareij */
2997: for(h=0; h<=nhstepm; h++){
2998: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2999: }
3000:
3001: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3002: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3003: }
3004:
3005: } /* End theta */
3006:
3007: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3008:
3009: for(h=0; h<=nhstepm; h++) /* veij */
3010: for(j=1; j<=nlstate;j++)
3011: for(theta=1; theta <=npar; theta++)
3012: trgradg[h][j][theta]=gradg[h][theta][j];
3013:
3014: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3015: for(theta=1; theta <=npar; theta++)
3016: trgradgp[j][theta]=gradgp[theta][j];
3017:
3018:
3019: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3020: for(i=1;i<=nlstate;i++)
3021: for(j=1;j<=nlstate;j++)
3022: vareij[i][j][(int)age] =0.;
3023:
3024: for(h=0;h<=nhstepm;h++){
3025: for(k=0;k<=nhstepm;k++){
3026: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3027: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3028: for(i=1;i<=nlstate;i++)
3029: for(j=1;j<=nlstate;j++)
3030: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3031: }
3032: }
3033:
3034: /* pptj */
3035: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3036: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3037: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3038: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3039: varppt[j][i]=doldmp[j][i];
3040: /* end ppptj */
3041: /* x centered again */
3042: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3043: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3044:
3045: if (popbased==1) {
3046: if(mobilav ==0){
3047: for(i=1; i<=nlstate;i++)
3048: prlim[i][i]=probs[(int)age][i][ij];
3049: }else{ /* mobilav */
3050: for(i=1; i<=nlstate;i++)
3051: prlim[i][i]=mobaverage[(int)age][i][ij];
3052: }
3053: }
3054:
3055: /* This for computing probability of death (h=1 means
3056: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3057: as a weighted average of prlim.
3058: */
3059: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3060: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3061: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3062: }
3063: /* end probability of death */
3064:
3065: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3066: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3067: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3068: for(i=1; i<=nlstate;i++){
3069: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3070: }
3071: }
3072: fprintf(ficresprobmorprev,"\n");
3073:
3074: fprintf(ficresvij,"%.0f ",age );
3075: for(i=1; i<=nlstate;i++)
3076: for(j=1; j<=nlstate;j++){
3077: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3078: }
3079: fprintf(ficresvij,"\n");
3080: free_matrix(gp,0,nhstepm,1,nlstate);
3081: free_matrix(gm,0,nhstepm,1,nlstate);
3082: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3083: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3084: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3085: } /* End age */
3086: free_vector(gpp,nlstate+1,nlstate+ndeath);
3087: free_vector(gmp,nlstate+1,nlstate+ndeath);
3088: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3089: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3090: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3091: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3092: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3093: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3094: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3095: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3096: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3097: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3098: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3099: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3100: 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);
3101: /* 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);
3102: */
3103: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3104: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3105:
3106: free_vector(xp,1,npar);
3107: free_matrix(doldm,1,nlstate,1,nlstate);
3108: free_matrix(dnewm,1,nlstate,1,npar);
3109: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3110: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3111: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3112: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3113: fclose(ficresprobmorprev);
3114: fflush(ficgp);
3115: fflush(fichtm);
3116: } /* end varevsij */
3117:
3118: /************ Variance of prevlim ******************/
3119: 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[])
3120: {
3121: /* Variance of prevalence limit */
3122: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3123: double **newm;
3124: double **dnewm,**doldm;
3125: int i, j, nhstepm, hstepm;
3126: int k, cptcode;
3127: double *xp;
3128: double *gp, *gm;
3129: double **gradg, **trgradg;
3130: double age,agelim;
3131: int theta;
3132:
3133: pstamp(ficresvpl);
3134: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3135: fprintf(ficresvpl,"# Age");
3136: for(i=1; i<=nlstate;i++)
3137: fprintf(ficresvpl," %1d-%1d",i,i);
3138: fprintf(ficresvpl,"\n");
3139:
3140: xp=vector(1,npar);
3141: dnewm=matrix(1,nlstate,1,npar);
3142: doldm=matrix(1,nlstate,1,nlstate);
3143:
3144: hstepm=1*YEARM; /* Every year of age */
3145: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3146: agelim = AGESUP;
3147: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3148: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3149: if (stepm >= YEARM) hstepm=1;
3150: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3151: gradg=matrix(1,npar,1,nlstate);
3152: gp=vector(1,nlstate);
3153: gm=vector(1,nlstate);
3154:
3155: for(theta=1; theta <=npar; theta++){
3156: for(i=1; i<=npar; i++){ /* Computes gradient */
3157: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3158: }
3159: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3160: for(i=1;i<=nlstate;i++)
3161: gp[i] = prlim[i][i];
3162:
3163: for(i=1; i<=npar; i++) /* Computes gradient */
3164: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3165: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3166: for(i=1;i<=nlstate;i++)
3167: gm[i] = prlim[i][i];
3168:
3169: for(i=1;i<=nlstate;i++)
3170: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3171: } /* End theta */
3172:
3173: trgradg =matrix(1,nlstate,1,npar);
3174:
3175: for(j=1; j<=nlstate;j++)
3176: for(theta=1; theta <=npar; theta++)
3177: trgradg[j][theta]=gradg[theta][j];
3178:
3179: for(i=1;i<=nlstate;i++)
3180: varpl[i][(int)age] =0.;
3181: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3182: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3183: for(i=1;i<=nlstate;i++)
3184: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3185:
3186: fprintf(ficresvpl,"%.0f ",age );
3187: for(i=1; i<=nlstate;i++)
3188: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3189: fprintf(ficresvpl,"\n");
3190: free_vector(gp,1,nlstate);
3191: free_vector(gm,1,nlstate);
3192: free_matrix(gradg,1,npar,1,nlstate);
3193: free_matrix(trgradg,1,nlstate,1,npar);
3194: } /* End age */
3195:
3196: free_vector(xp,1,npar);
3197: free_matrix(doldm,1,nlstate,1,npar);
3198: free_matrix(dnewm,1,nlstate,1,nlstate);
3199:
3200: }
3201:
3202: /************ Variance of one-step probabilities ******************/
3203: 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[])
3204: {
3205: int i, j=0, i1, k1, l1, t, tj;
3206: int k2, l2, j1, z1;
3207: int k=0,l, cptcode;
3208: int first=1, first1;
3209: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3210: double **dnewm,**doldm;
3211: double *xp;
3212: double *gp, *gm;
3213: double **gradg, **trgradg;
3214: double **mu;
3215: double age,agelim, cov[NCOVMAX];
3216: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3217: int theta;
3218: char fileresprob[FILENAMELENGTH];
3219: char fileresprobcov[FILENAMELENGTH];
3220: char fileresprobcor[FILENAMELENGTH];
3221:
3222: double ***varpij;
3223:
3224: strcpy(fileresprob,"prob");
3225: strcat(fileresprob,fileres);
3226: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3227: printf("Problem with resultfile: %s\n", fileresprob);
3228: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3229: }
3230: strcpy(fileresprobcov,"probcov");
3231: strcat(fileresprobcov,fileres);
3232: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3233: printf("Problem with resultfile: %s\n", fileresprobcov);
3234: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3235: }
3236: strcpy(fileresprobcor,"probcor");
3237: strcat(fileresprobcor,fileres);
3238: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3239: printf("Problem with resultfile: %s\n", fileresprobcor);
3240: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3241: }
3242: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3243: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3244: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3245: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3246: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3247: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3248: pstamp(ficresprob);
3249: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3250: fprintf(ficresprob,"# Age");
3251: pstamp(ficresprobcov);
3252: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3253: fprintf(ficresprobcov,"# Age");
3254: pstamp(ficresprobcor);
3255: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3256: fprintf(ficresprobcor,"# Age");
3257:
3258:
3259: for(i=1; i<=nlstate;i++)
3260: for(j=1; j<=(nlstate+ndeath);j++){
3261: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3262: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3263: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3264: }
3265: /* fprintf(ficresprob,"\n");
3266: fprintf(ficresprobcov,"\n");
3267: fprintf(ficresprobcor,"\n");
3268: */
3269: xp=vector(1,npar);
3270: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3271: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3272: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3273: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3274: first=1;
3275: fprintf(ficgp,"\n# Routine varprob");
3276: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3277: fprintf(fichtm,"\n");
3278:
3279: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3280: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3281: file %s<br>\n",optionfilehtmcov);
3282: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3283: and drawn. It helps understanding how is the covariance between two incidences.\
3284: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3285: 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. \
3286: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3287: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3288: standard deviations wide on each axis. <br>\
3289: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3290: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3291: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3292:
3293: cov[1]=1;
3294: tj=cptcoveff;
3295: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3296: j1=0;
3297: for(t=1; t<=tj;t++){
3298: for(i1=1; i1<=ncodemax[t];i1++){
3299: j1++;
3300: if (cptcovn>0) {
3301: fprintf(ficresprob, "\n#********** Variable ");
3302: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3303: fprintf(ficresprob, "**********\n#\n");
3304: fprintf(ficresprobcov, "\n#********** Variable ");
3305: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3306: fprintf(ficresprobcov, "**********\n#\n");
3307:
3308: fprintf(ficgp, "\n#********** Variable ");
3309: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3310: fprintf(ficgp, "**********\n#\n");
3311:
3312:
3313: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3314: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3315: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3316:
3317: fprintf(ficresprobcor, "\n#********** Variable ");
3318: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3319: fprintf(ficresprobcor, "**********\n#");
3320: }
3321:
3322: for (age=bage; age<=fage; age ++){
3323: cov[2]=age;
3324: for (k=1; k<=cptcovn;k++) {
3325: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3326: }
3327: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3328: for (k=1; k<=cptcovprod;k++)
3329: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3330:
3331: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3332: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3333: gp=vector(1,(nlstate)*(nlstate+ndeath));
3334: gm=vector(1,(nlstate)*(nlstate+ndeath));
3335:
3336: for(theta=1; theta <=npar; theta++){
3337: for(i=1; i<=npar; i++)
3338: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3339:
3340: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3341:
3342: k=0;
3343: for(i=1; i<= (nlstate); i++){
3344: for(j=1; j<=(nlstate+ndeath);j++){
3345: k=k+1;
3346: gp[k]=pmmij[i][j];
3347: }
3348: }
3349:
3350: for(i=1; i<=npar; i++)
3351: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3352:
3353: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3354: k=0;
3355: for(i=1; i<=(nlstate); i++){
3356: for(j=1; j<=(nlstate+ndeath);j++){
3357: k=k+1;
3358: gm[k]=pmmij[i][j];
3359: }
3360: }
3361:
3362: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3363: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3364: }
3365:
3366: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3367: for(theta=1; theta <=npar; theta++)
3368: trgradg[j][theta]=gradg[theta][j];
3369:
3370: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3371: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3372: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3373: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3374: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3375: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3376:
3377: pmij(pmmij,cov,ncovmodel,x,nlstate);
3378:
3379: k=0;
3380: for(i=1; i<=(nlstate); i++){
3381: for(j=1; j<=(nlstate+ndeath);j++){
3382: k=k+1;
3383: mu[k][(int) age]=pmmij[i][j];
3384: }
3385: }
3386: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3387: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3388: varpij[i][j][(int)age] = doldm[i][j];
3389:
3390: /*printf("\n%d ",(int)age);
3391: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3392: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3393: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3394: }*/
3395:
3396: fprintf(ficresprob,"\n%d ",(int)age);
3397: fprintf(ficresprobcov,"\n%d ",(int)age);
3398: fprintf(ficresprobcor,"\n%d ",(int)age);
3399:
3400: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3401: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3402: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3403: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3404: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3405: }
3406: i=0;
3407: for (k=1; k<=(nlstate);k++){
3408: for (l=1; l<=(nlstate+ndeath);l++){
3409: i=i++;
3410: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3411: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3412: for (j=1; j<=i;j++){
3413: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3414: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3415: }
3416: }
3417: }/* end of loop for state */
3418: } /* end of loop for age */
3419:
3420: /* Confidence intervalle of pij */
3421: /*
3422: fprintf(ficgp,"\nset noparametric;unset label");
3423: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3424: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3425: 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);
3426: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3427: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3428: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3429: */
3430:
3431: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3432: first1=1;
3433: for (k2=1; k2<=(nlstate);k2++){
3434: for (l2=1; l2<=(nlstate+ndeath);l2++){
3435: if(l2==k2) continue;
3436: j=(k2-1)*(nlstate+ndeath)+l2;
3437: for (k1=1; k1<=(nlstate);k1++){
3438: for (l1=1; l1<=(nlstate+ndeath);l1++){
3439: if(l1==k1) continue;
3440: i=(k1-1)*(nlstate+ndeath)+l1;
3441: if(i<=j) continue;
3442: for (age=bage; age<=fage; age ++){
3443: if ((int)age %5==0){
3444: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3445: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3446: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3447: mu1=mu[i][(int) age]/stepm*YEARM ;
3448: mu2=mu[j][(int) age]/stepm*YEARM;
3449: c12=cv12/sqrt(v1*v2);
3450: /* Computing eigen value of matrix of covariance */
3451: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3452: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3453: /* Eigen vectors */
3454: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3455: /*v21=sqrt(1.-v11*v11); *//* error */
3456: v21=(lc1-v1)/cv12*v11;
3457: v12=-v21;
3458: v22=v11;
3459: tnalp=v21/v11;
3460: if(first1==1){
3461: first1=0;
3462: 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);
3463: }
3464: 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);
3465: /*printf(fignu*/
3466: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3467: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3468: if(first==1){
3469: first=0;
3470: fprintf(ficgp,"\nset parametric;unset label");
3471: 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);
3472: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3473: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3474: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3475: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3476: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3477: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3478: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3479: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3480: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3481: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3482: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3483: 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",\
3484: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3485: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3486: }else{
3487: first=0;
3488: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3489: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3490: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3491: 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",\
3492: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3493: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3494: }/* if first */
3495: } /* age mod 5 */
3496: } /* end loop age */
3497: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3498: first=1;
3499: } /*l12 */
3500: } /* k12 */
3501: } /*l1 */
3502: }/* k1 */
3503: } /* loop covariates */
3504: }
3505: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3506: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3507: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3508: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3509: free_vector(xp,1,npar);
3510: fclose(ficresprob);
3511: fclose(ficresprobcov);
3512: fclose(ficresprobcor);
3513: fflush(ficgp);
3514: fflush(fichtmcov);
3515: }
3516:
3517:
3518: /******************* Printing html file ***********/
3519: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3520: int lastpass, int stepm, int weightopt, char model[],\
3521: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3522: int popforecast, int estepm ,\
3523: double jprev1, double mprev1,double anprev1, \
3524: double jprev2, double mprev2,double anprev2){
3525: int jj1, k1, i1, cpt;
3526:
3527: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3528: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3529: </ul>");
3530: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3531: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3532: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3533: fprintf(fichtm,"\
3534: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3535: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3536: fprintf(fichtm,"\
3537: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3538: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3539: fprintf(fichtm,"\
3540: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
3541: <a href=\"%s\">%s</a> <br>\n",
3542: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3543: fprintf(fichtm,"\
3544: - Population projections by age and states: \
3545: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3546:
3547: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3548:
3549: m=cptcoveff;
3550: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3551:
3552: jj1=0;
3553: for(k1=1; k1<=m;k1++){
3554: for(i1=1; i1<=ncodemax[k1];i1++){
3555: jj1++;
3556: if (cptcovn > 0) {
3557: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3558: for (cpt=1; cpt<=cptcoveff;cpt++)
3559: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3560: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3561: }
3562: /* Pij */
3563: 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> \
3564: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3565: /* Quasi-incidences */
3566: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3567: 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> \
3568: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3569: /* Period (stable) prevalence in each health state */
3570: for(cpt=1; cpt<nlstate;cpt++){
3571: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3572: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3573: }
3574: for(cpt=1; cpt<=nlstate;cpt++) {
3575: 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> \
3576: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3577: }
3578: } /* end i1 */
3579: }/* End k1 */
3580: fprintf(fichtm,"</ul>");
3581:
3582:
3583: fprintf(fichtm,"\
3584: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3585: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3586:
3587: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3588: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3589: fprintf(fichtm,"\
3590: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3591: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3592:
3593: fprintf(fichtm,"\
3594: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3595: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3596: fprintf(fichtm,"\
3597: - 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): \
3598: <a href=\"%s\">%s</a> <br>\n</li>",
3599: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3600: fprintf(fichtm,"\
3601: - (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): \
3602: <a href=\"%s\">%s</a> <br>\n</li>",
3603: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3604: fprintf(fichtm,"\
3605: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> 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",
3606: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3607: fprintf(fichtm,"\
3608: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
3609: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3610: fprintf(fichtm,"\
3611: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3612: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3613:
3614: /* if(popforecast==1) fprintf(fichtm,"\n */
3615: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3616: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3617: /* <br>",fileres,fileres,fileres,fileres); */
3618: /* else */
3619: /* 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); */
3620: fflush(fichtm);
3621: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3622:
3623: m=cptcoveff;
3624: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3625:
3626: jj1=0;
3627: for(k1=1; k1<=m;k1++){
3628: for(i1=1; i1<=ncodemax[k1];i1++){
3629: jj1++;
3630: if (cptcovn > 0) {
3631: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3632: for (cpt=1; cpt<=cptcoveff;cpt++)
3633: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3634: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3635: }
3636: for(cpt=1; cpt<=nlstate;cpt++) {
3637: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3638: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3639: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3640: }
3641: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3642: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3643: true period expectancies (those weighted with period prevalences are also\
3644: drawn in addition to the population based expectancies computed using\
3645: observed and cahotic prevalences: %s%d.png<br>\
3646: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3647: } /* end i1 */
3648: }/* End k1 */
3649: fprintf(fichtm,"</ul>");
3650: fflush(fichtm);
3651: }
3652:
3653: /******************* Gnuplot file **************/
3654: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3655:
3656: char dirfileres[132],optfileres[132];
3657: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3658: int ng=0;
3659: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3660: /* printf("Problem with file %s",optionfilegnuplot); */
3661: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3662: /* } */
3663:
3664: /*#ifdef windows */
3665: fprintf(ficgp,"cd \"%s\" \n",pathc);
3666: /*#endif */
3667: m=pow(2,cptcoveff);
3668:
3669: strcpy(dirfileres,optionfilefiname);
3670: strcpy(optfileres,"vpl");
3671: /* 1eme*/
3672: for (cpt=1; cpt<= nlstate ; cpt ++) {
3673: for (k1=1; k1<= m ; k1 ++) {
3674: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3675: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3676: fprintf(ficgp,"set xlabel \"Age\" \n\
3677: set ylabel \"Probability\" \n\
3678: set ter png small\n\
3679: set size 0.65,0.65\n\
3680: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3681:
3682: for (i=1; i<= nlstate ; i ++) {
3683: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3684: else fprintf(ficgp," \%%*lf (\%%*lf)");
3685: }
3686: 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);
3687: for (i=1; i<= nlstate ; i ++) {
3688: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3689: else fprintf(ficgp," \%%*lf (\%%*lf)");
3690: }
3691: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3692: for (i=1; i<= nlstate ; i ++) {
3693: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3694: else fprintf(ficgp," \%%*lf (\%%*lf)");
3695: }
3696: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3697: }
3698: }
3699: /*2 eme*/
3700:
3701: for (k1=1; k1<= m ; k1 ++) {
3702: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3703: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3704:
3705: for (i=1; i<= nlstate+1 ; i ++) {
3706: k=2*i;
3707: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3708: for (j=1; j<= nlstate+1 ; j ++) {
3709: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3710: else fprintf(ficgp," \%%*lf (\%%*lf)");
3711: }
3712: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3713: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3714: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3715: for (j=1; j<= nlstate+1 ; j ++) {
3716: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3717: else fprintf(ficgp," \%%*lf (\%%*lf)");
3718: }
3719: fprintf(ficgp,"\" t\"\" w l 0,");
3720: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3721: for (j=1; j<= nlstate+1 ; j ++) {
3722: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3723: else fprintf(ficgp," \%%*lf (\%%*lf)");
3724: }
3725: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3726: else fprintf(ficgp,"\" t\"\" w l 0,");
3727: }
3728: }
3729:
3730: /*3eme*/
3731:
3732: for (k1=1; k1<= m ; k1 ++) {
3733: for (cpt=1; cpt<= nlstate ; cpt ++) {
3734: /* k=2+nlstate*(2*cpt-2); */
3735: k=2+(nlstate+1)*(cpt-1);
3736: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3737: fprintf(ficgp,"set ter png small\n\
3738: set size 0.65,0.65\n\
3739: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3740: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3741: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3742: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3743: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3744: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3745: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3746:
3747: */
3748: for (i=1; i< nlstate ; i ++) {
3749: 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);
3750: /* 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);*/
3751:
3752: }
3753: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3754: }
3755: }
3756:
3757: /* CV preval stable (period) */
3758: for (k1=1; k1<= m ; k1 ++) {
3759: for (cpt=1; cpt<=nlstate ; cpt ++) {
3760: k=3;
3761: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3762: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3763: set ter png small\nset size 0.65,0.65\n\
3764: unset log y\n\
3765: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3766:
3767: for (i=1; i< nlstate ; i ++)
3768: fprintf(ficgp,"+$%d",k+i+1);
3769: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3770:
3771: l=3+(nlstate+ndeath)*cpt;
3772: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3773: for (i=1; i< nlstate ; i ++) {
3774: l=3+(nlstate+ndeath)*cpt;
3775: fprintf(ficgp,"+$%d",l+i+1);
3776: }
3777: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3778: }
3779: }
3780:
3781: /* proba elementaires */
3782: for(i=1,jk=1; i <=nlstate; i++){
3783: for(k=1; k <=(nlstate+ndeath); k++){
3784: if (k != i) {
3785: for(j=1; j <=ncovmodel; j++){
3786: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3787: jk++;
3788: fprintf(ficgp,"\n");
3789: }
3790: }
3791: }
3792: }
3793:
3794: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3795: for(jk=1; jk <=m; jk++) {
3796: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3797: if (ng==2)
3798: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3799: else
3800: fprintf(ficgp,"\nset title \"Probability\"\n");
3801: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3802: i=1;
3803: for(k2=1; k2<=nlstate; k2++) {
3804: k3=i;
3805: for(k=1; k<=(nlstate+ndeath); k++) {
3806: if (k != k2){
3807: if(ng==2)
3808: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3809: else
3810: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3811: ij=1;
3812: for(j=3; j <=ncovmodel; j++) {
3813: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3814: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3815: ij++;
3816: }
3817: else
3818: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3819: }
3820: fprintf(ficgp,")/(1");
3821:
3822: for(k1=1; k1 <=nlstate; k1++){
3823: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3824: ij=1;
3825: for(j=3; j <=ncovmodel; j++){
3826: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3827: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3828: ij++;
3829: }
3830: else
3831: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3832: }
3833: fprintf(ficgp,")");
3834: }
3835: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3836: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3837: i=i+ncovmodel;
3838: }
3839: } /* end k */
3840: } /* end k2 */
3841: } /* end jk */
3842: } /* end ng */
3843: fflush(ficgp);
3844: } /* end gnuplot */
3845:
3846:
3847: /*************** Moving average **************/
3848: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3849:
3850: int i, cpt, cptcod;
3851: int modcovmax =1;
3852: int mobilavrange, mob;
3853: double age;
3854:
3855: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3856: a covariate has 2 modalities */
3857: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3858:
3859: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3860: if(mobilav==1) mobilavrange=5; /* default */
3861: else mobilavrange=mobilav;
3862: for (age=bage; age<=fage; age++)
3863: for (i=1; i<=nlstate;i++)
3864: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3865: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3866: /* We keep the original values on the extreme ages bage, fage and for
3867: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3868: we use a 5 terms etc. until the borders are no more concerned.
3869: */
3870: for (mob=3;mob <=mobilavrange;mob=mob+2){
3871: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3872: for (i=1; i<=nlstate;i++){
3873: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3874: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3875: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3876: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3877: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3878: }
3879: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3880: }
3881: }
3882: }/* end age */
3883: }/* end mob */
3884: }else return -1;
3885: return 0;
3886: }/* End movingaverage */
3887:
3888:
3889: /************** Forecasting ******************/
3890: 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){
3891: /* proj1, year, month, day of starting projection
3892: agemin, agemax range of age
3893: dateprev1 dateprev2 range of dates during which prevalence is computed
3894: anproj2 year of en of projection (same day and month as proj1).
3895: */
3896: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3897: int *popage;
3898: double agec; /* generic age */
3899: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3900: double *popeffectif,*popcount;
3901: double ***p3mat;
3902: double ***mobaverage;
3903: char fileresf[FILENAMELENGTH];
3904:
3905: agelim=AGESUP;
3906: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3907:
3908: strcpy(fileresf,"f");
3909: strcat(fileresf,fileres);
3910: if((ficresf=fopen(fileresf,"w"))==NULL) {
3911: printf("Problem with forecast resultfile: %s\n", fileresf);
3912: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3913: }
3914: printf("Computing forecasting: result on file '%s' \n", fileresf);
3915: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3916:
3917: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3918:
3919: if (mobilav!=0) {
3920: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3921: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3922: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3923: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3924: }
3925: }
3926:
3927: stepsize=(int) (stepm+YEARM-1)/YEARM;
3928: if (stepm<=12) stepsize=1;
3929: if(estepm < stepm){
3930: printf ("Problem %d lower than %d\n",estepm, stepm);
3931: }
3932: else hstepm=estepm;
3933:
3934: hstepm=hstepm/stepm;
3935: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3936: fractional in yp1 */
3937: anprojmean=yp;
3938: yp2=modf((yp1*12),&yp);
3939: mprojmean=yp;
3940: yp1=modf((yp2*30.5),&yp);
3941: jprojmean=yp;
3942: if(jprojmean==0) jprojmean=1;
3943: if(mprojmean==0) jprojmean=1;
3944:
3945: i1=cptcoveff;
3946: if (cptcovn < 1){i1=1;}
3947:
3948: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3949:
3950: fprintf(ficresf,"#****** Routine prevforecast **\n");
3951:
3952: /* if (h==(int)(YEARM*yearp)){ */
3953: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3954: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3955: k=k+1;
3956: fprintf(ficresf,"\n#******");
3957: for(j=1;j<=cptcoveff;j++) {
3958: 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]]);
3959: }
3960: fprintf(ficresf,"******\n");
3961: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3962: for(j=1; j<=nlstate+ndeath;j++){
3963: for(i=1; i<=nlstate;i++)
3964: fprintf(ficresf," p%d%d",i,j);
3965: fprintf(ficresf," p.%d",j);
3966: }
3967: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3968: fprintf(ficresf,"\n");
3969: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3970:
3971: for (agec=fage; agec>=(ageminpar-1); agec--){
3972: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3973: nhstepm = nhstepm/hstepm;
3974: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3975: oldm=oldms;savm=savms;
3976: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3977:
3978: for (h=0; h<=nhstepm; h++){
3979: if (h*hstepm/YEARM*stepm ==yearp) {
3980: fprintf(ficresf,"\n");
3981: for(j=1;j<=cptcoveff;j++)
3982: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3983: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3984: }
3985: for(j=1; j<=nlstate+ndeath;j++) {
3986: ppij=0.;
3987: for(i=1; i<=nlstate;i++) {
3988: if (mobilav==1)
3989: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3990: else {
3991: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3992: }
3993: if (h*hstepm/YEARM*stepm== yearp) {
3994: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3995: }
3996: } /* end i */
3997: if (h*hstepm/YEARM*stepm==yearp) {
3998: fprintf(ficresf," %.3f", ppij);
3999: }
4000: }/* end j */
4001: } /* end h */
4002: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4003: } /* end agec */
4004: } /* end yearp */
4005: } /* end cptcod */
4006: } /* end cptcov */
4007:
4008: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4009:
4010: fclose(ficresf);
4011: }
4012:
4013: /************** Forecasting *****not tested NB*************/
4014: 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){
4015:
4016: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4017: int *popage;
4018: double calagedatem, agelim, kk1, kk2;
4019: double *popeffectif,*popcount;
4020: double ***p3mat,***tabpop,***tabpopprev;
4021: double ***mobaverage;
4022: char filerespop[FILENAMELENGTH];
4023:
4024: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4025: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4026: agelim=AGESUP;
4027: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4028:
4029: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4030:
4031:
4032: strcpy(filerespop,"pop");
4033: strcat(filerespop,fileres);
4034: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4035: printf("Problem with forecast resultfile: %s\n", filerespop);
4036: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4037: }
4038: printf("Computing forecasting: result on file '%s' \n", filerespop);
4039: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4040:
4041: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4042:
4043: if (mobilav!=0) {
4044: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4045: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4046: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4047: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4048: }
4049: }
4050:
4051: stepsize=(int) (stepm+YEARM-1)/YEARM;
4052: if (stepm<=12) stepsize=1;
4053:
4054: agelim=AGESUP;
4055:
4056: hstepm=1;
4057: hstepm=hstepm/stepm;
4058:
4059: if (popforecast==1) {
4060: if((ficpop=fopen(popfile,"r"))==NULL) {
4061: printf("Problem with population file : %s\n",popfile);exit(0);
4062: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4063: }
4064: popage=ivector(0,AGESUP);
4065: popeffectif=vector(0,AGESUP);
4066: popcount=vector(0,AGESUP);
4067:
4068: i=1;
4069: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4070:
4071: imx=i;
4072: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4073: }
4074:
4075: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4076: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4077: k=k+1;
4078: fprintf(ficrespop,"\n#******");
4079: for(j=1;j<=cptcoveff;j++) {
4080: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4081: }
4082: fprintf(ficrespop,"******\n");
4083: fprintf(ficrespop,"# Age");
4084: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4085: if (popforecast==1) fprintf(ficrespop," [Population]");
4086:
4087: for (cpt=0; cpt<=0;cpt++) {
4088: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4089:
4090: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4091: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4092: nhstepm = nhstepm/hstepm;
4093:
4094: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4095: oldm=oldms;savm=savms;
4096: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4097:
4098: for (h=0; h<=nhstepm; h++){
4099: if (h==(int) (calagedatem+YEARM*cpt)) {
4100: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4101: }
4102: for(j=1; j<=nlstate+ndeath;j++) {
4103: kk1=0.;kk2=0;
4104: for(i=1; i<=nlstate;i++) {
4105: if (mobilav==1)
4106: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4107: else {
4108: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4109: }
4110: }
4111: if (h==(int)(calagedatem+12*cpt)){
4112: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4113: /*fprintf(ficrespop," %.3f", kk1);
4114: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4115: }
4116: }
4117: for(i=1; i<=nlstate;i++){
4118: kk1=0.;
4119: for(j=1; j<=nlstate;j++){
4120: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4121: }
4122: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4123: }
4124:
4125: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4126: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4127: }
4128: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4129: }
4130: }
4131:
4132: /******/
4133:
4134: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4135: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4136: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4137: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4138: nhstepm = nhstepm/hstepm;
4139:
4140: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4141: oldm=oldms;savm=savms;
4142: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4143: for (h=0; h<=nhstepm; h++){
4144: if (h==(int) (calagedatem+YEARM*cpt)) {
4145: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4146: }
4147: for(j=1; j<=nlstate+ndeath;j++) {
4148: kk1=0.;kk2=0;
4149: for(i=1; i<=nlstate;i++) {
4150: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4151: }
4152: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4153: }
4154: }
4155: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4156: }
4157: }
4158: }
4159: }
4160:
4161: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4162:
4163: if (popforecast==1) {
4164: free_ivector(popage,0,AGESUP);
4165: free_vector(popeffectif,0,AGESUP);
4166: free_vector(popcount,0,AGESUP);
4167: }
4168: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4169: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4170: fclose(ficrespop);
4171: } /* End of popforecast */
4172:
4173: int fileappend(FILE *fichier, char *optionfich)
4174: {
4175: if((fichier=fopen(optionfich,"a"))==NULL) {
4176: printf("Problem with file: %s\n", optionfich);
4177: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4178: return (0);
4179: }
4180: fflush(fichier);
4181: return (1);
4182: }
4183:
4184:
4185: /**************** function prwizard **********************/
4186: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4187: {
4188:
4189: /* Wizard to print covariance matrix template */
4190:
4191: char ca[32], cb[32], cc[32];
4192: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4193: int numlinepar;
4194:
4195: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4196: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4197: for(i=1; i <=nlstate; i++){
4198: jj=0;
4199: for(j=1; j <=nlstate+ndeath; j++){
4200: if(j==i) continue;
4201: jj++;
4202: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4203: printf("%1d%1d",i,j);
4204: fprintf(ficparo,"%1d%1d",i,j);
4205: for(k=1; k<=ncovmodel;k++){
4206: /* printf(" %lf",param[i][j][k]); */
4207: /* fprintf(ficparo," %lf",param[i][j][k]); */
4208: printf(" 0.");
4209: fprintf(ficparo," 0.");
4210: }
4211: printf("\n");
4212: fprintf(ficparo,"\n");
4213: }
4214: }
4215: printf("# Scales (for hessian or gradient estimation)\n");
4216: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4217: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4218: for(i=1; i <=nlstate; i++){
4219: jj=0;
4220: for(j=1; j <=nlstate+ndeath; j++){
4221: if(j==i) continue;
4222: jj++;
4223: fprintf(ficparo,"%1d%1d",i,j);
4224: printf("%1d%1d",i,j);
4225: fflush(stdout);
4226: for(k=1; k<=ncovmodel;k++){
4227: /* printf(" %le",delti3[i][j][k]); */
4228: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4229: printf(" 0.");
4230: fprintf(ficparo," 0.");
4231: }
4232: numlinepar++;
4233: printf("\n");
4234: fprintf(ficparo,"\n");
4235: }
4236: }
4237: printf("# Covariance matrix\n");
4238: /* # 121 Var(a12)\n\ */
4239: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4240: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4241: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4242: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4243: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4244: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4245: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4246: fflush(stdout);
4247: fprintf(ficparo,"# Covariance matrix\n");
4248: /* # 121 Var(a12)\n\ */
4249: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4250: /* # ...\n\ */
4251: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4252:
4253: for(itimes=1;itimes<=2;itimes++){
4254: jj=0;
4255: for(i=1; i <=nlstate; i++){
4256: for(j=1; j <=nlstate+ndeath; j++){
4257: if(j==i) continue;
4258: for(k=1; k<=ncovmodel;k++){
4259: jj++;
4260: ca[0]= k+'a'-1;ca[1]='\0';
4261: if(itimes==1){
4262: printf("#%1d%1d%d",i,j,k);
4263: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4264: }else{
4265: printf("%1d%1d%d",i,j,k);
4266: fprintf(ficparo,"%1d%1d%d",i,j,k);
4267: /* printf(" %.5le",matcov[i][j]); */
4268: }
4269: ll=0;
4270: for(li=1;li <=nlstate; li++){
4271: for(lj=1;lj <=nlstate+ndeath; lj++){
4272: if(lj==li) continue;
4273: for(lk=1;lk<=ncovmodel;lk++){
4274: ll++;
4275: if(ll<=jj){
4276: cb[0]= lk +'a'-1;cb[1]='\0';
4277: if(ll<jj){
4278: if(itimes==1){
4279: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4280: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4281: }else{
4282: printf(" 0.");
4283: fprintf(ficparo," 0.");
4284: }
4285: }else{
4286: if(itimes==1){
4287: printf(" Var(%s%1d%1d)",ca,i,j);
4288: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4289: }else{
4290: printf(" 0.");
4291: fprintf(ficparo," 0.");
4292: }
4293: }
4294: }
4295: } /* end lk */
4296: } /* end lj */
4297: } /* end li */
4298: printf("\n");
4299: fprintf(ficparo,"\n");
4300: numlinepar++;
4301: } /* end k*/
4302: } /*end j */
4303: } /* end i */
4304: } /* end itimes */
4305:
4306: } /* end of prwizard */
4307: /******************* Gompertz Likelihood ******************************/
4308: double gompertz(double x[])
4309: {
4310: double A,B,L=0.0,sump=0.,num=0.;
4311: int i,n=0; /* n is the size of the sample */
4312:
4313: for (i=0;i<=imx-1 ; i++) {
4314: sump=sump+weight[i];
4315: /* sump=sump+1;*/
4316: num=num+1;
4317: }
4318:
4319:
4320: /* for (i=0; i<=imx; i++)
4321: 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]);*/
4322:
4323: for (i=1;i<=imx ; i++)
4324: {
4325: if (cens[i] == 1 && wav[i]>1)
4326: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4327:
4328: if (cens[i] == 0 && wav[i]>1)
4329: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4330: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4331:
4332: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4333: if (wav[i] > 1 ) { /* ??? */
4334: L=L+A*weight[i];
4335: /* 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]);*/
4336: }
4337: }
4338:
4339: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4340:
4341: return -2*L*num/sump;
4342: }
4343:
4344: /******************* Printing html file ***********/
4345: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4346: int lastpass, int stepm, int weightopt, char model[],\
4347: int imx, double p[],double **matcov,double agemortsup){
4348: int i,k;
4349:
4350: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4351: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4352: for (i=1;i<=2;i++)
4353: 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]));
4354: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4355: fprintf(fichtm,"</ul>");
4356:
4357: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4358:
4359: 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>");
4360:
4361: for (k=agegomp;k<(agemortsup-2);k++)
4362: 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]);
4363:
4364:
4365: fflush(fichtm);
4366: }
4367:
4368: /******************* Gnuplot file **************/
4369: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4370:
4371: char dirfileres[132],optfileres[132];
4372: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4373: int ng;
4374:
4375:
4376: /*#ifdef windows */
4377: fprintf(ficgp,"cd \"%s\" \n",pathc);
4378: /*#endif */
4379:
4380:
4381: strcpy(dirfileres,optionfilefiname);
4382: strcpy(optfileres,"vpl");
4383: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4384: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4385: fprintf(ficgp, "set ter png small\n set log y\n");
4386: fprintf(ficgp, "set size 0.65,0.65\n");
4387: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4388:
4389: }
4390:
4391:
4392:
4393:
4394:
4395: /***********************************************/
4396: /**************** Main Program *****************/
4397: /***********************************************/
4398:
4399: int main(int argc, char *argv[])
4400: {
4401: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4402: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4403: int linei, month, year,iout;
4404: int jj, ll, li, lj, lk, imk;
4405: int numlinepar=0; /* Current linenumber of parameter file */
4406: int itimes;
4407: int NDIM=2;
4408: int vpopbased=0;
4409:
4410: char ca[32], cb[32], cc[32];
4411: char dummy[]=" ";
4412: /* FILE *fichtm; *//* Html File */
4413: /* FILE *ficgp;*/ /*Gnuplot File */
4414: struct stat info;
4415: double agedeb, agefin,hf;
4416: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4417:
4418: double fret;
4419: double **xi,tmp,delta;
4420:
4421: double dum; /* Dummy variable */
4422: double ***p3mat;
4423: double ***mobaverage;
4424: int *indx;
4425: char line[MAXLINE], linepar[MAXLINE];
4426: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4427: char pathr[MAXLINE], pathimach[MAXLINE];
4428: char **bp, *tok, *val; /* pathtot */
4429: int firstobs=1, lastobs=10;
4430: int sdeb, sfin; /* Status at beginning and end */
4431: int c, h , cpt,l;
4432: int ju,jl, mi;
4433: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4434: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4435: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4436: int mobilav=0,popforecast=0;
4437: int hstepm, nhstepm;
4438: int agemortsup;
4439: float sumlpop=0.;
4440: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4441: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4442:
4443: double bage, fage, age, agelim, agebase;
4444: double ftolpl=FTOL;
4445: double **prlim;
4446: double *severity;
4447: double ***param; /* Matrix of parameters */
4448: double *p;
4449: double **matcov; /* Matrix of covariance */
4450: double ***delti3; /* Scale */
4451: double *delti; /* Scale */
4452: double ***eij, ***vareij;
4453: double **varpl; /* Variances of prevalence limits by age */
4454: double *epj, vepp;
4455: double kk1, kk2;
4456: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4457: double **ximort;
4458: char *alph[]={"a","a","b","c","d","e"}, str[4];
4459: int *dcwave;
4460:
4461: char z[1]="c", occ;
4462:
4463: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4464: char *strt, strtend[80];
4465: char *stratrunc;
4466: int lstra;
4467:
4468: long total_usecs;
4469:
4470: /* setlocale (LC_ALL, ""); */
4471: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4472: /* textdomain (PACKAGE); */
4473: /* setlocale (LC_CTYPE, ""); */
4474: /* setlocale (LC_MESSAGES, ""); */
4475:
4476: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4477: (void) gettimeofday(&start_time,&tzp);
4478: curr_time=start_time;
4479: tm = *localtime(&start_time.tv_sec);
4480: tmg = *gmtime(&start_time.tv_sec);
4481: strcpy(strstart,asctime(&tm));
4482:
4483: /* printf("Localtime (at start)=%s",strstart); */
4484: /* tp.tv_sec = tp.tv_sec +86400; */
4485: /* tm = *localtime(&start_time.tv_sec); */
4486: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4487: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4488: /* tmg.tm_hour=tmg.tm_hour + 1; */
4489: /* tp.tv_sec = mktime(&tmg); */
4490: /* strt=asctime(&tmg); */
4491: /* printf("Time(after) =%s",strstart); */
4492: /* (void) time (&time_value);
4493: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4494: * tm = *localtime(&time_value);
4495: * strstart=asctime(&tm);
4496: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4497: */
4498:
4499: nberr=0; /* Number of errors and warnings */
4500: nbwarn=0;
4501: getcwd(pathcd, size);
4502:
4503: printf("\n%s\n%s",version,fullversion);
4504: if(argc <=1){
4505: printf("\nEnter the parameter file name: ");
4506: fgets(pathr,FILENAMELENGTH,stdin);
4507: i=strlen(pathr);
4508: if(pathr[i-1]=='\n')
4509: pathr[i-1]='\0';
4510: for (tok = pathr; tok != NULL; ){
4511: printf("Pathr |%s|\n",pathr);
4512: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4513: printf("val= |%s| pathr=%s\n",val,pathr);
4514: strcpy (pathtot, val);
4515: if(pathr[0] == '\0') break; /* Dirty */
4516: }
4517: }
4518: else{
4519: strcpy(pathtot,argv[1]);
4520: }
4521: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4522: /*cygwin_split_path(pathtot,path,optionfile);
4523: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4524: /* cutv(path,optionfile,pathtot,'\\');*/
4525:
4526: /* Split argv[0], imach program to get pathimach */
4527: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4528: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4529: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4530: /* strcpy(pathimach,argv[0]); */
4531: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4532: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4533: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4534: chdir(path); /* Can be a relative path */
4535: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4536: printf("Current directory %s!\n",pathcd);
4537: strcpy(command,"mkdir ");
4538: strcat(command,optionfilefiname);
4539: if((outcmd=system(command)) != 0){
4540: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4541: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4542: /* fclose(ficlog); */
4543: /* exit(1); */
4544: }
4545: /* if((imk=mkdir(optionfilefiname))<0){ */
4546: /* perror("mkdir"); */
4547: /* } */
4548:
4549: /*-------- arguments in the command line --------*/
4550:
4551: /* Log file */
4552: strcat(filelog, optionfilefiname);
4553: strcat(filelog,".log"); /* */
4554: if((ficlog=fopen(filelog,"w"))==NULL) {
4555: printf("Problem with logfile %s\n",filelog);
4556: goto end;
4557: }
4558: fprintf(ficlog,"Log filename:%s\n",filelog);
4559: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4560: fprintf(ficlog,"\nEnter the parameter file name: \n");
4561: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4562: path=%s \n\
4563: optionfile=%s\n\
4564: optionfilext=%s\n\
4565: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4566:
4567: printf("Local time (at start):%s",strstart);
4568: fprintf(ficlog,"Local time (at start): %s",strstart);
4569: fflush(ficlog);
4570: /* (void) gettimeofday(&curr_time,&tzp); */
4571: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4572:
4573: /* */
4574: strcpy(fileres,"r");
4575: strcat(fileres, optionfilefiname);
4576: strcat(fileres,".txt"); /* Other files have txt extension */
4577:
4578: /*---------arguments file --------*/
4579:
4580: if((ficpar=fopen(optionfile,"r"))==NULL) {
4581: printf("Problem with optionfile %s\n",optionfile);
4582: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4583: fflush(ficlog);
4584: goto end;
4585: }
4586:
4587:
4588:
4589: strcpy(filereso,"o");
4590: strcat(filereso,fileres);
4591: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4592: printf("Problem with Output resultfile: %s\n", filereso);
4593: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4594: fflush(ficlog);
4595: goto end;
4596: }
4597:
4598: /* Reads comments: lines beginning with '#' */
4599: numlinepar=0;
4600: while((c=getc(ficpar))=='#' && c!= EOF){
4601: ungetc(c,ficpar);
4602: fgets(line, MAXLINE, ficpar);
4603: numlinepar++;
4604: puts(line);
4605: fputs(line,ficparo);
4606: fputs(line,ficlog);
4607: }
4608: ungetc(c,ficpar);
4609:
4610: 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);
4611: numlinepar++;
4612: 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);
4613: 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);
4614: 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);
4615: fflush(ficlog);
4616: while((c=getc(ficpar))=='#' && c!= EOF){
4617: ungetc(c,ficpar);
4618: fgets(line, MAXLINE, ficpar);
4619: numlinepar++;
4620: puts(line);
4621: fputs(line,ficparo);
4622: fputs(line,ficlog);
4623: }
4624: ungetc(c,ficpar);
4625:
4626:
4627: covar=matrix(0,NCOVMAX,1,n);
4628: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4629: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4630:
4631: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4632: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4633: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4634:
4635: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4636: delti=delti3[1][1];
4637: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4638: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4639: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4640: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4641: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4642: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4643: fclose (ficparo);
4644: fclose (ficlog);
4645: goto end;
4646: exit(0);
4647: }
4648: else if(mle==-3) {
4649: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4650: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4651: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4652: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4653: matcov=matrix(1,npar,1,npar);
4654: }
4655: else{
4656: /* Read guess parameters */
4657: /* Reads comments: lines beginning with '#' */
4658: while((c=getc(ficpar))=='#' && c!= EOF){
4659: ungetc(c,ficpar);
4660: fgets(line, MAXLINE, ficpar);
4661: numlinepar++;
4662: puts(line);
4663: fputs(line,ficparo);
4664: fputs(line,ficlog);
4665: }
4666: ungetc(c,ficpar);
4667:
4668: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4669: for(i=1; i <=nlstate; i++){
4670: j=0;
4671: for(jj=1; jj <=nlstate+ndeath; jj++){
4672: if(jj==i) continue;
4673: j++;
4674: fscanf(ficpar,"%1d%1d",&i1,&j1);
4675: if ((i1 != i) && (j1 != j)){
4676: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4677: It might be a problem of design; if ncovcol and the model are correct\n \
4678: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4679: exit(1);
4680: }
4681: fprintf(ficparo,"%1d%1d",i1,j1);
4682: if(mle==1)
4683: printf("%1d%1d",i,j);
4684: fprintf(ficlog,"%1d%1d",i,j);
4685: for(k=1; k<=ncovmodel;k++){
4686: fscanf(ficpar," %lf",¶m[i][j][k]);
4687: if(mle==1){
4688: printf(" %lf",param[i][j][k]);
4689: fprintf(ficlog," %lf",param[i][j][k]);
4690: }
4691: else
4692: fprintf(ficlog," %lf",param[i][j][k]);
4693: fprintf(ficparo," %lf",param[i][j][k]);
4694: }
4695: fscanf(ficpar,"\n");
4696: numlinepar++;
4697: if(mle==1)
4698: printf("\n");
4699: fprintf(ficlog,"\n");
4700: fprintf(ficparo,"\n");
4701: }
4702: }
4703: fflush(ficlog);
4704:
4705: p=param[1][1];
4706:
4707: /* Reads comments: lines beginning with '#' */
4708: while((c=getc(ficpar))=='#' && c!= EOF){
4709: ungetc(c,ficpar);
4710: fgets(line, MAXLINE, ficpar);
4711: numlinepar++;
4712: puts(line);
4713: fputs(line,ficparo);
4714: fputs(line,ficlog);
4715: }
4716: ungetc(c,ficpar);
4717:
4718: for(i=1; i <=nlstate; i++){
4719: for(j=1; j <=nlstate+ndeath-1; j++){
4720: fscanf(ficpar,"%1d%1d",&i1,&j1);
4721: if ((i1-i)*(j1-j)!=0){
4722: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4723: exit(1);
4724: }
4725: printf("%1d%1d",i,j);
4726: fprintf(ficparo,"%1d%1d",i1,j1);
4727: fprintf(ficlog,"%1d%1d",i1,j1);
4728: for(k=1; k<=ncovmodel;k++){
4729: fscanf(ficpar,"%le",&delti3[i][j][k]);
4730: printf(" %le",delti3[i][j][k]);
4731: fprintf(ficparo," %le",delti3[i][j][k]);
4732: fprintf(ficlog," %le",delti3[i][j][k]);
4733: }
4734: fscanf(ficpar,"\n");
4735: numlinepar++;
4736: printf("\n");
4737: fprintf(ficparo,"\n");
4738: fprintf(ficlog,"\n");
4739: }
4740: }
4741: fflush(ficlog);
4742:
4743: delti=delti3[1][1];
4744:
4745:
4746: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4747:
4748: /* Reads comments: lines beginning with '#' */
4749: while((c=getc(ficpar))=='#' && c!= EOF){
4750: ungetc(c,ficpar);
4751: fgets(line, MAXLINE, ficpar);
4752: numlinepar++;
4753: puts(line);
4754: fputs(line,ficparo);
4755: fputs(line,ficlog);
4756: }
4757: ungetc(c,ficpar);
4758:
4759: matcov=matrix(1,npar,1,npar);
4760: for(i=1; i <=npar; i++){
4761: fscanf(ficpar,"%s",&str);
4762: if(mle==1)
4763: printf("%s",str);
4764: fprintf(ficlog,"%s",str);
4765: fprintf(ficparo,"%s",str);
4766: for(j=1; j <=i; j++){
4767: fscanf(ficpar," %le",&matcov[i][j]);
4768: if(mle==1){
4769: printf(" %.5le",matcov[i][j]);
4770: }
4771: fprintf(ficlog," %.5le",matcov[i][j]);
4772: fprintf(ficparo," %.5le",matcov[i][j]);
4773: }
4774: fscanf(ficpar,"\n");
4775: numlinepar++;
4776: if(mle==1)
4777: printf("\n");
4778: fprintf(ficlog,"\n");
4779: fprintf(ficparo,"\n");
4780: }
4781: for(i=1; i <=npar; i++)
4782: for(j=i+1;j<=npar;j++)
4783: matcov[i][j]=matcov[j][i];
4784:
4785: if(mle==1)
4786: printf("\n");
4787: fprintf(ficlog,"\n");
4788:
4789: fflush(ficlog);
4790:
4791: /*-------- Rewriting parameter file ----------*/
4792: strcpy(rfileres,"r"); /* "Rparameterfile */
4793: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4794: strcat(rfileres,"."); /* */
4795: strcat(rfileres,optionfilext); /* Other files have txt extension */
4796: if((ficres =fopen(rfileres,"w"))==NULL) {
4797: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4798: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4799: }
4800: fprintf(ficres,"#%s\n",version);
4801: } /* End of mle != -3 */
4802:
4803: /*-------- data file ----------*/
4804: if((fic=fopen(datafile,"r"))==NULL) {
4805: printf("Problem while opening datafile: %s\n", datafile);goto end;
4806: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4807: }
4808:
4809: n= lastobs;
4810: severity = vector(1,maxwav);
4811: outcome=imatrix(1,maxwav+1,1,n);
4812: num=lvector(1,n);
4813: moisnais=vector(1,n);
4814: annais=vector(1,n);
4815: moisdc=vector(1,n);
4816: andc=vector(1,n);
4817: agedc=vector(1,n);
4818: cod=ivector(1,n);
4819: weight=vector(1,n);
4820: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4821: mint=matrix(1,maxwav,1,n);
4822: anint=matrix(1,maxwav,1,n);
4823: s=imatrix(1,maxwav+1,1,n);
4824: tab=ivector(1,NCOVMAX);
4825: ncodemax=ivector(1,8);
4826:
4827: i=1;
4828: linei=0;
4829: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4830: linei=linei+1;
4831: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4832: if(line[j] == '\t')
4833: line[j] = ' ';
4834: }
4835: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4836: ;
4837: };
4838: line[j+1]=0; /* Trims blanks at end of line */
4839: if(line[0]=='#'){
4840: fprintf(ficlog,"Comment line\n%s\n",line);
4841: printf("Comment line\n%s\n",line);
4842: continue;
4843: }
4844:
4845: for (j=maxwav;j>=1;j--){
4846: cutv(stra, strb,line,' ');
4847: errno=0;
4848: lval=strtol(strb,&endptr,10);
4849: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4850: if( strb[0]=='\0' || (*endptr != '\0')){
4851: 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);
4852: exit(1);
4853: }
4854: s[j][i]=lval;
4855:
4856: strcpy(line,stra);
4857: cutv(stra, strb,line,' ');
4858: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4859: }
4860: else if(iout=sscanf(strb,"%s.") != 0){
4861: month=99;
4862: year=9999;
4863: }else{
4864: 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);
4865: exit(1);
4866: }
4867: anint[j][i]= (double) year;
4868: mint[j][i]= (double)month;
4869: strcpy(line,stra);
4870: } /* ENd Waves */
4871:
4872: cutv(stra, strb,line,' ');
4873: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4874: }
4875: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4876: month=99;
4877: year=9999;
4878: }else{
4879: 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);
4880: exit(1);
4881: }
4882: andc[i]=(double) year;
4883: moisdc[i]=(double) month;
4884: strcpy(line,stra);
4885:
4886: cutv(stra, strb,line,' ');
4887: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4888: }
4889: else if(iout=sscanf(strb,"%s.") != 0){
4890: month=99;
4891: year=9999;
4892: }else{
4893: 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);
4894: exit(1);
4895: }
4896: annais[i]=(double)(year);
4897: moisnais[i]=(double)(month);
4898: strcpy(line,stra);
4899:
4900: cutv(stra, strb,line,' ');
4901: errno=0;
4902: dval=strtod(strb,&endptr);
4903: if( strb[0]=='\0' || (*endptr != '\0')){
4904: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4905: exit(1);
4906: }
4907: weight[i]=dval;
4908: strcpy(line,stra);
4909:
4910: for (j=ncovcol;j>=1;j--){
4911: cutv(stra, strb,line,' ');
4912: errno=0;
4913: lval=strtol(strb,&endptr,10);
4914: if( strb[0]=='\0' || (*endptr != '\0')){
4915: 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);
4916: exit(1);
4917: }
4918: if(lval <-1 || lval >1){
4919: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4920: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4921: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4922: For example, for multinomial values like 1, 2 and 3,\n \
4923: build V1=0 V2=0 for the reference value (1),\n \
4924: V1=1 V2=0 for (2) \n \
4925: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4926: output of IMaCh is often meaningless.\n \
4927: Exiting.\n",lval,linei, i,line,j);
4928: goto end;
4929: }
4930: covar[j][i]=(double)(lval);
4931: strcpy(line,stra);
4932: }
4933: lstra=strlen(stra);
4934:
4935: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4936: stratrunc = &(stra[lstra-9]);
4937: num[i]=atol(stratrunc);
4938: }
4939: else
4940: num[i]=atol(stra);
4941: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4942: 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;}*/
4943:
4944: i=i+1;
4945: } /* End loop reading data */
4946: fclose(fic);
4947: /* printf("ii=%d", ij);
4948: scanf("%d",i);*/
4949: imx=i-1; /* Number of individuals */
4950:
4951: /* for (i=1; i<=imx; i++){
4952: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4953: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4954: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4955: }*/
4956: /* for (i=1; i<=imx; i++){
4957: if (s[4][i]==9) s[4][i]=-1;
4958: 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]));}*/
4959:
4960: /* for (i=1; i<=imx; i++) */
4961:
4962: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4963: else weight[i]=1;*/
4964:
4965: /* Calculation of the number of parameters from char model */
4966: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4967: Tprod=ivector(1,15);
4968: Tvaraff=ivector(1,15);
4969: Tvard=imatrix(1,15,1,2);
4970: Tage=ivector(1,15);
4971:
4972: if (strlen(model) >1){ /* If there is at least 1 covariate */
4973: j=0, j1=0, k1=1, k2=1;
4974: j=nbocc(model,'+'); /* j=Number of '+' */
4975: j1=nbocc(model,'*'); /* j1=Number of '*' */
4976: cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
4977: cptcovprod=j1; /*Number of products V1*V2 =1 */
4978:
4979: strcpy(modelsav,model);
4980: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4981: printf("Error. Non available option model=%s ",model);
4982: fprintf(ficlog,"Error. Non available option model=%s ",model);
4983: goto end;
4984: }
4985:
4986: /* This loop fills the array Tvar from the string 'model'.*/
4987: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
4988: for(i=(j+1); i>=1;i--){
4989: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
4990: modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
4991: stra=V2
4992: */
4993: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4994: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4995: /*scanf("%d",i);*/
4996: if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/
4997: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
4998: if (strcmp(strc,"age")==0) { /* Vn*age */
4999: cptcovprod--;
5000: cutv(strb,stre,strd,'V');
5001: Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
5002: cptcovage++; /* Sum the number of covariates including ages as a product */
5003: Tage[cptcovage]=i; /* Tage[1] =2 */
5004: /*printf("stre=%s ", stre);*/
5005: }
5006: else if (strcmp(strd,"age")==0) { /* or age*Vn */
5007: cptcovprod--;
5008: cutv(strb,stre,strc,'V');
5009: Tvar[i]=atoi(stre);
5010: cptcovage++;
5011: Tage[cptcovage]=i;
5012: }
5013: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
5014: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5015: Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
5016: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
5017: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
5018: Tprod[k1]=i; /* Tprod[1] */
5019: Tvard[k1][1]=atoi(strc); /* m*/
5020: Tvard[k1][2]=atoi(stre); /* n */
5021: Tvar[cptcovn+k2]=Tvard[k1][1];
5022: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5023: for (k=1; k<=lastobs;k++)
5024: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5025: k1++;
5026: k2=k2+2;
5027: }
5028: }
5029: else { /* no more sum */
5030: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5031: /* scanf("%d",i);*/
5032: cutv(strd,strc,strb,'V');
5033: Tvar[i]=atoi(strc);
5034: }
5035: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
5036: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5037: scanf("%d",i);*/
5038: } /* end of loop + */
5039: } /* end model */
5040:
5041: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5042: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5043:
5044: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5045: printf("cptcovprod=%d ", cptcovprod);
5046: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5047:
5048: scanf("%d ",i);*/
5049:
5050: /* if(mle==1){*/
5051: if (weightopt != 1) { /* Maximisation without weights*/
5052: for(i=1;i<=n;i++) weight[i]=1.0;
5053: }
5054: /*-calculation of age at interview from date of interview and age at death -*/
5055: agev=matrix(1,maxwav,1,imx);
5056:
5057: for (i=1; i<=imx; i++) {
5058: for(m=2; (m<= maxwav); m++) {
5059: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5060: anint[m][i]=9999;
5061: s[m][i]=-1;
5062: }
5063: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5064: nberr++;
5065: 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);
5066: 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);
5067: s[m][i]=-1;
5068: }
5069: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5070: nberr++;
5071: 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]);
5072: 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]);
5073: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5074: }
5075: }
5076: }
5077:
5078: for (i=1; i<=imx; i++) {
5079: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5080: for(m=firstpass; (m<= lastpass); m++){
5081: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5082: if (s[m][i] >= nlstate+1) {
5083: if(agedc[i]>0)
5084: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5085: agev[m][i]=agedc[i];
5086: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5087: else {
5088: if ((int)andc[i]!=9999){
5089: nbwarn++;
5090: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5091: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5092: agev[m][i]=-1;
5093: }
5094: }
5095: }
5096: else if(s[m][i] !=9){ /* Standard case, age in fractional
5097: years but with the precision of a month */
5098: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5099: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5100: agev[m][i]=1;
5101: else if(agev[m][i] <agemin){
5102: agemin=agev[m][i];
5103: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5104: }
5105: else if(agev[m][i] >agemax){
5106: agemax=agev[m][i];
5107: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5108: }
5109: /*agev[m][i]=anint[m][i]-annais[i];*/
5110: /* agev[m][i] = age[i]+2*m;*/
5111: }
5112: else { /* =9 */
5113: agev[m][i]=1;
5114: s[m][i]=-1;
5115: }
5116: }
5117: else /*= 0 Unknown */
5118: agev[m][i]=1;
5119: }
5120:
5121: }
5122: for (i=1; i<=imx; i++) {
5123: for(m=firstpass; (m<=lastpass); m++){
5124: if (s[m][i] > (nlstate+ndeath)) {
5125: nberr++;
5126: 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);
5127: 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);
5128: goto end;
5129: }
5130: }
5131: }
5132:
5133: /*for (i=1; i<=imx; i++){
5134: for (m=firstpass; (m<lastpass); m++){
5135: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5136: }
5137:
5138: }*/
5139:
5140:
5141: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5142: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5143:
5144: agegomp=(int)agemin;
5145: free_vector(severity,1,maxwav);
5146: free_imatrix(outcome,1,maxwav+1,1,n);
5147: free_vector(moisnais,1,n);
5148: free_vector(annais,1,n);
5149: /* free_matrix(mint,1,maxwav,1,n);
5150: free_matrix(anint,1,maxwav,1,n);*/
5151: free_vector(moisdc,1,n);
5152: free_vector(andc,1,n);
5153:
5154:
5155: wav=ivector(1,imx);
5156: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5157: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5158: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5159:
5160: /* Concatenates waves */
5161: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5162:
5163: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5164:
5165: Tcode=ivector(1,100);
5166: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5167: ncodemax[1]=1;
5168: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5169:
5170: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5171: the estimations*/
5172: h=0;
5173: m=pow(2,cptcoveff);
5174:
5175: for(k=1;k<=cptcoveff; k++){
5176: for(i=1; i <=(m/pow(2,k));i++){
5177: for(j=1; j <= ncodemax[k]; j++){
5178: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5179: h++;
5180: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5181: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
5182: }
5183: }
5184: }
5185: }
5186: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5187: codtab[1][2]=1;codtab[2][2]=2; */
5188: /* for(i=1; i <=m ;i++){
5189: for(k=1; k <=cptcovn; k++){
5190: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5191: }
5192: printf("\n");
5193: }
5194: scanf("%d",i);*/
5195:
5196: /*------------ gnuplot -------------*/
5197: strcpy(optionfilegnuplot,optionfilefiname);
5198: if(mle==-3)
5199: strcat(optionfilegnuplot,"-mort");
5200: strcat(optionfilegnuplot,".gp");
5201:
5202: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5203: printf("Problem with file %s",optionfilegnuplot);
5204: }
5205: else{
5206: fprintf(ficgp,"\n# %s\n", version);
5207: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5208: fprintf(ficgp,"set missing 'NaNq'\n");
5209: }
5210: /* fclose(ficgp);*/
5211: /*--------- index.htm --------*/
5212:
5213: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5214: if(mle==-3)
5215: strcat(optionfilehtm,"-mort");
5216: strcat(optionfilehtm,".htm");
5217: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5218: printf("Problem with %s \n",optionfilehtm), exit(0);
5219: }
5220:
5221: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5222: strcat(optionfilehtmcov,"-cov.htm");
5223: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5224: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5225: }
5226: else{
5227: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5228: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5229: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5230: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5231: }
5232:
5233: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5234: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5235: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5236: \n\
5237: <hr size=\"2\" color=\"#EC5E5E\">\
5238: <ul><li><h4>Parameter files</h4>\n\
5239: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5240: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5241: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5242: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5243: - Date and time at start: %s</ul>\n",\
5244: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5245: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5246: fileres,fileres,\
5247: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5248: fflush(fichtm);
5249:
5250: strcpy(pathr,path);
5251: strcat(pathr,optionfilefiname);
5252: chdir(optionfilefiname); /* Move to directory named optionfile */
5253:
5254: /* Calculates basic frequencies. Computes observed prevalence at single age
5255: and prints on file fileres'p'. */
5256: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5257:
5258: fprintf(fichtm,"\n");
5259: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5260: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5261: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5262: imx,agemin,agemax,jmin,jmax,jmean);
5263: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5264: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5265: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5266: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5267: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5268:
5269:
5270: /* For Powell, parameters are in a vector p[] starting at p[1]
5271: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5272: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5273:
5274: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5275:
5276: if (mle==-3){
5277: ximort=matrix(1,NDIM,1,NDIM);
5278: cens=ivector(1,n);
5279: ageexmed=vector(1,n);
5280: agecens=vector(1,n);
5281: dcwave=ivector(1,n);
5282:
5283: for (i=1; i<=imx; i++){
5284: dcwave[i]=-1;
5285: for (m=firstpass; m<=lastpass; m++)
5286: if (s[m][i]>nlstate) {
5287: dcwave[i]=m;
5288: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5289: break;
5290: }
5291: }
5292:
5293: for (i=1; i<=imx; i++) {
5294: if (wav[i]>0){
5295: ageexmed[i]=agev[mw[1][i]][i];
5296: j=wav[i];
5297: agecens[i]=1.;
5298:
5299: if (ageexmed[i]> 1 && wav[i] > 0){
5300: agecens[i]=agev[mw[j][i]][i];
5301: cens[i]= 1;
5302: }else if (ageexmed[i]< 1)
5303: cens[i]= -1;
5304: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5305: cens[i]=0 ;
5306: }
5307: else cens[i]=-1;
5308: }
5309:
5310: for (i=1;i<=NDIM;i++) {
5311: for (j=1;j<=NDIM;j++)
5312: ximort[i][j]=(i == j ? 1.0 : 0.0);
5313: }
5314:
5315: p[1]=0.0268; p[NDIM]=0.083;
5316: /*printf("%lf %lf", p[1], p[2]);*/
5317:
5318:
5319: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5320: strcpy(filerespow,"pow-mort");
5321: strcat(filerespow,fileres);
5322: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5323: printf("Problem with resultfile: %s\n", filerespow);
5324: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5325: }
5326: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5327: /* for (i=1;i<=nlstate;i++)
5328: for(j=1;j<=nlstate+ndeath;j++)
5329: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5330: */
5331: fprintf(ficrespow,"\n");
5332:
5333: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5334: fclose(ficrespow);
5335:
5336: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5337:
5338: for(i=1; i <=NDIM; i++)
5339: for(j=i+1;j<=NDIM;j++)
5340: matcov[i][j]=matcov[j][i];
5341:
5342: printf("\nCovariance matrix\n ");
5343: for(i=1; i <=NDIM; i++) {
5344: for(j=1;j<=NDIM;j++){
5345: printf("%f ",matcov[i][j]);
5346: }
5347: printf("\n ");
5348: }
5349:
5350: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5351: for (i=1;i<=NDIM;i++)
5352: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5353:
5354: lsurv=vector(1,AGESUP);
5355: lpop=vector(1,AGESUP);
5356: tpop=vector(1,AGESUP);
5357: lsurv[agegomp]=100000;
5358:
5359: for (k=agegomp;k<=AGESUP;k++) {
5360: agemortsup=k;
5361: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5362: }
5363:
5364: for (k=agegomp;k<agemortsup;k++)
5365: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5366:
5367: for (k=agegomp;k<agemortsup;k++){
5368: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5369: sumlpop=sumlpop+lpop[k];
5370: }
5371:
5372: tpop[agegomp]=sumlpop;
5373: for (k=agegomp;k<(agemortsup-3);k++){
5374: /* tpop[k+1]=2;*/
5375: tpop[k+1]=tpop[k]-lpop[k];
5376: }
5377:
5378:
5379: printf("\nAge lx qx dx Lx Tx e(x)\n");
5380: for (k=agegomp;k<(agemortsup-2);k++)
5381: 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]);
5382:
5383:
5384: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5385: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5386:
5387: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5388: stepm, weightopt,\
5389: model,imx,p,matcov,agemortsup);
5390:
5391: free_vector(lsurv,1,AGESUP);
5392: free_vector(lpop,1,AGESUP);
5393: free_vector(tpop,1,AGESUP);
5394: } /* Endof if mle==-3 */
5395:
5396: else{ /* For mle >=1 */
5397:
5398: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5399: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5400: for (k=1; k<=npar;k++)
5401: printf(" %d %8.5f",k,p[k]);
5402: printf("\n");
5403: globpr=1; /* to print the contributions */
5404: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5405: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5406: for (k=1; k<=npar;k++)
5407: printf(" %d %8.5f",k,p[k]);
5408: printf("\n");
5409: if(mle>=1){ /* Could be 1 or 2 */
5410: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5411: }
5412:
5413: /*--------- results files --------------*/
5414: 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);
5415:
5416:
5417: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5418: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5419: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5420: for(i=1,jk=1; i <=nlstate; i++){
5421: for(k=1; k <=(nlstate+ndeath); k++){
5422: if (k != i) {
5423: printf("%d%d ",i,k);
5424: fprintf(ficlog,"%d%d ",i,k);
5425: fprintf(ficres,"%1d%1d ",i,k);
5426: for(j=1; j <=ncovmodel; j++){
5427: printf("%lf ",p[jk]);
5428: fprintf(ficlog,"%lf ",p[jk]);
5429: fprintf(ficres,"%lf ",p[jk]);
5430: jk++;
5431: }
5432: printf("\n");
5433: fprintf(ficlog,"\n");
5434: fprintf(ficres,"\n");
5435: }
5436: }
5437: }
5438: if(mle!=0){
5439: /* Computing hessian and covariance matrix */
5440: ftolhess=ftol; /* Usually correct */
5441: hesscov(matcov, p, npar, delti, ftolhess, func);
5442: }
5443: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5444: printf("# Scales (for hessian or gradient estimation)\n");
5445: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5446: for(i=1,jk=1; i <=nlstate; i++){
5447: for(j=1; j <=nlstate+ndeath; j++){
5448: if (j!=i) {
5449: fprintf(ficres,"%1d%1d",i,j);
5450: printf("%1d%1d",i,j);
5451: fprintf(ficlog,"%1d%1d",i,j);
5452: for(k=1; k<=ncovmodel;k++){
5453: printf(" %.5e",delti[jk]);
5454: fprintf(ficlog," %.5e",delti[jk]);
5455: fprintf(ficres," %.5e",delti[jk]);
5456: jk++;
5457: }
5458: printf("\n");
5459: fprintf(ficlog,"\n");
5460: fprintf(ficres,"\n");
5461: }
5462: }
5463: }
5464:
5465: 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");
5466: if(mle>=1)
5467: 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");
5468: 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");
5469: /* # 121 Var(a12)\n\ */
5470: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5471: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5472: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5473: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5474: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5475: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5476: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5477:
5478:
5479: /* Just to have a covariance matrix which will be more understandable
5480: even is we still don't want to manage dictionary of variables
5481: */
5482: for(itimes=1;itimes<=2;itimes++){
5483: jj=0;
5484: for(i=1; i <=nlstate; i++){
5485: for(j=1; j <=nlstate+ndeath; j++){
5486: if(j==i) continue;
5487: for(k=1; k<=ncovmodel;k++){
5488: jj++;
5489: ca[0]= k+'a'-1;ca[1]='\0';
5490: if(itimes==1){
5491: if(mle>=1)
5492: printf("#%1d%1d%d",i,j,k);
5493: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5494: fprintf(ficres,"#%1d%1d%d",i,j,k);
5495: }else{
5496: if(mle>=1)
5497: printf("%1d%1d%d",i,j,k);
5498: fprintf(ficlog,"%1d%1d%d",i,j,k);
5499: fprintf(ficres,"%1d%1d%d",i,j,k);
5500: }
5501: ll=0;
5502: for(li=1;li <=nlstate; li++){
5503: for(lj=1;lj <=nlstate+ndeath; lj++){
5504: if(lj==li) continue;
5505: for(lk=1;lk<=ncovmodel;lk++){
5506: ll++;
5507: if(ll<=jj){
5508: cb[0]= lk +'a'-1;cb[1]='\0';
5509: if(ll<jj){
5510: if(itimes==1){
5511: if(mle>=1)
5512: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5513: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5514: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5515: }else{
5516: if(mle>=1)
5517: printf(" %.5e",matcov[jj][ll]);
5518: fprintf(ficlog," %.5e",matcov[jj][ll]);
5519: fprintf(ficres," %.5e",matcov[jj][ll]);
5520: }
5521: }else{
5522: if(itimes==1){
5523: if(mle>=1)
5524: printf(" Var(%s%1d%1d)",ca,i,j);
5525: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5526: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5527: }else{
5528: if(mle>=1)
5529: printf(" %.5e",matcov[jj][ll]);
5530: fprintf(ficlog," %.5e",matcov[jj][ll]);
5531: fprintf(ficres," %.5e",matcov[jj][ll]);
5532: }
5533: }
5534: }
5535: } /* end lk */
5536: } /* end lj */
5537: } /* end li */
5538: if(mle>=1)
5539: printf("\n");
5540: fprintf(ficlog,"\n");
5541: fprintf(ficres,"\n");
5542: numlinepar++;
5543: } /* end k*/
5544: } /*end j */
5545: } /* end i */
5546: } /* end itimes */
5547:
5548: fflush(ficlog);
5549: fflush(ficres);
5550:
5551: while((c=getc(ficpar))=='#' && c!= EOF){
5552: ungetc(c,ficpar);
5553: fgets(line, MAXLINE, ficpar);
5554: puts(line);
5555: fputs(line,ficparo);
5556: }
5557: ungetc(c,ficpar);
5558:
5559: estepm=0;
5560: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5561: if (estepm==0 || estepm < stepm) estepm=stepm;
5562: if (fage <= 2) {
5563: bage = ageminpar;
5564: fage = agemaxpar;
5565: }
5566:
5567: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5568: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5569: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5570:
5571: while((c=getc(ficpar))=='#' && c!= EOF){
5572: ungetc(c,ficpar);
5573: fgets(line, MAXLINE, ficpar);
5574: puts(line);
5575: fputs(line,ficparo);
5576: }
5577: ungetc(c,ficpar);
5578:
5579: 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);
5580: 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);
5581: 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);
5582: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5583: 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);
5584:
5585: while((c=getc(ficpar))=='#' && c!= EOF){
5586: ungetc(c,ficpar);
5587: fgets(line, MAXLINE, ficpar);
5588: puts(line);
5589: fputs(line,ficparo);
5590: }
5591: ungetc(c,ficpar);
5592:
5593:
5594: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5595: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5596:
5597: fscanf(ficpar,"pop_based=%d\n",&popbased);
5598: fprintf(ficparo,"pop_based=%d\n",popbased);
5599: fprintf(ficres,"pop_based=%d\n",popbased);
5600:
5601: while((c=getc(ficpar))=='#' && c!= EOF){
5602: ungetc(c,ficpar);
5603: fgets(line, MAXLINE, ficpar);
5604: puts(line);
5605: fputs(line,ficparo);
5606: }
5607: ungetc(c,ficpar);
5608:
5609: 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);
5610: 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);
5611: 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);
5612: 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);
5613: 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);
5614: /* day and month of proj2 are not used but only year anproj2.*/
5615:
5616:
5617:
5618: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5619: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5620:
5621: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5622: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5623:
5624: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5625: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5626: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5627:
5628: /*------------ free_vector -------------*/
5629: /* chdir(path); */
5630:
5631: free_ivector(wav,1,imx);
5632: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5633: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5634: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5635: free_lvector(num,1,n);
5636: free_vector(agedc,1,n);
5637: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5638: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5639: fclose(ficparo);
5640: fclose(ficres);
5641:
5642:
5643: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5644:
5645: strcpy(filerespl,"pl");
5646: strcat(filerespl,fileres);
5647: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5648: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5649: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5650: }
5651: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5652: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5653: pstamp(ficrespl);
5654: fprintf(ficrespl,"# Period (stable) prevalence \n");
5655: fprintf(ficrespl,"#Age ");
5656: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5657: fprintf(ficrespl,"\n");
5658:
5659: prlim=matrix(1,nlstate,1,nlstate);
5660:
5661: agebase=ageminpar;
5662: agelim=agemaxpar;
5663: ftolpl=1.e-10;
5664: i1=cptcoveff;
5665: if (cptcovn < 1){i1=1;}
5666:
5667: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5668: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5669: k=k+1;
5670: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5671: fprintf(ficrespl,"\n#******");
5672: printf("\n#******");
5673: fprintf(ficlog,"\n#******");
5674: for(j=1;j<=cptcoveff;j++) {
5675: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5676: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5677: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5678: }
5679: fprintf(ficrespl,"******\n");
5680: printf("******\n");
5681: fprintf(ficlog,"******\n");
5682:
5683: for (age=agebase; age<=agelim; age++){
5684: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5685: fprintf(ficrespl,"%.0f ",age );
5686: for(j=1;j<=cptcoveff;j++)
5687: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5688: for(i=1; i<=nlstate;i++)
5689: fprintf(ficrespl," %.5f", prlim[i][i]);
5690: fprintf(ficrespl,"\n");
5691: }
5692: }
5693: }
5694: fclose(ficrespl);
5695:
5696: /*------------- h Pij x at various ages ------------*/
5697:
5698: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5699: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5700: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5701: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5702: }
5703: printf("Computing pij: result on file '%s' \n", filerespij);
5704: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5705:
5706: stepsize=(int) (stepm+YEARM-1)/YEARM;
5707: /*if (stepm<=24) stepsize=2;*/
5708:
5709: agelim=AGESUP;
5710: hstepm=stepsize*YEARM; /* Every year of age */
5711: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5712:
5713: /* hstepm=1; aff par mois*/
5714: pstamp(ficrespij);
5715: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5716: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5717: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5718: k=k+1;
5719: fprintf(ficrespij,"\n#****** ");
5720: for(j=1;j<=cptcoveff;j++)
5721: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5722: fprintf(ficrespij,"******\n");
5723:
5724: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5725: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5726: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5727:
5728: /* nhstepm=nhstepm*YEARM; aff par mois*/
5729:
5730: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5731: oldm=oldms;savm=savms;
5732: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5733: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5734: for(i=1; i<=nlstate;i++)
5735: for(j=1; j<=nlstate+ndeath;j++)
5736: fprintf(ficrespij," %1d-%1d",i,j);
5737: fprintf(ficrespij,"\n");
5738: for (h=0; h<=nhstepm; h++){
5739: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5740: for(i=1; i<=nlstate;i++)
5741: for(j=1; j<=nlstate+ndeath;j++)
5742: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5743: fprintf(ficrespij,"\n");
5744: }
5745: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5746: fprintf(ficrespij,"\n");
5747: }
5748: }
5749: }
5750:
5751: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5752:
5753: fclose(ficrespij);
5754:
5755: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5756: for(i=1;i<=AGESUP;i++)
5757: for(j=1;j<=NCOVMAX;j++)
5758: for(k=1;k<=NCOVMAX;k++)
5759: probs[i][j][k]=0.;
5760:
5761: /*---------- Forecasting ------------------*/
5762: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5763: if(prevfcast==1){
5764: /* if(stepm ==1){*/
5765: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5766: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5767: /* } */
5768: /* else{ */
5769: /* erreur=108; */
5770: /* 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); */
5771: /* 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); */
5772: /* } */
5773: }
5774:
5775:
5776: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5777:
5778: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5779: /* 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",\
5780: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5781: */
5782:
5783: if (mobilav!=0) {
5784: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5785: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5786: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5787: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5788: }
5789: }
5790:
5791:
5792: /*---------- Health expectancies, no variances ------------*/
5793:
5794: strcpy(filerese,"e");
5795: strcat(filerese,fileres);
5796: if((ficreseij=fopen(filerese,"w"))==NULL) {
5797: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5798: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5799: }
5800: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5801: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5802: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5803: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5804: k=k+1;
5805: fprintf(ficreseij,"\n#****** ");
5806: for(j=1;j<=cptcoveff;j++) {
5807: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5808: }
5809: fprintf(ficreseij,"******\n");
5810:
5811: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5812: oldm=oldms;savm=savms;
5813: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5814:
5815: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5816: }
5817: }
5818: fclose(ficreseij);
5819:
5820:
5821: /*---------- Health expectancies and variances ------------*/
5822:
5823:
5824: strcpy(filerest,"t");
5825: strcat(filerest,fileres);
5826: if((ficrest=fopen(filerest,"w"))==NULL) {
5827: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5828: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5829: }
5830: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5831: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5832:
5833:
5834: strcpy(fileresstde,"stde");
5835: strcat(fileresstde,fileres);
5836: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5837: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5838: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5839: }
5840: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5841: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5842:
5843: strcpy(filerescve,"cve");
5844: strcat(filerescve,fileres);
5845: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5846: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5847: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5848: }
5849: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5850: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5851:
5852: strcpy(fileresv,"v");
5853: strcat(fileresv,fileres);
5854: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5855: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5856: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5857: }
5858: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5859: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5860:
5861: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5862: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5863: k=k+1;
5864: fprintf(ficrest,"\n#****** ");
5865: for(j=1;j<=cptcoveff;j++)
5866: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5867: fprintf(ficrest,"******\n");
5868:
5869: fprintf(ficresstdeij,"\n#****** ");
5870: fprintf(ficrescveij,"\n#****** ");
5871: for(j=1;j<=cptcoveff;j++) {
5872: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5873: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5874: }
5875: fprintf(ficresstdeij,"******\n");
5876: fprintf(ficrescveij,"******\n");
5877:
5878: fprintf(ficresvij,"\n#****** ");
5879: for(j=1;j<=cptcoveff;j++)
5880: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5881: fprintf(ficresvij,"******\n");
5882:
5883: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5884: oldm=oldms;savm=savms;
5885: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5886:
5887: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5888: pstamp(ficrest);
5889: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5890: oldm=oldms;savm=savms;
5891: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
5892: if(vpopbased==1)
5893: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
5894: else
5895: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5896: fprintf(ficrest,"# Age e.. (std) ");
5897: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5898: fprintf(ficrest,"\n");
5899:
5900: epj=vector(1,nlstate+1);
5901: for(age=bage; age <=fage ;age++){
5902: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5903: if (vpopbased==1) {
5904: if(mobilav ==0){
5905: for(i=1; i<=nlstate;i++)
5906: prlim[i][i]=probs[(int)age][i][k];
5907: }else{ /* mobilav */
5908: for(i=1; i<=nlstate;i++)
5909: prlim[i][i]=mobaverage[(int)age][i][k];
5910: }
5911: }
5912:
5913: fprintf(ficrest," %4.0f",age);
5914: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5915: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5916: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5917: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5918: }
5919: epj[nlstate+1] +=epj[j];
5920: }
5921:
5922: for(i=1, vepp=0.;i <=nlstate;i++)
5923: for(j=1;j <=nlstate;j++)
5924: vepp += vareij[i][j][(int)age];
5925: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5926: for(j=1;j <=nlstate;j++){
5927: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5928: }
5929: fprintf(ficrest,"\n");
5930: }
5931: }
5932: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5933: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5934: free_vector(epj,1,nlstate+1);
5935: }
5936: }
5937: free_vector(weight,1,n);
5938: free_imatrix(Tvard,1,15,1,2);
5939: free_imatrix(s,1,maxwav+1,1,n);
5940: free_matrix(anint,1,maxwav,1,n);
5941: free_matrix(mint,1,maxwav,1,n);
5942: free_ivector(cod,1,n);
5943: free_ivector(tab,1,NCOVMAX);
5944: fclose(ficresstdeij);
5945: fclose(ficrescveij);
5946: fclose(ficresvij);
5947: fclose(ficrest);
5948: fclose(ficpar);
5949:
5950: /*------- Variance of period (stable) prevalence------*/
5951:
5952: strcpy(fileresvpl,"vpl");
5953: strcat(fileresvpl,fileres);
5954: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5955: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5956: exit(0);
5957: }
5958: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5959:
5960: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5961: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5962: k=k+1;
5963: fprintf(ficresvpl,"\n#****** ");
5964: for(j=1;j<=cptcoveff;j++)
5965: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5966: fprintf(ficresvpl,"******\n");
5967:
5968: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5969: oldm=oldms;savm=savms;
5970: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5971: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5972: }
5973: }
5974:
5975: fclose(ficresvpl);
5976:
5977: /*---------- End : free ----------------*/
5978: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5979: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5980:
5981: } /* mle==-3 arrives here for freeing */
5982: free_matrix(prlim,1,nlstate,1,nlstate);
5983: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5984: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5985: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5986: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5987: free_matrix(covar,0,NCOVMAX,1,n);
5988: free_matrix(matcov,1,npar,1,npar);
5989: /*free_vector(delti,1,npar);*/
5990: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5991: free_matrix(agev,1,maxwav,1,imx);
5992: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5993:
5994: free_ivector(ncodemax,1,8);
5995: free_ivector(Tvar,1,15);
5996: free_ivector(Tprod,1,15);
5997: free_ivector(Tvaraff,1,15);
5998: free_ivector(Tage,1,15);
5999: free_ivector(Tcode,1,100);
6000:
6001: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6002: free_imatrix(codtab,1,100,1,10);
6003: fflush(fichtm);
6004: fflush(ficgp);
6005:
6006:
6007: if((nberr >0) || (nbwarn>0)){
6008: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6009: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6010: }else{
6011: printf("End of Imach\n");
6012: fprintf(ficlog,"End of Imach\n");
6013: }
6014: printf("See log file on %s\n",filelog);
6015: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6016: (void) gettimeofday(&end_time,&tzp);
6017: tm = *localtime(&end_time.tv_sec);
6018: tmg = *gmtime(&end_time.tv_sec);
6019: strcpy(strtend,asctime(&tm));
6020: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6021: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6022: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6023:
6024: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6025: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6026: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6027: /* printf("Total time was %d uSec.\n", total_usecs);*/
6028: /* if(fileappend(fichtm,optionfilehtm)){ */
6029: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6030: fclose(fichtm);
6031: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6032: fclose(fichtmcov);
6033: fclose(ficgp);
6034: fclose(ficlog);
6035: /*------ End -----------*/
6036:
6037:
6038: printf("Before Current directory %s!\n",pathcd);
6039: if(chdir(pathcd) != 0)
6040: printf("Can't move to directory %s!\n",path);
6041: if(getcwd(pathcd,MAXLINE) > 0)
6042: printf("Current directory %s!\n",pathcd);
6043: /*strcat(plotcmd,CHARSEPARATOR);*/
6044: sprintf(plotcmd,"gnuplot");
6045: #ifndef UNIX
6046: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6047: #endif
6048: if(!stat(plotcmd,&info)){
6049: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6050: if(!stat(getenv("GNUPLOTBIN"),&info)){
6051: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6052: }else
6053: strcpy(pplotcmd,plotcmd);
6054: #ifdef UNIX
6055: strcpy(plotcmd,GNUPLOTPROGRAM);
6056: if(!stat(plotcmd,&info)){
6057: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6058: }else
6059: strcpy(pplotcmd,plotcmd);
6060: #endif
6061: }else
6062: strcpy(pplotcmd,plotcmd);
6063:
6064: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6065: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6066:
6067: if((outcmd=system(plotcmd)) != 0){
6068: printf("\n Problem with gnuplot\n");
6069: }
6070: printf(" Wait...");
6071: while (z[0] != 'q') {
6072: /* chdir(path); */
6073: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6074: scanf("%s",z);
6075: /* if (z[0] == 'c') system("./imach"); */
6076: if (z[0] == 'e') {
6077: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6078: system(optionfilehtm);
6079: }
6080: else if (z[0] == 'g') system(plotcmd);
6081: else if (z[0] == 'q') exit(0);
6082: }
6083: end:
6084: while (z[0] != 'q') {
6085: printf("\nType q for exiting: ");
6086: scanf("%s",z);
6087: }
6088: }
6089:
6090:
6091:
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