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