1: /* $Id: imach.c,v 1.142 2014/01/26 03:57:36 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.142 2014/01/26 03:57:36 brouard
5: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
6:
7: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
8:
9: Revision 1.141 2014/01/26 02:42:01 brouard
10: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
11:
12: Revision 1.140 2011/09/02 10:37:54 brouard
13: Summary: times.h is ok with mingw32 now.
14:
15: Revision 1.139 2010/06/14 07:50:17 brouard
16: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
17: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
18:
19: Revision 1.138 2010/04/30 18:19:40 brouard
20: *** empty log message ***
21:
22: Revision 1.137 2010/04/29 18:11:38 brouard
23: (Module): Checking covariates for more complex models
24: than V1+V2. A lot of change to be done. Unstable.
25:
26: Revision 1.136 2010/04/26 20:30:53 brouard
27: (Module): merging some libgsl code. Fixing computation
28: of likelione (using inter/intrapolation if mle = 0) in order to
29: get same likelihood as if mle=1.
30: Some cleaning of code and comments added.
31:
32: Revision 1.135 2009/10/29 15:33:14 brouard
33: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
34:
35: Revision 1.134 2009/10/29 13:18:53 brouard
36: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
37:
38: Revision 1.133 2009/07/06 10:21:25 brouard
39: just nforces
40:
41: Revision 1.132 2009/07/06 08:22:05 brouard
42: Many tings
43:
44: Revision 1.131 2009/06/20 16:22:47 brouard
45: Some dimensions resccaled
46:
47: Revision 1.130 2009/05/26 06:44:34 brouard
48: (Module): Max Covariate is now set to 20 instead of 8. A
49: lot of cleaning with variables initialized to 0. Trying to make
50: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
51:
52: Revision 1.129 2007/08/31 13:49:27 lievre
53: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
54:
55: Revision 1.128 2006/06/30 13:02:05 brouard
56: (Module): Clarifications on computing e.j
57:
58: Revision 1.127 2006/04/28 18:11:50 brouard
59: (Module): Yes the sum of survivors was wrong since
60: imach-114 because nhstepm was no more computed in the age
61: loop. Now we define nhstepma in the age loop.
62: (Module): In order to speed up (in case of numerous covariates) we
63: compute health expectancies (without variances) in a first step
64: and then all the health expectancies with variances or standard
65: deviation (needs data from the Hessian matrices) which slows the
66: computation.
67: In the future we should be able to stop the program is only health
68: expectancies and graph are needed without standard deviations.
69:
70: Revision 1.126 2006/04/28 17:23:28 brouard
71: (Module): Yes the sum of survivors was wrong since
72: imach-114 because nhstepm was no more computed in the age
73: loop. Now we define nhstepma in the age loop.
74: Version 0.98h
75:
76: Revision 1.125 2006/04/04 15:20:31 lievre
77: Errors in calculation of health expectancies. Age was not initialized.
78: Forecasting file added.
79:
80: Revision 1.124 2006/03/22 17:13:53 lievre
81: Parameters are printed with %lf instead of %f (more numbers after the comma).
82: The log-likelihood is printed in the log file
83:
84: Revision 1.123 2006/03/20 10:52:43 brouard
85: * imach.c (Module): <title> changed, corresponds to .htm file
86: name. <head> headers where missing.
87:
88: * imach.c (Module): Weights can have a decimal point as for
89: English (a comma might work with a correct LC_NUMERIC environment,
90: otherwise the weight is truncated).
91: Modification of warning when the covariates values are not 0 or
92: 1.
93: Version 0.98g
94:
95: Revision 1.122 2006/03/20 09:45:41 brouard
96: (Module): Weights can have a decimal point as for
97: English (a comma might work with a correct LC_NUMERIC environment,
98: otherwise the weight is truncated).
99: Modification of warning when the covariates values are not 0 or
100: 1.
101: Version 0.98g
102:
103: Revision 1.121 2006/03/16 17:45:01 lievre
104: * imach.c (Module): Comments concerning covariates added
105:
106: * imach.c (Module): refinements in the computation of lli if
107: status=-2 in order to have more reliable computation if stepm is
108: not 1 month. Version 0.98f
109:
110: Revision 1.120 2006/03/16 15:10:38 lievre
111: (Module): refinements in the computation of lli if
112: status=-2 in order to have more reliable computation if stepm is
113: not 1 month. Version 0.98f
114:
115: Revision 1.119 2006/03/15 17:42:26 brouard
116: (Module): Bug if status = -2, the loglikelihood was
117: computed as likelihood omitting the logarithm. Version O.98e
118:
119: Revision 1.118 2006/03/14 18:20:07 brouard
120: (Module): varevsij Comments added explaining the second
121: table of variances if popbased=1 .
122: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
123: (Module): Function pstamp added
124: (Module): Version 0.98d
125:
126: Revision 1.117 2006/03/14 17:16:22 brouard
127: (Module): varevsij Comments added explaining the second
128: table of variances if popbased=1 .
129: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
130: (Module): Function pstamp added
131: (Module): Version 0.98d
132:
133: Revision 1.116 2006/03/06 10:29:27 brouard
134: (Module): Variance-covariance wrong links and
135: varian-covariance of ej. is needed (Saito).
136:
137: Revision 1.115 2006/02/27 12:17:45 brouard
138: (Module): One freematrix added in mlikeli! 0.98c
139:
140: Revision 1.114 2006/02/26 12:57:58 brouard
141: (Module): Some improvements in processing parameter
142: filename with strsep.
143:
144: Revision 1.113 2006/02/24 14:20:24 brouard
145: (Module): Memory leaks checks with valgrind and:
146: datafile was not closed, some imatrix were not freed and on matrix
147: allocation too.
148:
149: Revision 1.112 2006/01/30 09:55:26 brouard
150: (Module): Back to gnuplot.exe instead of wgnuplot.exe
151:
152: Revision 1.111 2006/01/25 20:38:18 brouard
153: (Module): Lots of cleaning and bugs added (Gompertz)
154: (Module): Comments can be added in data file. Missing date values
155: can be a simple dot '.'.
156:
157: Revision 1.110 2006/01/25 00:51:50 brouard
158: (Module): Lots of cleaning and bugs added (Gompertz)
159:
160: Revision 1.109 2006/01/24 19:37:15 brouard
161: (Module): Comments (lines starting with a #) are allowed in data.
162:
163: Revision 1.108 2006/01/19 18:05:42 lievre
164: Gnuplot problem appeared...
165: To be fixed
166:
167: Revision 1.107 2006/01/19 16:20:37 brouard
168: Test existence of gnuplot in imach path
169:
170: Revision 1.106 2006/01/19 13:24:36 brouard
171: Some cleaning and links added in html output
172:
173: Revision 1.105 2006/01/05 20:23:19 lievre
174: *** empty log message ***
175:
176: Revision 1.104 2005/09/30 16:11:43 lievre
177: (Module): sump fixed, loop imx fixed, and simplifications.
178: (Module): If the status is missing at the last wave but we know
179: that the person is alive, then we can code his/her status as -2
180: (instead of missing=-1 in earlier versions) and his/her
181: contributions to the likelihood is 1 - Prob of dying from last
182: health status (= 1-p13= p11+p12 in the easiest case of somebody in
183: the healthy state at last known wave). Version is 0.98
184:
185: Revision 1.103 2005/09/30 15:54:49 lievre
186: (Module): sump fixed, loop imx fixed, and simplifications.
187:
188: Revision 1.102 2004/09/15 17:31:30 brouard
189: Add the possibility to read data file including tab characters.
190:
191: Revision 1.101 2004/09/15 10:38:38 brouard
192: Fix on curr_time
193:
194: Revision 1.100 2004/07/12 18:29:06 brouard
195: Add version for Mac OS X. Just define UNIX in Makefile
196:
197: Revision 1.99 2004/06/05 08:57:40 brouard
198: *** empty log message ***
199:
200: Revision 1.98 2004/05/16 15:05:56 brouard
201: New version 0.97 . First attempt to estimate force of mortality
202: directly from the data i.e. without the need of knowing the health
203: state at each age, but using a Gompertz model: log u =a + b*age .
204: This is the basic analysis of mortality and should be done before any
205: other analysis, in order to test if the mortality estimated from the
206: cross-longitudinal survey is different from the mortality estimated
207: from other sources like vital statistic data.
208:
209: The same imach parameter file can be used but the option for mle should be -3.
210:
211: Agnès, who wrote this part of the code, tried to keep most of the
212: former routines in order to include the new code within the former code.
213:
214: The output is very simple: only an estimate of the intercept and of
215: the slope with 95% confident intervals.
216:
217: Current limitations:
218: A) Even if you enter covariates, i.e. with the
219: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
220: B) There is no computation of Life Expectancy nor Life Table.
221:
222: Revision 1.97 2004/02/20 13:25:42 lievre
223: Version 0.96d. Population forecasting command line is (temporarily)
224: suppressed.
225:
226: Revision 1.96 2003/07/15 15:38:55 brouard
227: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
228: rewritten within the same printf. Workaround: many printfs.
229:
230: Revision 1.95 2003/07/08 07:54:34 brouard
231: * imach.c (Repository):
232: (Repository): Using imachwizard code to output a more meaningful covariance
233: matrix (cov(a12,c31) instead of numbers.
234:
235: Revision 1.94 2003/06/27 13:00:02 brouard
236: Just cleaning
237:
238: Revision 1.93 2003/06/25 16:33:55 brouard
239: (Module): On windows (cygwin) function asctime_r doesn't
240: exist so I changed back to asctime which exists.
241: (Module): Version 0.96b
242:
243: Revision 1.92 2003/06/25 16:30:45 brouard
244: (Module): On windows (cygwin) function asctime_r doesn't
245: exist so I changed back to asctime which exists.
246:
247: Revision 1.91 2003/06/25 15:30:29 brouard
248: * imach.c (Repository): Duplicated warning errors corrected.
249: (Repository): Elapsed time after each iteration is now output. It
250: helps to forecast when convergence will be reached. Elapsed time
251: is stamped in powell. We created a new html file for the graphs
252: concerning matrix of covariance. It has extension -cov.htm.
253:
254: Revision 1.90 2003/06/24 12:34:15 brouard
255: (Module): Some bugs corrected for windows. Also, when
256: mle=-1 a template is output in file "or"mypar.txt with the design
257: of the covariance matrix to be input.
258:
259: Revision 1.89 2003/06/24 12:30:52 brouard
260: (Module): Some bugs corrected for windows. Also, when
261: mle=-1 a template is output in file "or"mypar.txt with the design
262: of the covariance matrix to be input.
263:
264: Revision 1.88 2003/06/23 17:54:56 brouard
265: * 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.
266:
267: Revision 1.87 2003/06/18 12:26:01 brouard
268: Version 0.96
269:
270: Revision 1.86 2003/06/17 20:04:08 brouard
271: (Module): Change position of html and gnuplot routines and added
272: routine fileappend.
273:
274: Revision 1.85 2003/06/17 13:12:43 brouard
275: * imach.c (Repository): Check when date of death was earlier that
276: current date of interview. It may happen when the death was just
277: prior to the death. In this case, dh was negative and likelihood
278: was wrong (infinity). We still send an "Error" but patch by
279: assuming that the date of death was just one stepm after the
280: interview.
281: (Repository): Because some people have very long ID (first column)
282: we changed int to long in num[] and we added a new lvector for
283: memory allocation. But we also truncated to 8 characters (left
284: truncation)
285: (Repository): No more line truncation errors.
286:
287: Revision 1.84 2003/06/13 21:44:43 brouard
288: * imach.c (Repository): Replace "freqsummary" at a correct
289: place. It differs from routine "prevalence" which may be called
290: many times. Probs is memory consuming and must be used with
291: parcimony.
292: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
293:
294: Revision 1.83 2003/06/10 13:39:11 lievre
295: *** empty log message ***
296:
297: Revision 1.82 2003/06/05 15:57:20 brouard
298: Add log in imach.c and fullversion number is now printed.
299:
300: */
301: /*
302: Interpolated Markov Chain
303:
304: Short summary of the programme:
305:
306: This program computes Healthy Life Expectancies from
307: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
308: first survey ("cross") where individuals from different ages are
309: interviewed on their health status or degree of disability (in the
310: case of a health survey which is our main interest) -2- at least a
311: second wave of interviews ("longitudinal") which measure each change
312: (if any) in individual health status. Health expectancies are
313: computed from the time spent in each health state according to a
314: model. More health states you consider, more time is necessary to reach the
315: Maximum Likelihood of the parameters involved in the model. The
316: simplest model is the multinomial logistic model where pij is the
317: probability to be observed in state j at the second wave
318: conditional to be observed in state i at the first wave. Therefore
319: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
320: 'age' is age and 'sex' is a covariate. If you want to have a more
321: complex model than "constant and age", you should modify the program
322: where the markup *Covariates have to be included here again* invites
323: you to do it. More covariates you add, slower the
324: convergence.
325:
326: The advantage of this computer programme, compared to a simple
327: multinomial logistic model, is clear when the delay between waves is not
328: identical for each individual. Also, if a individual missed an
329: intermediate interview, the information is lost, but taken into
330: account using an interpolation or extrapolation.
331:
332: hPijx is the probability to be observed in state i at age x+h
333: conditional to the observed state i at age x. The delay 'h' can be
334: split into an exact number (nh*stepm) of unobserved intermediate
335: states. This elementary transition (by month, quarter,
336: semester or year) is modelled as a multinomial logistic. The hPx
337: matrix is simply the matrix product of nh*stepm elementary matrices
338: and the contribution of each individual to the likelihood is simply
339: hPijx.
340:
341: Also this programme outputs the covariance matrix of the parameters but also
342: of the life expectancies. It also computes the period (stable) prevalence.
343:
344: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
345: Institut national d'études démographiques, Paris.
346: This software have been partly granted by Euro-REVES, a concerted action
347: from the European Union.
348: It is copyrighted identically to a GNU software product, ie programme and
349: software can be distributed freely for non commercial use. Latest version
350: can be accessed at http://euroreves.ined.fr/imach .
351:
352: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
353: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
354:
355: **********************************************************************/
356: /*
357: main
358: read parameterfile
359: read datafile
360: concatwav
361: freqsummary
362: if (mle >= 1)
363: mlikeli
364: print results files
365: if mle==1
366: computes hessian
367: read end of parameter file: agemin, agemax, bage, fage, estepm
368: begin-prev-date,...
369: open gnuplot file
370: open html file
371: period (stable) prevalence
372: for age prevalim()
373: h Pij x
374: variance of p varprob
375: forecasting if prevfcast==1 prevforecast call prevalence()
376: health expectancies
377: Variance-covariance of DFLE
378: prevalence()
379: movingaverage()
380: varevsij()
381: if popbased==1 varevsij(,popbased)
382: total life expectancies
383: Variance of period (stable) prevalence
384: end
385: */
386:
387:
388:
389:
390: #include <math.h>
391: #include <stdio.h>
392: #include <stdlib.h>
393: #include <string.h>
394: #include <unistd.h>
395:
396: #include <limits.h>
397: #include <sys/types.h>
398: #include <sys/stat.h>
399: #include <errno.h>
400: extern int errno;
401:
402: #ifdef LINUX
403: #include <time.h>
404: #include "timeval.h"
405: #else
406: #include <sys/time.h>
407: #endif
408:
409: #ifdef GSL
410: #include <gsl/gsl_errno.h>
411: #include <gsl/gsl_multimin.h>
412: #endif
413:
414: /* #include <libintl.h> */
415: /* #define _(String) gettext (String) */
416:
417: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
418:
419: #define GNUPLOTPROGRAM "gnuplot"
420: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
421: #define FILENAMELENGTH 132
422:
423: #define GLOCK_ERROR_NOPATH -1 /* empty path */
424: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
425:
426: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
427: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
428:
429: #define NINTERVMAX 8
430: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
431: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
432: #define NCOVMAX 20 /* Maximum number of covariates */
433: #define MAXN 20000
434: #define YEARM 12. /* Number of months per year */
435: #define AGESUP 130
436: #define AGEBASE 40
437: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
438: #ifdef UNIX
439: #define DIRSEPARATOR '/'
440: #define CHARSEPARATOR "/"
441: #define ODIRSEPARATOR '\\'
442: #else
443: #define DIRSEPARATOR '\\'
444: #define CHARSEPARATOR "\\"
445: #define ODIRSEPARATOR '/'
446: #endif
447:
448: /* $Id: imach.c,v 1.142 2014/01/26 03:57:36 brouard Exp $ */
449: /* $State: Exp $ */
450:
451: char version[]="Imach version 0.98nR, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
452: char fullversion[]="$Revision: 1.142 $ $Date: 2014/01/26 03:57:36 $";
453: char strstart[80];
454: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
455: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
456: int nvar=0, nforce=0; /* Number of variables, number of forces */
457: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
458: int npar=NPARMAX;
459: int nlstate=2; /* Number of live states */
460: int ndeath=1; /* Number of dead states */
461: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
462: int popbased=0;
463:
464: int *wav; /* Number of waves for this individuual 0 is possible */
465: int maxwav=0; /* Maxim number of waves */
466: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
467: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
468: int gipmx=0, gsw=0; /* Global variables on the number of contributions
469: to the likelihood and the sum of weights (done by funcone)*/
470: int mle=1, weightopt=0;
471: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
472: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
473: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
474: * wave mi and wave mi+1 is not an exact multiple of stepm. */
475: double jmean=1; /* Mean space between 2 waves */
476: double **oldm, **newm, **savm; /* Working pointers to matrices */
477: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
478: /*FILE *fic ; */ /* Used in readdata only */
479: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
480: FILE *ficlog, *ficrespow;
481: int globpr=0; /* Global variable for printing or not */
482: double fretone; /* Only one call to likelihood */
483: long ipmx=0; /* Number of contributions */
484: double sw; /* Sum of weights */
485: char filerespow[FILENAMELENGTH];
486: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
487: FILE *ficresilk;
488: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
489: FILE *ficresprobmorprev;
490: FILE *fichtm, *fichtmcov; /* Html File */
491: FILE *ficreseij;
492: char filerese[FILENAMELENGTH];
493: FILE *ficresstdeij;
494: char fileresstde[FILENAMELENGTH];
495: FILE *ficrescveij;
496: char filerescve[FILENAMELENGTH];
497: FILE *ficresvij;
498: char fileresv[FILENAMELENGTH];
499: FILE *ficresvpl;
500: char fileresvpl[FILENAMELENGTH];
501: char title[MAXLINE];
502: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
503: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
504: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
505: char command[FILENAMELENGTH];
506: int outcmd=0;
507:
508: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
509:
510: char filelog[FILENAMELENGTH]; /* Log file */
511: char filerest[FILENAMELENGTH];
512: char fileregp[FILENAMELENGTH];
513: char popfile[FILENAMELENGTH];
514:
515: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
516:
517: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
518: struct timezone tzp;
519: extern int gettimeofday();
520: struct tm tmg, tm, tmf, *gmtime(), *localtime();
521: long time_value;
522: extern long time();
523: char strcurr[80], strfor[80];
524:
525: char *endptr;
526: long lval;
527: double dval;
528:
529: #define NR_END 1
530: #define FREE_ARG char*
531: #define FTOL 1.0e-10
532:
533: #define NRANSI
534: #define ITMAX 200
535:
536: #define TOL 2.0e-4
537:
538: #define CGOLD 0.3819660
539: #define ZEPS 1.0e-10
540: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
541:
542: #define GOLD 1.618034
543: #define GLIMIT 100.0
544: #define TINY 1.0e-20
545:
546: static double maxarg1,maxarg2;
547: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
548: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
549:
550: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
551: #define rint(a) floor(a+0.5)
552:
553: static double sqrarg;
554: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
555: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
556: int agegomp= AGEGOMP;
557:
558: int imx;
559: int stepm=1;
560: /* Stepm, step in month: minimum step interpolation*/
561:
562: int estepm;
563: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
564:
565: int m,nb;
566: long *num;
567: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
568: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
569: double **pmmij, ***probs;
570: double *ageexmed,*agecens;
571: double dateintmean=0;
572:
573: double *weight;
574: int **s; /* Status */
575: double *agedc;
576: double **covar; /**< covar[i,j], value of jth covariate for individual i,
577: * covar=matrix(0,NCOVMAX,1,n);
578: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
579: double idx;
580: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
581: int **codtab; /**< codtab=imatrix(1,100,1,10); */
582: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
583: double *lsurv, *lpop, *tpop;
584:
585: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
586: double ftolhess; /* Tolerance for computing hessian */
587:
588: /**************** split *************************/
589: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
590: {
591: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
592: the name of the file (name), its extension only (ext) and its first part of the name (finame)
593: */
594: char *ss; /* pointer */
595: int l1, l2; /* length counters */
596:
597: l1 = strlen(path ); /* length of path */
598: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
599: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
600: if ( ss == NULL ) { /* no directory, so determine current directory */
601: strcpy( name, path ); /* we got the fullname name because no directory */
602: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
603: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
604: /* get current working directory */
605: /* extern char* getcwd ( char *buf , int len);*/
606: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
607: return( GLOCK_ERROR_GETCWD );
608: }
609: /* got dirc from getcwd*/
610: printf(" DIRC = %s \n",dirc);
611: } else { /* strip direcotry from path */
612: ss++; /* after this, the filename */
613: l2 = strlen( ss ); /* length of filename */
614: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
615: strcpy( name, ss ); /* save file name */
616: strncpy( dirc, path, l1 - l2 ); /* now the directory */
617: dirc[l1-l2] = 0; /* add zero */
618: printf(" DIRC2 = %s \n",dirc);
619: }
620: /* We add a separator at the end of dirc if not exists */
621: l1 = strlen( dirc ); /* length of directory */
622: if( dirc[l1-1] != DIRSEPARATOR ){
623: dirc[l1] = DIRSEPARATOR;
624: dirc[l1+1] = 0;
625: printf(" DIRC3 = %s \n",dirc);
626: }
627: ss = strrchr( name, '.' ); /* find last / */
628: if (ss >0){
629: ss++;
630: strcpy(ext,ss); /* save extension */
631: l1= strlen( name);
632: l2= strlen(ss)+1;
633: strncpy( finame, name, l1-l2);
634: finame[l1-l2]= 0;
635: }
636:
637: return( 0 ); /* we're done */
638: }
639:
640:
641: /******************************************/
642:
643: void replace_back_to_slash(char *s, char*t)
644: {
645: int i;
646: int lg=0;
647: i=0;
648: lg=strlen(t);
649: for(i=0; i<= lg; i++) {
650: (s[i] = t[i]);
651: if (t[i]== '\\') s[i]='/';
652: }
653: }
654:
655: char *trimbb(char *out, char *in)
656: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
657: char *s;
658: s=out;
659: while (*in != '\0'){
660: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
661: in++;
662: }
663: *out++ = *in++;
664: }
665: *out='\0';
666: return s;
667: }
668:
669: char *cutv(char *blocc, char *alocc, char *in, char occ)
670: {
671: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
672: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
673: gives blocc="abcdef2ghi" and alocc="j".
674: If occ is not found blocc is null and alocc is equal to in. Returns alocc
675: */
676: char *s, *t;
677: t=in;s=in;
678: while (*in != '\0'){
679: while( *in == occ){
680: *blocc++ = *in++;
681: s=in;
682: }
683: *blocc++ = *in++;
684: }
685: if (s == t) /* occ not found */
686: *(blocc-(in-s))='\0';
687: else
688: *(blocc-(in-s)-1)='\0';
689: in=s;
690: while ( *in != '\0'){
691: *alocc++ = *in++;
692: }
693:
694: *alocc='\0';
695: return s;
696: }
697:
698: int nbocc(char *s, char occ)
699: {
700: int i,j=0;
701: int lg=20;
702: i=0;
703: lg=strlen(s);
704: for(i=0; i<= lg; i++) {
705: if (s[i] == occ ) j++;
706: }
707: return j;
708: }
709:
710: /* void cutv(char *u,char *v, char*t, char occ) */
711: /* { */
712: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
713: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
714: /* gives u="abcdef2ghi" and v="j" *\/ */
715: /* int i,lg,j,p=0; */
716: /* i=0; */
717: /* lg=strlen(t); */
718: /* for(j=0; j<=lg-1; j++) { */
719: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
720: /* } */
721:
722: /* for(j=0; j<p; j++) { */
723: /* (u[j] = t[j]); */
724: /* } */
725: /* u[p]='\0'; */
726:
727: /* for(j=0; j<= lg; j++) { */
728: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
729: /* } */
730: /* } */
731:
732: /********************** nrerror ********************/
733:
734: void nrerror(char error_text[])
735: {
736: fprintf(stderr,"ERREUR ...\n");
737: fprintf(stderr,"%s\n",error_text);
738: exit(EXIT_FAILURE);
739: }
740: /*********************** vector *******************/
741: double *vector(int nl, int nh)
742: {
743: double *v;
744: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
745: if (!v) nrerror("allocation failure in vector");
746: return v-nl+NR_END;
747: }
748:
749: /************************ free vector ******************/
750: void free_vector(double*v, int nl, int nh)
751: {
752: free((FREE_ARG)(v+nl-NR_END));
753: }
754:
755: /************************ivector *******************************/
756: int *ivector(long nl,long nh)
757: {
758: int *v;
759: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
760: if (!v) nrerror("allocation failure in ivector");
761: return v-nl+NR_END;
762: }
763:
764: /******************free ivector **************************/
765: void free_ivector(int *v, long nl, long nh)
766: {
767: free((FREE_ARG)(v+nl-NR_END));
768: }
769:
770: /************************lvector *******************************/
771: long *lvector(long nl,long nh)
772: {
773: long *v;
774: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
775: if (!v) nrerror("allocation failure in ivector");
776: return v-nl+NR_END;
777: }
778:
779: /******************free lvector **************************/
780: void free_lvector(long *v, long nl, long nh)
781: {
782: free((FREE_ARG)(v+nl-NR_END));
783: }
784:
785: /******************* imatrix *******************************/
786: int **imatrix(long nrl, long nrh, long ncl, long nch)
787: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
788: {
789: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
790: int **m;
791:
792: /* allocate pointers to rows */
793: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
794: if (!m) nrerror("allocation failure 1 in matrix()");
795: m += NR_END;
796: m -= nrl;
797:
798:
799: /* allocate rows and set pointers to them */
800: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
801: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
802: m[nrl] += NR_END;
803: m[nrl] -= ncl;
804:
805: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
806:
807: /* return pointer to array of pointers to rows */
808: return m;
809: }
810:
811: /****************** free_imatrix *************************/
812: void free_imatrix(m,nrl,nrh,ncl,nch)
813: int **m;
814: long nch,ncl,nrh,nrl;
815: /* free an int matrix allocated by imatrix() */
816: {
817: free((FREE_ARG) (m[nrl]+ncl-NR_END));
818: free((FREE_ARG) (m+nrl-NR_END));
819: }
820:
821: /******************* matrix *******************************/
822: double **matrix(long nrl, long nrh, long ncl, long nch)
823: {
824: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
825: double **m;
826:
827: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
828: if (!m) nrerror("allocation failure 1 in matrix()");
829: m += NR_END;
830: m -= nrl;
831:
832: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
833: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
834: m[nrl] += NR_END;
835: m[nrl] -= ncl;
836:
837: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
838: return m;
839: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
840: */
841: }
842:
843: /*************************free matrix ************************/
844: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
845: {
846: free((FREE_ARG)(m[nrl]+ncl-NR_END));
847: free((FREE_ARG)(m+nrl-NR_END));
848: }
849:
850: /******************* ma3x *******************************/
851: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
852: {
853: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
854: double ***m;
855:
856: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
857: if (!m) nrerror("allocation failure 1 in matrix()");
858: m += NR_END;
859: m -= nrl;
860:
861: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
862: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
863: m[nrl] += NR_END;
864: m[nrl] -= ncl;
865:
866: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
867:
868: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
869: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
870: m[nrl][ncl] += NR_END;
871: m[nrl][ncl] -= nll;
872: for (j=ncl+1; j<=nch; j++)
873: m[nrl][j]=m[nrl][j-1]+nlay;
874:
875: for (i=nrl+1; i<=nrh; i++) {
876: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
877: for (j=ncl+1; j<=nch; j++)
878: m[i][j]=m[i][j-1]+nlay;
879: }
880: return m;
881: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
882: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
883: */
884: }
885:
886: /*************************free ma3x ************************/
887: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
888: {
889: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
890: free((FREE_ARG)(m[nrl]+ncl-NR_END));
891: free((FREE_ARG)(m+nrl-NR_END));
892: }
893:
894: /*************** function subdirf ***********/
895: char *subdirf(char fileres[])
896: {
897: /* Caution optionfilefiname is hidden */
898: strcpy(tmpout,optionfilefiname);
899: strcat(tmpout,"/"); /* Add to the right */
900: strcat(tmpout,fileres);
901: return tmpout;
902: }
903:
904: /*************** function subdirf2 ***********/
905: char *subdirf2(char fileres[], char *preop)
906: {
907:
908: /* Caution optionfilefiname is hidden */
909: strcpy(tmpout,optionfilefiname);
910: strcat(tmpout,"/");
911: strcat(tmpout,preop);
912: strcat(tmpout,fileres);
913: return tmpout;
914: }
915:
916: /*************** function subdirf3 ***********/
917: char *subdirf3(char fileres[], char *preop, char *preop2)
918: {
919:
920: /* Caution optionfilefiname is hidden */
921: strcpy(tmpout,optionfilefiname);
922: strcat(tmpout,"/");
923: strcat(tmpout,preop);
924: strcat(tmpout,preop2);
925: strcat(tmpout,fileres);
926: return tmpout;
927: }
928:
929: /***************** f1dim *************************/
930: extern int ncom;
931: extern double *pcom,*xicom;
932: extern double (*nrfunc)(double []);
933:
934: double f1dim(double x)
935: {
936: int j;
937: double f;
938: double *xt;
939:
940: xt=vector(1,ncom);
941: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
942: f=(*nrfunc)(xt);
943: free_vector(xt,1,ncom);
944: return f;
945: }
946:
947: /*****************brent *************************/
948: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
949: {
950: int iter;
951: double a,b,d,etemp;
952: double fu,fv,fw,fx;
953: double ftemp;
954: double p,q,r,tol1,tol2,u,v,w,x,xm;
955: double e=0.0;
956:
957: a=(ax < cx ? ax : cx);
958: b=(ax > cx ? ax : cx);
959: x=w=v=bx;
960: fw=fv=fx=(*f)(x);
961: for (iter=1;iter<=ITMAX;iter++) {
962: xm=0.5*(a+b);
963: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
964: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
965: printf(".");fflush(stdout);
966: fprintf(ficlog,".");fflush(ficlog);
967: #ifdef DEBUG
968: 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);
969: 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);
970: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
971: #endif
972: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
973: *xmin=x;
974: return fx;
975: }
976: ftemp=fu;
977: if (fabs(e) > tol1) {
978: r=(x-w)*(fx-fv);
979: q=(x-v)*(fx-fw);
980: p=(x-v)*q-(x-w)*r;
981: q=2.0*(q-r);
982: if (q > 0.0) p = -p;
983: q=fabs(q);
984: etemp=e;
985: e=d;
986: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
987: d=CGOLD*(e=(x >= xm ? a-x : b-x));
988: else {
989: d=p/q;
990: u=x+d;
991: if (u-a < tol2 || b-u < tol2)
992: d=SIGN(tol1,xm-x);
993: }
994: } else {
995: d=CGOLD*(e=(x >= xm ? a-x : b-x));
996: }
997: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
998: fu=(*f)(u);
999: if (fu <= fx) {
1000: if (u >= x) a=x; else b=x;
1001: SHFT(v,w,x,u)
1002: SHFT(fv,fw,fx,fu)
1003: } else {
1004: if (u < x) a=u; else b=u;
1005: if (fu <= fw || w == x) {
1006: v=w;
1007: w=u;
1008: fv=fw;
1009: fw=fu;
1010: } else if (fu <= fv || v == x || v == w) {
1011: v=u;
1012: fv=fu;
1013: }
1014: }
1015: }
1016: nrerror("Too many iterations in brent");
1017: *xmin=x;
1018: return fx;
1019: }
1020:
1021: /****************** mnbrak ***********************/
1022:
1023: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1024: double (*func)(double))
1025: {
1026: double ulim,u,r,q, dum;
1027: double fu;
1028:
1029: *fa=(*func)(*ax);
1030: *fb=(*func)(*bx);
1031: if (*fb > *fa) {
1032: SHFT(dum,*ax,*bx,dum)
1033: SHFT(dum,*fb,*fa,dum)
1034: }
1035: *cx=(*bx)+GOLD*(*bx-*ax);
1036: *fc=(*func)(*cx);
1037: while (*fb > *fc) {
1038: r=(*bx-*ax)*(*fb-*fc);
1039: q=(*bx-*cx)*(*fb-*fa);
1040: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1041: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1042: ulim=(*bx)+GLIMIT*(*cx-*bx);
1043: if ((*bx-u)*(u-*cx) > 0.0) {
1044: fu=(*func)(u);
1045: } else if ((*cx-u)*(u-ulim) > 0.0) {
1046: fu=(*func)(u);
1047: if (fu < *fc) {
1048: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1049: SHFT(*fb,*fc,fu,(*func)(u))
1050: }
1051: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1052: u=ulim;
1053: fu=(*func)(u);
1054: } else {
1055: u=(*cx)+GOLD*(*cx-*bx);
1056: fu=(*func)(u);
1057: }
1058: SHFT(*ax,*bx,*cx,u)
1059: SHFT(*fa,*fb,*fc,fu)
1060: }
1061: }
1062:
1063: /*************** linmin ************************/
1064:
1065: int ncom;
1066: double *pcom,*xicom;
1067: double (*nrfunc)(double []);
1068:
1069: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1070: {
1071: double brent(double ax, double bx, double cx,
1072: double (*f)(double), double tol, double *xmin);
1073: double f1dim(double x);
1074: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1075: double *fc, double (*func)(double));
1076: int j;
1077: double xx,xmin,bx,ax;
1078: double fx,fb,fa;
1079:
1080: ncom=n;
1081: pcom=vector(1,n);
1082: xicom=vector(1,n);
1083: nrfunc=func;
1084: for (j=1;j<=n;j++) {
1085: pcom[j]=p[j];
1086: xicom[j]=xi[j];
1087: }
1088: ax=0.0;
1089: xx=1.0;
1090: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1091: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1092: #ifdef DEBUG
1093: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1094: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1095: #endif
1096: for (j=1;j<=n;j++) {
1097: xi[j] *= xmin;
1098: p[j] += xi[j];
1099: }
1100: free_vector(xicom,1,n);
1101: free_vector(pcom,1,n);
1102: }
1103:
1104: char *asc_diff_time(long time_sec, char ascdiff[])
1105: {
1106: long sec_left, days, hours, minutes;
1107: days = (time_sec) / (60*60*24);
1108: sec_left = (time_sec) % (60*60*24);
1109: hours = (sec_left) / (60*60) ;
1110: sec_left = (sec_left) %(60*60);
1111: minutes = (sec_left) /60;
1112: sec_left = (sec_left) % (60);
1113: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1114: return ascdiff;
1115: }
1116:
1117: /*************** powell ************************/
1118: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1119: double (*func)(double []))
1120: {
1121: void linmin(double p[], double xi[], int n, double *fret,
1122: double (*func)(double []));
1123: int i,ibig,j;
1124: double del,t,*pt,*ptt,*xit;
1125: double fp,fptt;
1126: double *xits;
1127: int niterf, itmp;
1128:
1129: pt=vector(1,n);
1130: ptt=vector(1,n);
1131: xit=vector(1,n);
1132: xits=vector(1,n);
1133: *fret=(*func)(p);
1134: for (j=1;j<=n;j++) pt[j]=p[j];
1135: for (*iter=1;;++(*iter)) {
1136: fp=(*fret);
1137: ibig=0;
1138: del=0.0;
1139: last_time=curr_time;
1140: (void) gettimeofday(&curr_time,&tzp);
1141: 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);
1142: 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);
1143: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1144: for (i=1;i<=n;i++) {
1145: printf(" %d %.12f",i, p[i]);
1146: fprintf(ficlog," %d %.12lf",i, p[i]);
1147: fprintf(ficrespow," %.12lf", p[i]);
1148: }
1149: printf("\n");
1150: fprintf(ficlog,"\n");
1151: fprintf(ficrespow,"\n");fflush(ficrespow);
1152: if(*iter <=3){
1153: tm = *localtime(&curr_time.tv_sec);
1154: strcpy(strcurr,asctime(&tm));
1155: /* asctime_r(&tm,strcurr); */
1156: forecast_time=curr_time;
1157: itmp = strlen(strcurr);
1158: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1159: strcurr[itmp-1]='\0';
1160: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1161: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1162: for(niterf=10;niterf<=30;niterf+=10){
1163: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1164: tmf = *localtime(&forecast_time.tv_sec);
1165: /* asctime_r(&tmf,strfor); */
1166: strcpy(strfor,asctime(&tmf));
1167: itmp = strlen(strfor);
1168: if(strfor[itmp-1]=='\n')
1169: strfor[itmp-1]='\0';
1170: 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);
1171: 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);
1172: }
1173: }
1174: for (i=1;i<=n;i++) {
1175: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1176: fptt=(*fret);
1177: #ifdef DEBUG
1178: printf("fret=%lf \n",*fret);
1179: fprintf(ficlog,"fret=%lf \n",*fret);
1180: #endif
1181: printf("%d",i);fflush(stdout);
1182: fprintf(ficlog,"%d",i);fflush(ficlog);
1183: linmin(p,xit,n,fret,func);
1184: if (fabs(fptt-(*fret)) > del) {
1185: del=fabs(fptt-(*fret));
1186: ibig=i;
1187: }
1188: #ifdef DEBUG
1189: printf("%d %.12e",i,(*fret));
1190: fprintf(ficlog,"%d %.12e",i,(*fret));
1191: for (j=1;j<=n;j++) {
1192: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1193: printf(" x(%d)=%.12e",j,xit[j]);
1194: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1195: }
1196: for(j=1;j<=n;j++) {
1197: printf(" p=%.12e",p[j]);
1198: fprintf(ficlog," p=%.12e",p[j]);
1199: }
1200: printf("\n");
1201: fprintf(ficlog,"\n");
1202: #endif
1203: }
1204: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1205: #ifdef DEBUG
1206: int k[2],l;
1207: k[0]=1;
1208: k[1]=-1;
1209: printf("Max: %.12e",(*func)(p));
1210: fprintf(ficlog,"Max: %.12e",(*func)(p));
1211: for (j=1;j<=n;j++) {
1212: printf(" %.12e",p[j]);
1213: fprintf(ficlog," %.12e",p[j]);
1214: }
1215: printf("\n");
1216: fprintf(ficlog,"\n");
1217: for(l=0;l<=1;l++) {
1218: for (j=1;j<=n;j++) {
1219: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1220: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1221: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1222: }
1223: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1224: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1225: }
1226: #endif
1227:
1228:
1229: free_vector(xit,1,n);
1230: free_vector(xits,1,n);
1231: free_vector(ptt,1,n);
1232: free_vector(pt,1,n);
1233: return;
1234: }
1235: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1236: for (j=1;j<=n;j++) {
1237: ptt[j]=2.0*p[j]-pt[j];
1238: xit[j]=p[j]-pt[j];
1239: pt[j]=p[j];
1240: }
1241: fptt=(*func)(ptt);
1242: if (fptt < fp) {
1243: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1244: if (t < 0.0) {
1245: linmin(p,xit,n,fret,func);
1246: for (j=1;j<=n;j++) {
1247: xi[j][ibig]=xi[j][n];
1248: xi[j][n]=xit[j];
1249: }
1250: #ifdef DEBUG
1251: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1252: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1253: for(j=1;j<=n;j++){
1254: printf(" %.12e",xit[j]);
1255: fprintf(ficlog," %.12e",xit[j]);
1256: }
1257: printf("\n");
1258: fprintf(ficlog,"\n");
1259: #endif
1260: }
1261: }
1262: }
1263: }
1264:
1265: /**** Prevalence limit (stable or period prevalence) ****************/
1266:
1267: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1268: {
1269: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1270: matrix by transitions matrix until convergence is reached */
1271:
1272: int i, ii,j,k;
1273: double min, max, maxmin, maxmax,sumnew=0.;
1274: double **matprod2();
1275: double **out, cov[NCOVMAX+1], **pmij();
1276: double **newm;
1277: double agefin, delaymax=50 ; /* Max number of years to converge */
1278:
1279: for (ii=1;ii<=nlstate+ndeath;ii++)
1280: for (j=1;j<=nlstate+ndeath;j++){
1281: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1282: }
1283:
1284: cov[1]=1.;
1285:
1286: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1287: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1288: newm=savm;
1289: /* Covariates have to be included here again */
1290: cov[2]=agefin;
1291:
1292: for (k=1; k<=cptcovn;k++) {
1293: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1294: /* 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]]);*/
1295: }
1296: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1297: for (k=1; k<=cptcovprod;k++)
1298: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1299:
1300: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1301: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1302: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1303: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1304:
1305: savm=oldm;
1306: oldm=newm;
1307: maxmax=0.;
1308: for(j=1;j<=nlstate;j++){
1309: min=1.;
1310: max=0.;
1311: for(i=1; i<=nlstate; i++) {
1312: sumnew=0;
1313: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1314: prlim[i][j]= newm[i][j]/(1-sumnew);
1315: max=FMAX(max,prlim[i][j]);
1316: min=FMIN(min,prlim[i][j]);
1317: }
1318: maxmin=max-min;
1319: maxmax=FMAX(maxmax,maxmin);
1320: }
1321: if(maxmax < ftolpl){
1322: return prlim;
1323: }
1324: }
1325: }
1326:
1327: /*************** transition probabilities ***************/
1328:
1329: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1330: {
1331: /* According to parameters values stored in x and the covariate's values stored in cov,
1332: computes the probability to be observed in state j being in state i by appying the
1333: model to the ncovmodel covariates (including constant and age).
1334: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1335: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1336: ncth covariate in the global vector x is given by the formula:
1337: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1338: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1339: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1340: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1341: Outputs ps[i][j] the probability to be observed in j being in j according to
1342: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1343: */
1344: double s1, lnpijopii;
1345: /*double t34;*/
1346: int i,j,j1, nc, ii, jj;
1347:
1348: for(i=1; i<= nlstate; i++){
1349: for(j=1; j<i;j++){
1350: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1351: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1352: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1353: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1354: }
1355: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1356: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1357: }
1358: for(j=i+1; j<=nlstate+ndeath;j++){
1359: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1360: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1361: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1362: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1363: }
1364: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1365: }
1366: }
1367:
1368: for(i=1; i<= nlstate; i++){
1369: s1=0;
1370: for(j=1; j<i; j++){
1371: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1372: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1373: }
1374: for(j=i+1; j<=nlstate+ndeath; j++){
1375: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1376: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1377: }
1378: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1379: ps[i][i]=1./(s1+1.);
1380: /* Computing other pijs */
1381: for(j=1; j<i; j++)
1382: ps[i][j]= exp(ps[i][j])*ps[i][i];
1383: for(j=i+1; j<=nlstate+ndeath; j++)
1384: ps[i][j]= exp(ps[i][j])*ps[i][i];
1385: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1386: } /* end i */
1387:
1388: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1389: for(jj=1; jj<= nlstate+ndeath; jj++){
1390: ps[ii][jj]=0;
1391: ps[ii][ii]=1;
1392: }
1393: }
1394:
1395:
1396: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1397: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1398: /* printf("ddd %lf ",ps[ii][jj]); */
1399: /* } */
1400: /* printf("\n "); */
1401: /* } */
1402: /* printf("\n ");printf("%lf ",cov[2]); */
1403: /*
1404: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1405: goto end;*/
1406: return ps;
1407: }
1408:
1409: /**************** Product of 2 matrices ******************/
1410:
1411: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1412: {
1413: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1414: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1415: /* in, b, out are matrice of pointers which should have been initialized
1416: before: only the contents of out is modified. The function returns
1417: a pointer to pointers identical to out */
1418: long i, j, k;
1419: for(i=nrl; i<= nrh; i++)
1420: for(k=ncolol; k<=ncoloh; k++)
1421: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1422: out[i][k] +=in[i][j]*b[j][k];
1423:
1424: return out;
1425: }
1426:
1427:
1428: /************* Higher Matrix Product ***************/
1429:
1430: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1431: {
1432: /* Computes the transition matrix starting at age 'age' over
1433: 'nhstepm*hstepm*stepm' months (i.e. until
1434: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1435: nhstepm*hstepm matrices.
1436: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1437: (typically every 2 years instead of every month which is too big
1438: for the memory).
1439: Model is determined by parameters x and covariates have to be
1440: included manually here.
1441:
1442: */
1443:
1444: int i, j, d, h, k;
1445: double **out, cov[NCOVMAX+1];
1446: double **newm;
1447:
1448: /* Hstepm could be zero and should return the unit matrix */
1449: for (i=1;i<=nlstate+ndeath;i++)
1450: for (j=1;j<=nlstate+ndeath;j++){
1451: oldm[i][j]=(i==j ? 1.0 : 0.0);
1452: po[i][j][0]=(i==j ? 1.0 : 0.0);
1453: }
1454: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1455: for(h=1; h <=nhstepm; h++){
1456: for(d=1; d <=hstepm; d++){
1457: newm=savm;
1458: /* Covariates have to be included here again */
1459: cov[1]=1.;
1460: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1461: for (k=1; k<=cptcovn;k++)
1462: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1463: for (k=1; k<=cptcovage;k++)
1464: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1465: for (k=1; k<=cptcovprod;k++)
1466: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1467:
1468:
1469: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1470: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1471: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1472: pmij(pmmij,cov,ncovmodel,x,nlstate));
1473: savm=oldm;
1474: oldm=newm;
1475: }
1476: for(i=1; i<=nlstate+ndeath; i++)
1477: for(j=1;j<=nlstate+ndeath;j++) {
1478: po[i][j][h]=newm[i][j];
1479: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1480: }
1481: /*printf("h=%d ",h);*/
1482: } /* end h */
1483: /* printf("\n H=%d \n",h); */
1484: return po;
1485: }
1486:
1487:
1488: /*************** log-likelihood *************/
1489: double func( double *x)
1490: {
1491: int i, ii, j, k, mi, d, kk;
1492: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1493: double **out;
1494: double sw; /* Sum of weights */
1495: double lli; /* Individual log likelihood */
1496: int s1, s2;
1497: double bbh, survp;
1498: long ipmx;
1499: /*extern weight */
1500: /* We are differentiating ll according to initial status */
1501: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1502: /*for(i=1;i<imx;i++)
1503: printf(" %d\n",s[4][i]);
1504: */
1505: cov[1]=1.;
1506:
1507: for(k=1; k<=nlstate; k++) ll[k]=0.;
1508:
1509: if(mle==1){
1510: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1511: /* Computes the values of the ncovmodel covariates of the model
1512: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1513: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1514: to be observed in j being in i according to the model.
1515: */
1516: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1517: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1518: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1519: has been calculated etc */
1520: for(mi=1; mi<= wav[i]-1; mi++){
1521: for (ii=1;ii<=nlstate+ndeath;ii++)
1522: for (j=1;j<=nlstate+ndeath;j++){
1523: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1524: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1525: }
1526: for(d=0; d<dh[mi][i]; d++){
1527: newm=savm;
1528: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1529: for (kk=1; kk<=cptcovage;kk++) {
1530: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1531: }
1532: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1533: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1534: savm=oldm;
1535: oldm=newm;
1536: } /* end mult */
1537:
1538: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1539: /* But now since version 0.9 we anticipate for bias at large stepm.
1540: * If stepm is larger than one month (smallest stepm) and if the exact delay
1541: * (in months) between two waves is not a multiple of stepm, we rounded to
1542: * the nearest (and in case of equal distance, to the lowest) interval but now
1543: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1544: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1545: * probability in order to take into account the bias as a fraction of the way
1546: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1547: * -stepm/2 to stepm/2 .
1548: * For stepm=1 the results are the same as for previous versions of Imach.
1549: * For stepm > 1 the results are less biased than in previous versions.
1550: */
1551: s1=s[mw[mi][i]][i];
1552: s2=s[mw[mi+1][i]][i];
1553: bbh=(double)bh[mi][i]/(double)stepm;
1554: /* bias bh is positive if real duration
1555: * is higher than the multiple of stepm and negative otherwise.
1556: */
1557: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1558: if( s2 > nlstate){
1559: /* i.e. if s2 is a death state and if the date of death is known
1560: then the contribution to the likelihood is the probability to
1561: die between last step unit time and current step unit time,
1562: which is also equal to probability to die before dh
1563: minus probability to die before dh-stepm .
1564: In version up to 0.92 likelihood was computed
1565: as if date of death was unknown. Death was treated as any other
1566: health state: the date of the interview describes the actual state
1567: and not the date of a change in health state. The former idea was
1568: to consider that at each interview the state was recorded
1569: (healthy, disable or death) and IMaCh was corrected; but when we
1570: introduced the exact date of death then we should have modified
1571: the contribution of an exact death to the likelihood. This new
1572: contribution is smaller and very dependent of the step unit
1573: stepm. It is no more the probability to die between last interview
1574: and month of death but the probability to survive from last
1575: interview up to one month before death multiplied by the
1576: probability to die within a month. Thanks to Chris
1577: Jackson for correcting this bug. Former versions increased
1578: mortality artificially. The bad side is that we add another loop
1579: which slows down the processing. The difference can be up to 10%
1580: lower mortality.
1581: */
1582: lli=log(out[s1][s2] - savm[s1][s2]);
1583:
1584:
1585: } else if (s2==-2) {
1586: for (j=1,survp=0. ; j<=nlstate; j++)
1587: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1588: /*survp += out[s1][j]; */
1589: lli= log(survp);
1590: }
1591:
1592: else if (s2==-4) {
1593: for (j=3,survp=0. ; j<=nlstate; j++)
1594: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1595: lli= log(survp);
1596: }
1597:
1598: else if (s2==-5) {
1599: for (j=1,survp=0. ; j<=2; j++)
1600: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1601: lli= log(survp);
1602: }
1603:
1604: else{
1605: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1606: /* 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 */
1607: }
1608: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1609: /*if(lli ==000.0)*/
1610: /*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); */
1611: ipmx +=1;
1612: sw += weight[i];
1613: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1614: } /* end of wave */
1615: } /* end of individual */
1616: } else if(mle==2){
1617: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1618: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1619: for(mi=1; mi<= wav[i]-1; mi++){
1620: for (ii=1;ii<=nlstate+ndeath;ii++)
1621: for (j=1;j<=nlstate+ndeath;j++){
1622: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1623: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1624: }
1625: for(d=0; d<=dh[mi][i]; d++){
1626: newm=savm;
1627: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1628: for (kk=1; kk<=cptcovage;kk++) {
1629: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1630: }
1631: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1632: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1633: savm=oldm;
1634: oldm=newm;
1635: } /* end mult */
1636:
1637: s1=s[mw[mi][i]][i];
1638: s2=s[mw[mi+1][i]][i];
1639: bbh=(double)bh[mi][i]/(double)stepm;
1640: 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 */
1641: ipmx +=1;
1642: sw += weight[i];
1643: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1644: } /* end of wave */
1645: } /* end of individual */
1646: } else if(mle==3){ /* exponential inter-extrapolation */
1647: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1648: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1649: for(mi=1; mi<= wav[i]-1; mi++){
1650: for (ii=1;ii<=nlstate+ndeath;ii++)
1651: for (j=1;j<=nlstate+ndeath;j++){
1652: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1653: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1654: }
1655: for(d=0; d<dh[mi][i]; d++){
1656: newm=savm;
1657: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1658: for (kk=1; kk<=cptcovage;kk++) {
1659: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1660: }
1661: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1662: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1663: savm=oldm;
1664: oldm=newm;
1665: } /* end mult */
1666:
1667: s1=s[mw[mi][i]][i];
1668: s2=s[mw[mi+1][i]][i];
1669: bbh=(double)bh[mi][i]/(double)stepm;
1670: 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 */
1671: ipmx +=1;
1672: sw += weight[i];
1673: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1674: } /* end of wave */
1675: } /* end of individual */
1676: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1677: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1678: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1679: for(mi=1; mi<= wav[i]-1; mi++){
1680: for (ii=1;ii<=nlstate+ndeath;ii++)
1681: for (j=1;j<=nlstate+ndeath;j++){
1682: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1683: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1684: }
1685: for(d=0; d<dh[mi][i]; d++){
1686: newm=savm;
1687: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1688: for (kk=1; kk<=cptcovage;kk++) {
1689: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1690: }
1691:
1692: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1693: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1694: savm=oldm;
1695: oldm=newm;
1696: } /* end mult */
1697:
1698: s1=s[mw[mi][i]][i];
1699: s2=s[mw[mi+1][i]][i];
1700: if( s2 > nlstate){
1701: lli=log(out[s1][s2] - savm[s1][s2]);
1702: }else{
1703: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1704: }
1705: ipmx +=1;
1706: sw += weight[i];
1707: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1708: /* 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]); */
1709: } /* end of wave */
1710: } /* end of individual */
1711: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1712: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1713: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1714: for(mi=1; mi<= wav[i]-1; mi++){
1715: for (ii=1;ii<=nlstate+ndeath;ii++)
1716: for (j=1;j<=nlstate+ndeath;j++){
1717: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1718: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1719: }
1720: for(d=0; d<dh[mi][i]; d++){
1721: newm=savm;
1722: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1723: for (kk=1; kk<=cptcovage;kk++) {
1724: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1725: }
1726:
1727: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1728: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1729: savm=oldm;
1730: oldm=newm;
1731: } /* end mult */
1732:
1733: s1=s[mw[mi][i]][i];
1734: s2=s[mw[mi+1][i]][i];
1735: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1736: ipmx +=1;
1737: sw += weight[i];
1738: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1739: /*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]);*/
1740: } /* end of wave */
1741: } /* end of individual */
1742: } /* End of if */
1743: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1744: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1745: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1746: return -l;
1747: }
1748:
1749: /*************** log-likelihood *************/
1750: double funcone( double *x)
1751: {
1752: /* Same as likeli but slower because of a lot of printf and if */
1753: int i, ii, j, k, mi, d, kk;
1754: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1755: double **out;
1756: double lli; /* Individual log likelihood */
1757: double llt;
1758: int s1, s2;
1759: double bbh, survp;
1760: /*extern weight */
1761: /* We are differentiating ll according to initial status */
1762: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1763: /*for(i=1;i<imx;i++)
1764: printf(" %d\n",s[4][i]);
1765: */
1766: cov[1]=1.;
1767:
1768: for(k=1; k<=nlstate; k++) ll[k]=0.;
1769:
1770: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1771: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1772: for(mi=1; mi<= wav[i]-1; mi++){
1773: for (ii=1;ii<=nlstate+ndeath;ii++)
1774: for (j=1;j<=nlstate+ndeath;j++){
1775: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1776: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1777: }
1778: for(d=0; d<dh[mi][i]; d++){
1779: newm=savm;
1780: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1781: for (kk=1; kk<=cptcovage;kk++) {
1782: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1783: }
1784: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1785: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1786: savm=oldm;
1787: oldm=newm;
1788: } /* end mult */
1789:
1790: s1=s[mw[mi][i]][i];
1791: s2=s[mw[mi+1][i]][i];
1792: bbh=(double)bh[mi][i]/(double)stepm;
1793: /* bias is positive if real duration
1794: * is higher than the multiple of stepm and negative otherwise.
1795: */
1796: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1797: lli=log(out[s1][s2] - savm[s1][s2]);
1798: } else if (s2==-2) {
1799: for (j=1,survp=0. ; j<=nlstate; j++)
1800: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1801: lli= log(survp);
1802: }else if (mle==1){
1803: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1804: } else if(mle==2){
1805: 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 */
1806: } else if(mle==3){ /* exponential inter-extrapolation */
1807: 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 */
1808: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1809: lli=log(out[s1][s2]); /* Original formula */
1810: } else{ /* mle=0 back to 1 */
1811: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1812: /*lli=log(out[s1][s2]); */ /* Original formula */
1813: } /* End of if */
1814: ipmx +=1;
1815: sw += weight[i];
1816: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1817: /*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]); */
1818: if(globpr){
1819: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1820: %11.6f %11.6f %11.6f ", \
1821: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1822: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1823: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1824: llt +=ll[k]*gipmx/gsw;
1825: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1826: }
1827: fprintf(ficresilk," %10.6f\n", -llt);
1828: }
1829: } /* end of wave */
1830: } /* end of individual */
1831: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1832: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1833: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1834: if(globpr==0){ /* First time we count the contributions and weights */
1835: gipmx=ipmx;
1836: gsw=sw;
1837: }
1838: return -l;
1839: }
1840:
1841:
1842: /*************** function likelione ***********/
1843: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1844: {
1845: /* This routine should help understanding what is done with
1846: the selection of individuals/waves and
1847: to check the exact contribution to the likelihood.
1848: Plotting could be done.
1849: */
1850: int k;
1851:
1852: if(*globpri !=0){ /* Just counts and sums, no printings */
1853: strcpy(fileresilk,"ilk");
1854: strcat(fileresilk,fileres);
1855: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1856: printf("Problem with resultfile: %s\n", fileresilk);
1857: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1858: }
1859: 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");
1860: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1861: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1862: for(k=1; k<=nlstate; k++)
1863: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1864: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1865: }
1866:
1867: *fretone=(*funcone)(p);
1868: if(*globpri !=0){
1869: fclose(ficresilk);
1870: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1871: fflush(fichtm);
1872: }
1873: return;
1874: }
1875:
1876:
1877: /*********** Maximum Likelihood Estimation ***************/
1878:
1879: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1880: {
1881: int i,j, iter;
1882: double **xi;
1883: double fret;
1884: double fretone; /* Only one call to likelihood */
1885: /* char filerespow[FILENAMELENGTH];*/
1886: xi=matrix(1,npar,1,npar);
1887: for (i=1;i<=npar;i++)
1888: for (j=1;j<=npar;j++)
1889: xi[i][j]=(i==j ? 1.0 : 0.0);
1890: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1891: strcpy(filerespow,"pow");
1892: strcat(filerespow,fileres);
1893: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1894: printf("Problem with resultfile: %s\n", filerespow);
1895: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1896: }
1897: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1898: for (i=1;i<=nlstate;i++)
1899: for(j=1;j<=nlstate+ndeath;j++)
1900: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1901: fprintf(ficrespow,"\n");
1902:
1903: powell(p,xi,npar,ftol,&iter,&fret,func);
1904:
1905: free_matrix(xi,1,npar,1,npar);
1906: fclose(ficrespow);
1907: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1908: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1909: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1910:
1911: }
1912:
1913: /**** Computes Hessian and covariance matrix ***/
1914: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1915: {
1916: double **a,**y,*x,pd;
1917: double **hess;
1918: int i, j,jk;
1919: int *indx;
1920:
1921: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1922: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1923: void lubksb(double **a, int npar, int *indx, double b[]) ;
1924: void ludcmp(double **a, int npar, int *indx, double *d) ;
1925: double gompertz(double p[]);
1926: hess=matrix(1,npar,1,npar);
1927:
1928: printf("\nCalculation of the hessian matrix. Wait...\n");
1929: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1930: for (i=1;i<=npar;i++){
1931: printf("%d",i);fflush(stdout);
1932: fprintf(ficlog,"%d",i);fflush(ficlog);
1933:
1934: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1935:
1936: /* printf(" %f ",p[i]);
1937: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1938: }
1939:
1940: for (i=1;i<=npar;i++) {
1941: for (j=1;j<=npar;j++) {
1942: if (j>i) {
1943: printf(".%d%d",i,j);fflush(stdout);
1944: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1945: hess[i][j]=hessij(p,delti,i,j,func,npar);
1946:
1947: hess[j][i]=hess[i][j];
1948: /*printf(" %lf ",hess[i][j]);*/
1949: }
1950: }
1951: }
1952: printf("\n");
1953: fprintf(ficlog,"\n");
1954:
1955: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1956: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1957:
1958: a=matrix(1,npar,1,npar);
1959: y=matrix(1,npar,1,npar);
1960: x=vector(1,npar);
1961: indx=ivector(1,npar);
1962: for (i=1;i<=npar;i++)
1963: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1964: ludcmp(a,npar,indx,&pd);
1965:
1966: for (j=1;j<=npar;j++) {
1967: for (i=1;i<=npar;i++) x[i]=0;
1968: x[j]=1;
1969: lubksb(a,npar,indx,x);
1970: for (i=1;i<=npar;i++){
1971: matcov[i][j]=x[i];
1972: }
1973: }
1974:
1975: printf("\n#Hessian matrix#\n");
1976: fprintf(ficlog,"\n#Hessian matrix#\n");
1977: for (i=1;i<=npar;i++) {
1978: for (j=1;j<=npar;j++) {
1979: printf("%.3e ",hess[i][j]);
1980: fprintf(ficlog,"%.3e ",hess[i][j]);
1981: }
1982: printf("\n");
1983: fprintf(ficlog,"\n");
1984: }
1985:
1986: /* Recompute Inverse */
1987: for (i=1;i<=npar;i++)
1988: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1989: ludcmp(a,npar,indx,&pd);
1990:
1991: /* printf("\n#Hessian matrix recomputed#\n");
1992:
1993: for (j=1;j<=npar;j++) {
1994: for (i=1;i<=npar;i++) x[i]=0;
1995: x[j]=1;
1996: lubksb(a,npar,indx,x);
1997: for (i=1;i<=npar;i++){
1998: y[i][j]=x[i];
1999: printf("%.3e ",y[i][j]);
2000: fprintf(ficlog,"%.3e ",y[i][j]);
2001: }
2002: printf("\n");
2003: fprintf(ficlog,"\n");
2004: }
2005: */
2006:
2007: free_matrix(a,1,npar,1,npar);
2008: free_matrix(y,1,npar,1,npar);
2009: free_vector(x,1,npar);
2010: free_ivector(indx,1,npar);
2011: free_matrix(hess,1,npar,1,npar);
2012:
2013:
2014: }
2015:
2016: /*************** hessian matrix ****************/
2017: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2018: {
2019: int i;
2020: int l=1, lmax=20;
2021: double k1,k2;
2022: double p2[MAXPARM+1]; /* identical to x */
2023: double res;
2024: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2025: double fx;
2026: int k=0,kmax=10;
2027: double l1;
2028:
2029: fx=func(x);
2030: for (i=1;i<=npar;i++) p2[i]=x[i];
2031: for(l=0 ; l <=lmax; l++){
2032: l1=pow(10,l);
2033: delts=delt;
2034: for(k=1 ; k <kmax; k=k+1){
2035: delt = delta*(l1*k);
2036: p2[theta]=x[theta] +delt;
2037: k1=func(p2)-fx;
2038: p2[theta]=x[theta]-delt;
2039: k2=func(p2)-fx;
2040: /*res= (k1-2.0*fx+k2)/delt/delt; */
2041: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2042:
2043: #ifdef DEBUGHESS
2044: 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);
2045: 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);
2046: #endif
2047: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2048: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2049: k=kmax;
2050: }
2051: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2052: k=kmax; l=lmax*10.;
2053: }
2054: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2055: delts=delt;
2056: }
2057: }
2058: }
2059: delti[theta]=delts;
2060: return res;
2061:
2062: }
2063:
2064: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2065: {
2066: int i;
2067: int l=1, l1, lmax=20;
2068: double k1,k2,k3,k4,res,fx;
2069: double p2[MAXPARM+1];
2070: int k;
2071:
2072: fx=func(x);
2073: for (k=1; k<=2; k++) {
2074: for (i=1;i<=npar;i++) p2[i]=x[i];
2075: p2[thetai]=x[thetai]+delti[thetai]/k;
2076: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2077: k1=func(p2)-fx;
2078:
2079: p2[thetai]=x[thetai]+delti[thetai]/k;
2080: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2081: k2=func(p2)-fx;
2082:
2083: p2[thetai]=x[thetai]-delti[thetai]/k;
2084: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2085: k3=func(p2)-fx;
2086:
2087: p2[thetai]=x[thetai]-delti[thetai]/k;
2088: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2089: k4=func(p2)-fx;
2090: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2091: #ifdef DEBUG
2092: 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);
2093: 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);
2094: #endif
2095: }
2096: return res;
2097: }
2098:
2099: /************** Inverse of matrix **************/
2100: void ludcmp(double **a, int n, int *indx, double *d)
2101: {
2102: int i,imax,j,k;
2103: double big,dum,sum,temp;
2104: double *vv;
2105:
2106: vv=vector(1,n);
2107: *d=1.0;
2108: for (i=1;i<=n;i++) {
2109: big=0.0;
2110: for (j=1;j<=n;j++)
2111: if ((temp=fabs(a[i][j])) > big) big=temp;
2112: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2113: vv[i]=1.0/big;
2114: }
2115: for (j=1;j<=n;j++) {
2116: for (i=1;i<j;i++) {
2117: sum=a[i][j];
2118: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2119: a[i][j]=sum;
2120: }
2121: big=0.0;
2122: for (i=j;i<=n;i++) {
2123: sum=a[i][j];
2124: for (k=1;k<j;k++)
2125: sum -= a[i][k]*a[k][j];
2126: a[i][j]=sum;
2127: if ( (dum=vv[i]*fabs(sum)) >= big) {
2128: big=dum;
2129: imax=i;
2130: }
2131: }
2132: if (j != imax) {
2133: for (k=1;k<=n;k++) {
2134: dum=a[imax][k];
2135: a[imax][k]=a[j][k];
2136: a[j][k]=dum;
2137: }
2138: *d = -(*d);
2139: vv[imax]=vv[j];
2140: }
2141: indx[j]=imax;
2142: if (a[j][j] == 0.0) a[j][j]=TINY;
2143: if (j != n) {
2144: dum=1.0/(a[j][j]);
2145: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2146: }
2147: }
2148: free_vector(vv,1,n); /* Doesn't work */
2149: ;
2150: }
2151:
2152: void lubksb(double **a, int n, int *indx, double b[])
2153: {
2154: int i,ii=0,ip,j;
2155: double sum;
2156:
2157: for (i=1;i<=n;i++) {
2158: ip=indx[i];
2159: sum=b[ip];
2160: b[ip]=b[i];
2161: if (ii)
2162: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2163: else if (sum) ii=i;
2164: b[i]=sum;
2165: }
2166: for (i=n;i>=1;i--) {
2167: sum=b[i];
2168: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2169: b[i]=sum/a[i][i];
2170: }
2171: }
2172:
2173: void pstamp(FILE *fichier)
2174: {
2175: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2176: }
2177:
2178: /************ Frequencies ********************/
2179: 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[])
2180: { /* Some frequencies */
2181:
2182: int i, m, jk, k1,i1, j1, bool, z1,j;
2183: int first;
2184: double ***freq; /* Frequencies */
2185: double *pp, **prop;
2186: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2187: char fileresp[FILENAMELENGTH];
2188:
2189: pp=vector(1,nlstate);
2190: prop=matrix(1,nlstate,iagemin,iagemax+3);
2191: strcpy(fileresp,"p");
2192: strcat(fileresp,fileres);
2193: if((ficresp=fopen(fileresp,"w"))==NULL) {
2194: printf("Problem with prevalence resultfile: %s\n", fileresp);
2195: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2196: exit(0);
2197: }
2198: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2199: j1=0;
2200:
2201: j=cptcoveff;
2202: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2203:
2204: first=1;
2205:
2206: for(k1=1; k1<=j;k1++){
2207: for(i1=1; i1<=ncodemax[k1];i1++){
2208: j1++;
2209: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2210: scanf("%d", i);*/
2211: for (i=-5; i<=nlstate+ndeath; i++)
2212: for (jk=-5; jk<=nlstate+ndeath; jk++)
2213: for(m=iagemin; m <= iagemax+3; m++)
2214: freq[i][jk][m]=0;
2215:
2216: for (i=1; i<=nlstate; i++)
2217: for(m=iagemin; m <= iagemax+3; m++)
2218: prop[i][m]=0;
2219:
2220: dateintsum=0;
2221: k2cpt=0;
2222: for (i=1; i<=imx; i++) {
2223: bool=1;
2224: if (cptcovn>0) {
2225: for (z1=1; z1<=cptcoveff; z1++)
2226: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2227: bool=0;
2228: }
2229: if (bool==1){
2230: for(m=firstpass; m<=lastpass; m++){
2231: k2=anint[m][i]+(mint[m][i]/12.);
2232: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2233: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2234: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2235: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2236: if (m<lastpass) {
2237: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2238: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2239: }
2240:
2241: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2242: dateintsum=dateintsum+k2;
2243: k2cpt++;
2244: }
2245: /*}*/
2246: }
2247: }
2248: }
2249:
2250: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2251: pstamp(ficresp);
2252: if (cptcovn>0) {
2253: fprintf(ficresp, "\n#********** Variable ");
2254: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2255: fprintf(ficresp, "**********\n#");
2256: }
2257: for(i=1; i<=nlstate;i++)
2258: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2259: fprintf(ficresp, "\n");
2260:
2261: for(i=iagemin; i <= iagemax+3; i++){
2262: if(i==iagemax+3){
2263: fprintf(ficlog,"Total");
2264: }else{
2265: if(first==1){
2266: first=0;
2267: printf("See log file for details...\n");
2268: }
2269: fprintf(ficlog,"Age %d", i);
2270: }
2271: for(jk=1; jk <=nlstate ; jk++){
2272: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2273: pp[jk] += freq[jk][m][i];
2274: }
2275: for(jk=1; jk <=nlstate ; jk++){
2276: for(m=-1, pos=0; m <=0 ; m++)
2277: pos += freq[jk][m][i];
2278: if(pp[jk]>=1.e-10){
2279: if(first==1){
2280: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2281: }
2282: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2283: }else{
2284: if(first==1)
2285: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2286: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2287: }
2288: }
2289:
2290: for(jk=1; jk <=nlstate ; jk++){
2291: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2292: pp[jk] += freq[jk][m][i];
2293: }
2294: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2295: pos += pp[jk];
2296: posprop += prop[jk][i];
2297: }
2298: for(jk=1; jk <=nlstate ; jk++){
2299: if(pos>=1.e-5){
2300: if(first==1)
2301: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2302: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2303: }else{
2304: if(first==1)
2305: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2306: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2307: }
2308: if( i <= iagemax){
2309: if(pos>=1.e-5){
2310: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2311: /*probs[i][jk][j1]= pp[jk]/pos;*/
2312: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2313: }
2314: else
2315: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2316: }
2317: }
2318:
2319: for(jk=-1; jk <=nlstate+ndeath; jk++)
2320: for(m=-1; m <=nlstate+ndeath; m++)
2321: if(freq[jk][m][i] !=0 ) {
2322: if(first==1)
2323: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2324: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2325: }
2326: if(i <= iagemax)
2327: fprintf(ficresp,"\n");
2328: if(first==1)
2329: printf("Others in log...\n");
2330: fprintf(ficlog,"\n");
2331: }
2332: }
2333: }
2334: dateintmean=dateintsum/k2cpt;
2335:
2336: fclose(ficresp);
2337: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2338: free_vector(pp,1,nlstate);
2339: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2340: /* End of Freq */
2341: }
2342:
2343: /************ Prevalence ********************/
2344: 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)
2345: {
2346: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2347: in each health status at the date of interview (if between dateprev1 and dateprev2).
2348: We still use firstpass and lastpass as another selection.
2349: */
2350:
2351: int i, m, jk, k1, i1, j1, bool, z1,j;
2352: double ***freq; /* Frequencies */
2353: double *pp, **prop;
2354: double pos,posprop;
2355: double y2; /* in fractional years */
2356: int iagemin, iagemax;
2357:
2358: iagemin= (int) agemin;
2359: iagemax= (int) agemax;
2360: /*pp=vector(1,nlstate);*/
2361: prop=matrix(1,nlstate,iagemin,iagemax+3);
2362: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2363: j1=0;
2364:
2365: j=cptcoveff;
2366: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2367:
2368: for(k1=1; k1<=j;k1++){
2369: for(i1=1; i1<=ncodemax[k1];i1++){
2370: j1++;
2371:
2372: for (i=1; i<=nlstate; i++)
2373: for(m=iagemin; m <= iagemax+3; m++)
2374: prop[i][m]=0.0;
2375:
2376: for (i=1; i<=imx; i++) { /* Each individual */
2377: bool=1;
2378: if (cptcovn>0) {
2379: for (z1=1; z1<=cptcoveff; z1++)
2380: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2381: bool=0;
2382: }
2383: if (bool==1) {
2384: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2385: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2386: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2387: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2388: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2389: 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);
2390: if (s[m][i]>0 && s[m][i]<=nlstate) {
2391: /*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]]);*/
2392: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2393: prop[s[m][i]][iagemax+3] += weight[i];
2394: }
2395: }
2396: } /* end selection of waves */
2397: }
2398: }
2399: for(i=iagemin; i <= iagemax+3; i++){
2400:
2401: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2402: posprop += prop[jk][i];
2403: }
2404:
2405: for(jk=1; jk <=nlstate ; jk++){
2406: if( i <= iagemax){
2407: if(posprop>=1.e-5){
2408: probs[i][jk][j1]= prop[jk][i]/posprop;
2409: } else
2410: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2411: }
2412: }/* end jk */
2413: }/* end i */
2414: } /* end i1 */
2415: } /* end k1 */
2416:
2417: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2418: /*free_vector(pp,1,nlstate);*/
2419: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2420: } /* End of prevalence */
2421:
2422: /************* Waves Concatenation ***************/
2423:
2424: 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)
2425: {
2426: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2427: Death is a valid wave (if date is known).
2428: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2429: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2430: and mw[mi+1][i]. dh depends on stepm.
2431: */
2432:
2433: int i, mi, m;
2434: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2435: double sum=0., jmean=0.;*/
2436: int first;
2437: int j, k=0,jk, ju, jl;
2438: double sum=0.;
2439: first=0;
2440: jmin=1e+5;
2441: jmax=-1;
2442: jmean=0.;
2443: for(i=1; i<=imx; i++){
2444: mi=0;
2445: m=firstpass;
2446: while(s[m][i] <= nlstate){
2447: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2448: mw[++mi][i]=m;
2449: if(m >=lastpass)
2450: break;
2451: else
2452: m++;
2453: }/* end while */
2454: if (s[m][i] > nlstate){
2455: mi++; /* Death is another wave */
2456: /* if(mi==0) never been interviewed correctly before death */
2457: /* Only death is a correct wave */
2458: mw[mi][i]=m;
2459: }
2460:
2461: wav[i]=mi;
2462: if(mi==0){
2463: nbwarn++;
2464: if(first==0){
2465: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2466: first=1;
2467: }
2468: if(first==1){
2469: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2470: }
2471: } /* end mi==0 */
2472: } /* End individuals */
2473:
2474: for(i=1; i<=imx; i++){
2475: for(mi=1; mi<wav[i];mi++){
2476: if (stepm <=0)
2477: dh[mi][i]=1;
2478: else{
2479: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2480: if (agedc[i] < 2*AGESUP) {
2481: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2482: if(j==0) j=1; /* Survives at least one month after exam */
2483: else if(j<0){
2484: nberr++;
2485: 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]);
2486: j=1; /* Temporary Dangerous patch */
2487: 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);
2488: 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]);
2489: 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);
2490: }
2491: k=k+1;
2492: if (j >= jmax){
2493: jmax=j;
2494: ijmax=i;
2495: }
2496: if (j <= jmin){
2497: jmin=j;
2498: ijmin=i;
2499: }
2500: sum=sum+j;
2501: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2502: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2503: }
2504: }
2505: else{
2506: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2507: /* 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]); */
2508:
2509: k=k+1;
2510: if (j >= jmax) {
2511: jmax=j;
2512: ijmax=i;
2513: }
2514: else if (j <= jmin){
2515: jmin=j;
2516: ijmin=i;
2517: }
2518: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2519: /*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]);*/
2520: if(j<0){
2521: nberr++;
2522: 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]);
2523: 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]);
2524: }
2525: sum=sum+j;
2526: }
2527: jk= j/stepm;
2528: jl= j -jk*stepm;
2529: ju= j -(jk+1)*stepm;
2530: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2531: if(jl==0){
2532: dh[mi][i]=jk;
2533: bh[mi][i]=0;
2534: }else{ /* We want a negative bias in order to only have interpolation ie
2535: * to avoid the price of an extra matrix product in likelihood */
2536: dh[mi][i]=jk+1;
2537: bh[mi][i]=ju;
2538: }
2539: }else{
2540: if(jl <= -ju){
2541: dh[mi][i]=jk;
2542: bh[mi][i]=jl; /* bias is positive if real duration
2543: * is higher than the multiple of stepm and negative otherwise.
2544: */
2545: }
2546: else{
2547: dh[mi][i]=jk+1;
2548: bh[mi][i]=ju;
2549: }
2550: if(dh[mi][i]==0){
2551: dh[mi][i]=1; /* At least one step */
2552: bh[mi][i]=ju; /* At least one step */
2553: /* 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);*/
2554: }
2555: } /* end if mle */
2556: }
2557: } /* end wave */
2558: }
2559: jmean=sum/k;
2560: 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);
2561: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2562: }
2563:
2564: /*********** Tricode ****************************/
2565: void tricode(int *Tvar, int **nbcode, int imx)
2566: {
2567: /* Uses cptcovn+2*cptcovprod as the number of covariates */
2568: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2569:
2570: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2571: int modmaxcovj=0; /* Modality max of covariates j */
2572: cptcoveff=0;
2573:
2574: for (k=0; k<maxncov; k++) Ndum[k]=0;
2575: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
2576:
2577: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
2578: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
2579: modality of this covariate Vj*/
2580: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
2581: modality of the nth covariate of individual i. */
2582: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2583: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2584: if (ij > modmaxcovj) modmaxcovj=ij;
2585: /* getting the maximum value of the modality of the covariate
2586: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2587: female is 1, then modmaxcovj=1.*/
2588: }
2589: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2590: for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
2591: if( Ndum[i] != 0 )
2592: ncodemax[j]++;
2593: /* Number of modalities of the j th covariate. In fact
2594: ncodemax[j]=2 (dichotom. variables only) but it could be more for
2595: historical reasons */
2596: } /* Ndum[-1] number of undefined modalities */
2597:
2598: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2599: ij=1;
2600: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
2601: for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
2602: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2603: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2604: k is a modality. If we have model=V1+V1*sex
2605: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2606: ij++;
2607: }
2608: if (ij > ncodemax[j]) break;
2609: } /* end of loop on */
2610: } /* end of loop on modality */
2611: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2612:
2613: for (k=0; k< maxncov; k++) Ndum[k]=0;
2614:
2615: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2616: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2617: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2618: Ndum[ij]++;
2619: }
2620:
2621: ij=1;
2622: for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2623: if((Ndum[i]!=0) && (i<=ncovcol)){
2624: Tvaraff[ij]=i; /*For printing */
2625: ij++;
2626: }
2627: }
2628: ij--;
2629: cptcoveff=ij; /*Number of simple covariates*/
2630: }
2631:
2632: /*********** Health Expectancies ****************/
2633:
2634: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2635:
2636: {
2637: /* Health expectancies, no variances */
2638: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2639: int nhstepma, nstepma; /* Decreasing with age */
2640: double age, agelim, hf;
2641: double ***p3mat;
2642: double eip;
2643:
2644: pstamp(ficreseij);
2645: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2646: fprintf(ficreseij,"# Age");
2647: for(i=1; i<=nlstate;i++){
2648: for(j=1; j<=nlstate;j++){
2649: fprintf(ficreseij," e%1d%1d ",i,j);
2650: }
2651: fprintf(ficreseij," e%1d. ",i);
2652: }
2653: fprintf(ficreseij,"\n");
2654:
2655:
2656: if(estepm < stepm){
2657: printf ("Problem %d lower than %d\n",estepm, stepm);
2658: }
2659: else hstepm=estepm;
2660: /* We compute the life expectancy from trapezoids spaced every estepm months
2661: * This is mainly to measure the difference between two models: for example
2662: * if stepm=24 months pijx are given only every 2 years and by summing them
2663: * we are calculating an estimate of the Life Expectancy assuming a linear
2664: * progression in between and thus overestimating or underestimating according
2665: * to the curvature of the survival function. If, for the same date, we
2666: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2667: * to compare the new estimate of Life expectancy with the same linear
2668: * hypothesis. A more precise result, taking into account a more precise
2669: * curvature will be obtained if estepm is as small as stepm. */
2670:
2671: /* For example we decided to compute the life expectancy with the smallest unit */
2672: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2673: nhstepm is the number of hstepm from age to agelim
2674: nstepm is the number of stepm from age to agelin.
2675: Look at hpijx to understand the reason of that which relies in memory size
2676: and note for a fixed period like estepm months */
2677: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2678: survival function given by stepm (the optimization length). Unfortunately it
2679: means that if the survival funtion is printed only each two years of age and if
2680: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2681: results. So we changed our mind and took the option of the best precision.
2682: */
2683: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2684:
2685: agelim=AGESUP;
2686: /* If stepm=6 months */
2687: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2688: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2689:
2690: /* nhstepm age range expressed in number of stepm */
2691: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2692: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2693: /* if (stepm >= YEARM) hstepm=1;*/
2694: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2695: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2696:
2697: for (age=bage; age<=fage; age ++){
2698: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2699: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2700: /* if (stepm >= YEARM) hstepm=1;*/
2701: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2702:
2703: /* If stepm=6 months */
2704: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2705: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2706:
2707: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2708:
2709: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2710:
2711: printf("%d|",(int)age);fflush(stdout);
2712: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2713:
2714: /* Computing expectancies */
2715: for(i=1; i<=nlstate;i++)
2716: for(j=1; j<=nlstate;j++)
2717: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2718: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2719:
2720: /* 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]);*/
2721:
2722: }
2723:
2724: fprintf(ficreseij,"%3.0f",age );
2725: for(i=1; i<=nlstate;i++){
2726: eip=0;
2727: for(j=1; j<=nlstate;j++){
2728: eip +=eij[i][j][(int)age];
2729: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2730: }
2731: fprintf(ficreseij,"%9.4f", eip );
2732: }
2733: fprintf(ficreseij,"\n");
2734:
2735: }
2736: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2737: printf("\n");
2738: fprintf(ficlog,"\n");
2739:
2740: }
2741:
2742: 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[] )
2743:
2744: {
2745: /* Covariances of health expectancies eij and of total life expectancies according
2746: to initial status i, ei. .
2747: */
2748: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2749: int nhstepma, nstepma; /* Decreasing with age */
2750: double age, agelim, hf;
2751: double ***p3matp, ***p3matm, ***varhe;
2752: double **dnewm,**doldm;
2753: double *xp, *xm;
2754: double **gp, **gm;
2755: double ***gradg, ***trgradg;
2756: int theta;
2757:
2758: double eip, vip;
2759:
2760: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2761: xp=vector(1,npar);
2762: xm=vector(1,npar);
2763: dnewm=matrix(1,nlstate*nlstate,1,npar);
2764: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2765:
2766: pstamp(ficresstdeij);
2767: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2768: fprintf(ficresstdeij,"# Age");
2769: for(i=1; i<=nlstate;i++){
2770: for(j=1; j<=nlstate;j++)
2771: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2772: fprintf(ficresstdeij," e%1d. ",i);
2773: }
2774: fprintf(ficresstdeij,"\n");
2775:
2776: pstamp(ficrescveij);
2777: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2778: fprintf(ficrescveij,"# Age");
2779: for(i=1; i<=nlstate;i++)
2780: for(j=1; j<=nlstate;j++){
2781: cptj= (j-1)*nlstate+i;
2782: for(i2=1; i2<=nlstate;i2++)
2783: for(j2=1; j2<=nlstate;j2++){
2784: cptj2= (j2-1)*nlstate+i2;
2785: if(cptj2 <= cptj)
2786: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2787: }
2788: }
2789: fprintf(ficrescveij,"\n");
2790:
2791: if(estepm < stepm){
2792: printf ("Problem %d lower than %d\n",estepm, stepm);
2793: }
2794: else hstepm=estepm;
2795: /* We compute the life expectancy from trapezoids spaced every estepm months
2796: * This is mainly to measure the difference between two models: for example
2797: * if stepm=24 months pijx are given only every 2 years and by summing them
2798: * we are calculating an estimate of the Life Expectancy assuming a linear
2799: * progression in between and thus overestimating or underestimating according
2800: * to the curvature of the survival function. If, for the same date, we
2801: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2802: * to compare the new estimate of Life expectancy with the same linear
2803: * hypothesis. A more precise result, taking into account a more precise
2804: * curvature will be obtained if estepm is as small as stepm. */
2805:
2806: /* For example we decided to compute the life expectancy with the smallest unit */
2807: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2808: nhstepm is the number of hstepm from age to agelim
2809: nstepm is the number of stepm from age to agelin.
2810: Look at hpijx to understand the reason of that which relies in memory size
2811: and note for a fixed period like estepm months */
2812: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2813: survival function given by stepm (the optimization length). Unfortunately it
2814: means that if the survival funtion is printed only each two years of age and if
2815: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2816: results. So we changed our mind and took the option of the best precision.
2817: */
2818: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2819:
2820: /* If stepm=6 months */
2821: /* nhstepm age range expressed in number of stepm */
2822: agelim=AGESUP;
2823: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2824: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2825: /* if (stepm >= YEARM) hstepm=1;*/
2826: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2827:
2828: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2829: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2830: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2831: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2832: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2833: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2834:
2835: for (age=bage; age<=fage; age ++){
2836: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2837: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2838: /* if (stepm >= YEARM) hstepm=1;*/
2839: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2840:
2841: /* If stepm=6 months */
2842: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2843: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2844:
2845: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2846:
2847: /* Computing Variances of health expectancies */
2848: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2849: decrease memory allocation */
2850: for(theta=1; theta <=npar; theta++){
2851: for(i=1; i<=npar; i++){
2852: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2853: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2854: }
2855: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2856: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2857:
2858: for(j=1; j<= nlstate; j++){
2859: for(i=1; i<=nlstate; i++){
2860: for(h=0; h<=nhstepm-1; h++){
2861: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2862: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2863: }
2864: }
2865: }
2866:
2867: for(ij=1; ij<= nlstate*nlstate; ij++)
2868: for(h=0; h<=nhstepm-1; h++){
2869: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2870: }
2871: }/* End theta */
2872:
2873:
2874: for(h=0; h<=nhstepm-1; h++)
2875: for(j=1; j<=nlstate*nlstate;j++)
2876: for(theta=1; theta <=npar; theta++)
2877: trgradg[h][j][theta]=gradg[h][theta][j];
2878:
2879:
2880: for(ij=1;ij<=nlstate*nlstate;ij++)
2881: for(ji=1;ji<=nlstate*nlstate;ji++)
2882: varhe[ij][ji][(int)age] =0.;
2883:
2884: printf("%d|",(int)age);fflush(stdout);
2885: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2886: for(h=0;h<=nhstepm-1;h++){
2887: for(k=0;k<=nhstepm-1;k++){
2888: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2889: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2890: for(ij=1;ij<=nlstate*nlstate;ij++)
2891: for(ji=1;ji<=nlstate*nlstate;ji++)
2892: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2893: }
2894: }
2895:
2896: /* Computing expectancies */
2897: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2898: for(i=1; i<=nlstate;i++)
2899: for(j=1; j<=nlstate;j++)
2900: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2901: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2902:
2903: /* 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]);*/
2904:
2905: }
2906:
2907: fprintf(ficresstdeij,"%3.0f",age );
2908: for(i=1; i<=nlstate;i++){
2909: eip=0.;
2910: vip=0.;
2911: for(j=1; j<=nlstate;j++){
2912: eip += eij[i][j][(int)age];
2913: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2914: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2915: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2916: }
2917: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2918: }
2919: fprintf(ficresstdeij,"\n");
2920:
2921: fprintf(ficrescveij,"%3.0f",age );
2922: for(i=1; i<=nlstate;i++)
2923: for(j=1; j<=nlstate;j++){
2924: cptj= (j-1)*nlstate+i;
2925: for(i2=1; i2<=nlstate;i2++)
2926: for(j2=1; j2<=nlstate;j2++){
2927: cptj2= (j2-1)*nlstate+i2;
2928: if(cptj2 <= cptj)
2929: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2930: }
2931: }
2932: fprintf(ficrescveij,"\n");
2933:
2934: }
2935: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2936: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2937: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2938: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2939: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2940: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2941: printf("\n");
2942: fprintf(ficlog,"\n");
2943:
2944: free_vector(xm,1,npar);
2945: free_vector(xp,1,npar);
2946: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2947: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2948: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2949: }
2950:
2951: /************ Variance ******************/
2952: 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[])
2953: {
2954: /* Variance of health expectancies */
2955: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2956: /* double **newm;*/
2957: double **dnewm,**doldm;
2958: double **dnewmp,**doldmp;
2959: int i, j, nhstepm, hstepm, h, nstepm ;
2960: int k, cptcode;
2961: double *xp;
2962: double **gp, **gm; /* for var eij */
2963: double ***gradg, ***trgradg; /*for var eij */
2964: double **gradgp, **trgradgp; /* for var p point j */
2965: double *gpp, *gmp; /* for var p point j */
2966: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2967: double ***p3mat;
2968: double age,agelim, hf;
2969: double ***mobaverage;
2970: int theta;
2971: char digit[4];
2972: char digitp[25];
2973:
2974: char fileresprobmorprev[FILENAMELENGTH];
2975:
2976: if(popbased==1){
2977: if(mobilav!=0)
2978: strcpy(digitp,"-populbased-mobilav-");
2979: else strcpy(digitp,"-populbased-nomobil-");
2980: }
2981: else
2982: strcpy(digitp,"-stablbased-");
2983:
2984: if (mobilav!=0) {
2985: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2986: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2987: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2988: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2989: }
2990: }
2991:
2992: strcpy(fileresprobmorprev,"prmorprev");
2993: sprintf(digit,"%-d",ij);
2994: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2995: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2996: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2997: strcat(fileresprobmorprev,fileres);
2998: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2999: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3000: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3001: }
3002: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3003:
3004: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3005: pstamp(ficresprobmorprev);
3006: 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);
3007: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3008: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3009: fprintf(ficresprobmorprev," p.%-d SE",j);
3010: for(i=1; i<=nlstate;i++)
3011: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3012: }
3013: fprintf(ficresprobmorprev,"\n");
3014: fprintf(ficgp,"\n# Routine varevsij");
3015: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3016: 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");
3017: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3018: /* } */
3019: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3020: pstamp(ficresvij);
3021: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3022: if(popbased==1)
3023: 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);
3024: else
3025: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3026: fprintf(ficresvij,"# Age");
3027: for(i=1; i<=nlstate;i++)
3028: for(j=1; j<=nlstate;j++)
3029: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3030: fprintf(ficresvij,"\n");
3031:
3032: xp=vector(1,npar);
3033: dnewm=matrix(1,nlstate,1,npar);
3034: doldm=matrix(1,nlstate,1,nlstate);
3035: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3036: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3037:
3038: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3039: gpp=vector(nlstate+1,nlstate+ndeath);
3040: gmp=vector(nlstate+1,nlstate+ndeath);
3041: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3042:
3043: if(estepm < stepm){
3044: printf ("Problem %d lower than %d\n",estepm, stepm);
3045: }
3046: else hstepm=estepm;
3047: /* For example we decided to compute the life expectancy with the smallest unit */
3048: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3049: nhstepm is the number of hstepm from age to agelim
3050: nstepm is the number of stepm from age to agelin.
3051: Look at function hpijx to understand why (it is linked to memory size questions) */
3052: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3053: survival function given by stepm (the optimization length). Unfortunately it
3054: means that if the survival funtion is printed every two years of age and if
3055: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3056: results. So we changed our mind and took the option of the best precision.
3057: */
3058: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3059: agelim = AGESUP;
3060: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3061: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3062: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3063: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3064: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3065: gp=matrix(0,nhstepm,1,nlstate);
3066: gm=matrix(0,nhstepm,1,nlstate);
3067:
3068:
3069: for(theta=1; theta <=npar; theta++){
3070: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3071: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3072: }
3073: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3074: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3075:
3076: if (popbased==1) {
3077: if(mobilav ==0){
3078: for(i=1; i<=nlstate;i++)
3079: prlim[i][i]=probs[(int)age][i][ij];
3080: }else{ /* mobilav */
3081: for(i=1; i<=nlstate;i++)
3082: prlim[i][i]=mobaverage[(int)age][i][ij];
3083: }
3084: }
3085:
3086: for(j=1; j<= nlstate; j++){
3087: for(h=0; h<=nhstepm; h++){
3088: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3089: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3090: }
3091: }
3092: /* This for computing probability of death (h=1 means
3093: computed over hstepm matrices product = hstepm*stepm months)
3094: as a weighted average of prlim.
3095: */
3096: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3097: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3098: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3099: }
3100: /* end probability of death */
3101:
3102: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3103: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3104: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3105: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3106:
3107: if (popbased==1) {
3108: if(mobilav ==0){
3109: for(i=1; i<=nlstate;i++)
3110: prlim[i][i]=probs[(int)age][i][ij];
3111: }else{ /* mobilav */
3112: for(i=1; i<=nlstate;i++)
3113: prlim[i][i]=mobaverage[(int)age][i][ij];
3114: }
3115: }
3116:
3117: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3118: for(h=0; h<=nhstepm; h++){
3119: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3120: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3121: }
3122: }
3123: /* This for computing probability of death (h=1 means
3124: computed over hstepm matrices product = hstepm*stepm months)
3125: as a weighted average of prlim.
3126: */
3127: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3128: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3129: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3130: }
3131: /* end probability of death */
3132:
3133: for(j=1; j<= nlstate; j++) /* vareij */
3134: for(h=0; h<=nhstepm; h++){
3135: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3136: }
3137:
3138: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3139: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3140: }
3141:
3142: } /* End theta */
3143:
3144: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3145:
3146: for(h=0; h<=nhstepm; h++) /* veij */
3147: for(j=1; j<=nlstate;j++)
3148: for(theta=1; theta <=npar; theta++)
3149: trgradg[h][j][theta]=gradg[h][theta][j];
3150:
3151: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3152: for(theta=1; theta <=npar; theta++)
3153: trgradgp[j][theta]=gradgp[theta][j];
3154:
3155:
3156: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3157: for(i=1;i<=nlstate;i++)
3158: for(j=1;j<=nlstate;j++)
3159: vareij[i][j][(int)age] =0.;
3160:
3161: for(h=0;h<=nhstepm;h++){
3162: for(k=0;k<=nhstepm;k++){
3163: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3164: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3165: for(i=1;i<=nlstate;i++)
3166: for(j=1;j<=nlstate;j++)
3167: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3168: }
3169: }
3170:
3171: /* pptj */
3172: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3173: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3174: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3175: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3176: varppt[j][i]=doldmp[j][i];
3177: /* end ppptj */
3178: /* x centered again */
3179: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3180: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3181:
3182: if (popbased==1) {
3183: if(mobilav ==0){
3184: for(i=1; i<=nlstate;i++)
3185: prlim[i][i]=probs[(int)age][i][ij];
3186: }else{ /* mobilav */
3187: for(i=1; i<=nlstate;i++)
3188: prlim[i][i]=mobaverage[(int)age][i][ij];
3189: }
3190: }
3191:
3192: /* This for computing probability of death (h=1 means
3193: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3194: as a weighted average of prlim.
3195: */
3196: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3197: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3198: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3199: }
3200: /* end probability of death */
3201:
3202: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3203: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3204: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3205: for(i=1; i<=nlstate;i++){
3206: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3207: }
3208: }
3209: fprintf(ficresprobmorprev,"\n");
3210:
3211: fprintf(ficresvij,"%.0f ",age );
3212: for(i=1; i<=nlstate;i++)
3213: for(j=1; j<=nlstate;j++){
3214: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3215: }
3216: fprintf(ficresvij,"\n");
3217: free_matrix(gp,0,nhstepm,1,nlstate);
3218: free_matrix(gm,0,nhstepm,1,nlstate);
3219: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3220: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3221: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3222: } /* End age */
3223: free_vector(gpp,nlstate+1,nlstate+ndeath);
3224: free_vector(gmp,nlstate+1,nlstate+ndeath);
3225: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3226: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3227: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
3228: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3229: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3230: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3231: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3232: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3233: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
3234: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
3235: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
3236: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3237: 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);
3238: /* 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);
3239: */
3240: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3241: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3242:
3243: free_vector(xp,1,npar);
3244: free_matrix(doldm,1,nlstate,1,nlstate);
3245: free_matrix(dnewm,1,nlstate,1,npar);
3246: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3247: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3248: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3249: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3250: fclose(ficresprobmorprev);
3251: fflush(ficgp);
3252: fflush(fichtm);
3253: } /* end varevsij */
3254:
3255: /************ Variance of prevlim ******************/
3256: 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[])
3257: {
3258: /* Variance of prevalence limit */
3259: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3260: double **newm;
3261: double **dnewm,**doldm;
3262: int i, j, nhstepm, hstepm;
3263: int k, cptcode;
3264: double *xp;
3265: double *gp, *gm;
3266: double **gradg, **trgradg;
3267: double age,agelim;
3268: int theta;
3269:
3270: pstamp(ficresvpl);
3271: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3272: fprintf(ficresvpl,"# Age");
3273: for(i=1; i<=nlstate;i++)
3274: fprintf(ficresvpl," %1d-%1d",i,i);
3275: fprintf(ficresvpl,"\n");
3276:
3277: xp=vector(1,npar);
3278: dnewm=matrix(1,nlstate,1,npar);
3279: doldm=matrix(1,nlstate,1,nlstate);
3280:
3281: hstepm=1*YEARM; /* Every year of age */
3282: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3283: agelim = AGESUP;
3284: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3285: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3286: if (stepm >= YEARM) hstepm=1;
3287: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3288: gradg=matrix(1,npar,1,nlstate);
3289: gp=vector(1,nlstate);
3290: gm=vector(1,nlstate);
3291:
3292: for(theta=1; theta <=npar; theta++){
3293: for(i=1; i<=npar; i++){ /* Computes gradient */
3294: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3295: }
3296: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3297: for(i=1;i<=nlstate;i++)
3298: gp[i] = prlim[i][i];
3299:
3300: for(i=1; i<=npar; i++) /* Computes gradient */
3301: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3302: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3303: for(i=1;i<=nlstate;i++)
3304: gm[i] = prlim[i][i];
3305:
3306: for(i=1;i<=nlstate;i++)
3307: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3308: } /* End theta */
3309:
3310: trgradg =matrix(1,nlstate,1,npar);
3311:
3312: for(j=1; j<=nlstate;j++)
3313: for(theta=1; theta <=npar; theta++)
3314: trgradg[j][theta]=gradg[theta][j];
3315:
3316: for(i=1;i<=nlstate;i++)
3317: varpl[i][(int)age] =0.;
3318: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3319: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3320: for(i=1;i<=nlstate;i++)
3321: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3322:
3323: fprintf(ficresvpl,"%.0f ",age );
3324: for(i=1; i<=nlstate;i++)
3325: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3326: fprintf(ficresvpl,"\n");
3327: free_vector(gp,1,nlstate);
3328: free_vector(gm,1,nlstate);
3329: free_matrix(gradg,1,npar,1,nlstate);
3330: free_matrix(trgradg,1,nlstate,1,npar);
3331: } /* End age */
3332:
3333: free_vector(xp,1,npar);
3334: free_matrix(doldm,1,nlstate,1,npar);
3335: free_matrix(dnewm,1,nlstate,1,nlstate);
3336:
3337: }
3338:
3339: /************ Variance of one-step probabilities ******************/
3340: 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[])
3341: {
3342: int i, j=0, i1, k1, l1, t, tj;
3343: int k2, l2, j1, z1;
3344: int k=0,l, cptcode;
3345: int first=1, first1;
3346: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3347: double **dnewm,**doldm;
3348: double *xp;
3349: double *gp, *gm;
3350: double **gradg, **trgradg;
3351: double **mu;
3352: double age,agelim, cov[NCOVMAX];
3353: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3354: int theta;
3355: char fileresprob[FILENAMELENGTH];
3356: char fileresprobcov[FILENAMELENGTH];
3357: char fileresprobcor[FILENAMELENGTH];
3358:
3359: double ***varpij;
3360:
3361: strcpy(fileresprob,"prob");
3362: strcat(fileresprob,fileres);
3363: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3364: printf("Problem with resultfile: %s\n", fileresprob);
3365: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3366: }
3367: strcpy(fileresprobcov,"probcov");
3368: strcat(fileresprobcov,fileres);
3369: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3370: printf("Problem with resultfile: %s\n", fileresprobcov);
3371: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3372: }
3373: strcpy(fileresprobcor,"probcor");
3374: strcat(fileresprobcor,fileres);
3375: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3376: printf("Problem with resultfile: %s\n", fileresprobcor);
3377: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3378: }
3379: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3380: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3381: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3382: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3383: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3384: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3385: pstamp(ficresprob);
3386: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3387: fprintf(ficresprob,"# Age");
3388: pstamp(ficresprobcov);
3389: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3390: fprintf(ficresprobcov,"# Age");
3391: pstamp(ficresprobcor);
3392: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3393: fprintf(ficresprobcor,"# Age");
3394:
3395:
3396: for(i=1; i<=nlstate;i++)
3397: for(j=1; j<=(nlstate+ndeath);j++){
3398: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3399: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3400: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3401: }
3402: /* fprintf(ficresprob,"\n");
3403: fprintf(ficresprobcov,"\n");
3404: fprintf(ficresprobcor,"\n");
3405: */
3406: xp=vector(1,npar);
3407: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3408: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3409: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3410: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3411: first=1;
3412: fprintf(ficgp,"\n# Routine varprob");
3413: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3414: fprintf(fichtm,"\n");
3415:
3416: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3417: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3418: file %s<br>\n",optionfilehtmcov);
3419: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3420: and drawn. It helps understanding how is the covariance between two incidences.\
3421: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3422: 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. \
3423: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3424: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3425: standard deviations wide on each axis. <br>\
3426: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3427: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3428: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3429:
3430: cov[1]=1;
3431: tj=cptcoveff;
3432: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3433: j1=0;
3434: for(t=1; t<=tj;t++){
3435: for(i1=1; i1<=ncodemax[t];i1++){
3436: j1++;
3437: if (cptcovn>0) {
3438: fprintf(ficresprob, "\n#********** Variable ");
3439: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3440: fprintf(ficresprob, "**********\n#\n");
3441: fprintf(ficresprobcov, "\n#********** Variable ");
3442: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3443: fprintf(ficresprobcov, "**********\n#\n");
3444:
3445: fprintf(ficgp, "\n#********** Variable ");
3446: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3447: fprintf(ficgp, "**********\n#\n");
3448:
3449:
3450: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3451: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3452: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3453:
3454: fprintf(ficresprobcor, "\n#********** Variable ");
3455: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3456: fprintf(ficresprobcor, "**********\n#");
3457: }
3458:
3459: for (age=bage; age<=fage; age ++){
3460: cov[2]=age;
3461: for (k=1; k<=cptcovn;k++) {
3462: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3463: }
3464: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3465: for (k=1; k<=cptcovprod;k++)
3466: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3467:
3468: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3469: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3470: gp=vector(1,(nlstate)*(nlstate+ndeath));
3471: gm=vector(1,(nlstate)*(nlstate+ndeath));
3472:
3473: for(theta=1; theta <=npar; theta++){
3474: for(i=1; i<=npar; i++)
3475: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3476:
3477: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3478:
3479: k=0;
3480: for(i=1; i<= (nlstate); i++){
3481: for(j=1; j<=(nlstate+ndeath);j++){
3482: k=k+1;
3483: gp[k]=pmmij[i][j];
3484: }
3485: }
3486:
3487: for(i=1; i<=npar; i++)
3488: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3489:
3490: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3491: k=0;
3492: for(i=1; i<=(nlstate); i++){
3493: for(j=1; j<=(nlstate+ndeath);j++){
3494: k=k+1;
3495: gm[k]=pmmij[i][j];
3496: }
3497: }
3498:
3499: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3500: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3501: }
3502:
3503: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3504: for(theta=1; theta <=npar; theta++)
3505: trgradg[j][theta]=gradg[theta][j];
3506:
3507: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3508: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3509: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3510: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3511: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3512: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3513:
3514: pmij(pmmij,cov,ncovmodel,x,nlstate);
3515:
3516: k=0;
3517: for(i=1; i<=(nlstate); i++){
3518: for(j=1; j<=(nlstate+ndeath);j++){
3519: k=k+1;
3520: mu[k][(int) age]=pmmij[i][j];
3521: }
3522: }
3523: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3524: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3525: varpij[i][j][(int)age] = doldm[i][j];
3526:
3527: /*printf("\n%d ",(int)age);
3528: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3529: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3530: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3531: }*/
3532:
3533: fprintf(ficresprob,"\n%d ",(int)age);
3534: fprintf(ficresprobcov,"\n%d ",(int)age);
3535: fprintf(ficresprobcor,"\n%d ",(int)age);
3536:
3537: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3538: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3539: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3540: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3541: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3542: }
3543: i=0;
3544: for (k=1; k<=(nlstate);k++){
3545: for (l=1; l<=(nlstate+ndeath);l++){
3546: i=i++;
3547: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3548: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3549: for (j=1; j<=i;j++){
3550: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3551: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3552: }
3553: }
3554: }/* end of loop for state */
3555: } /* end of loop for age */
3556:
3557: /* Confidence intervalle of pij */
3558: /*
3559: fprintf(ficgp,"\nunset parametric;unset label");
3560: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3561: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3562: 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);
3563: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3564: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3565: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3566: */
3567:
3568: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3569: first1=1;
3570: for (k2=1; k2<=(nlstate);k2++){
3571: for (l2=1; l2<=(nlstate+ndeath);l2++){
3572: if(l2==k2) continue;
3573: j=(k2-1)*(nlstate+ndeath)+l2;
3574: for (k1=1; k1<=(nlstate);k1++){
3575: for (l1=1; l1<=(nlstate+ndeath);l1++){
3576: if(l1==k1) continue;
3577: i=(k1-1)*(nlstate+ndeath)+l1;
3578: if(i<=j) continue;
3579: for (age=bage; age<=fage; age ++){
3580: if ((int)age %5==0){
3581: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3582: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3583: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3584: mu1=mu[i][(int) age]/stepm*YEARM ;
3585: mu2=mu[j][(int) age]/stepm*YEARM;
3586: c12=cv12/sqrt(v1*v2);
3587: /* Computing eigen value of matrix of covariance */
3588: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3589: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3590: if ((lc2 <0) || (lc1 <0) ){
3591: printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3592: fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
3593: lc1=fabs(lc1);
3594: lc2=fabs(lc2);
3595: }
3596:
3597: /* Eigen vectors */
3598: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3599: /*v21=sqrt(1.-v11*v11); *//* error */
3600: v21=(lc1-v1)/cv12*v11;
3601: v12=-v21;
3602: v22=v11;
3603: tnalp=v21/v11;
3604: if(first1==1){
3605: first1=0;
3606: 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);
3607: }
3608: 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);
3609: /*printf(fignu*/
3610: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3611: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3612: if(first==1){
3613: first=0;
3614: fprintf(ficgp,"\nset parametric;unset label");
3615: 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);
3616: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3617: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3618: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3619: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3620: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3621: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3622: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3623: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3624: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3625: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3626: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3627: 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",\
3628: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3629: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3630: }else{
3631: first=0;
3632: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3633: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3634: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3635: 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",\
3636: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3637: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3638: }/* if first */
3639: } /* age mod 5 */
3640: } /* end loop age */
3641: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3642: first=1;
3643: } /*l12 */
3644: } /* k12 */
3645: } /*l1 */
3646: }/* k1 */
3647: } /* loop covariates */
3648: }
3649: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3650: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3651: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3652: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3653: free_vector(xp,1,npar);
3654: fclose(ficresprob);
3655: fclose(ficresprobcov);
3656: fclose(ficresprobcor);
3657: fflush(ficgp);
3658: fflush(fichtmcov);
3659: }
3660:
3661:
3662: /******************* Printing html file ***********/
3663: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3664: int lastpass, int stepm, int weightopt, char model[],\
3665: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3666: int popforecast, int estepm ,\
3667: double jprev1, double mprev1,double anprev1, \
3668: double jprev2, double mprev2,double anprev2){
3669: int jj1, k1, i1, cpt;
3670:
3671: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3672: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3673: </ul>");
3674: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3675: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3676: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3677: fprintf(fichtm,"\
3678: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3679: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3680: fprintf(fichtm,"\
3681: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3682: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3683: fprintf(fichtm,"\
3684: - (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): \
3685: <a href=\"%s\">%s</a> <br>\n",
3686: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3687: fprintf(fichtm,"\
3688: - Population projections by age and states: \
3689: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3690:
3691: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3692:
3693: m=cptcoveff;
3694: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3695:
3696: jj1=0;
3697: for(k1=1; k1<=m;k1++){
3698: for(i1=1; i1<=ncodemax[k1];i1++){
3699: jj1++;
3700: if (cptcovn > 0) {
3701: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3702: for (cpt=1; cpt<=cptcoveff;cpt++)
3703: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3704: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3705: }
3706: /* Pij */
3707: 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> \
3708: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3709: /* Quasi-incidences */
3710: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3711: 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> \
3712: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3713: /* Period (stable) prevalence in each health state */
3714: for(cpt=1; cpt<nlstate;cpt++){
3715: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3716: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3717: }
3718: for(cpt=1; cpt<=nlstate;cpt++) {
3719: 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> \
3720: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3721: }
3722: } /* end i1 */
3723: }/* End k1 */
3724: fprintf(fichtm,"</ul>");
3725:
3726:
3727: fprintf(fichtm,"\
3728: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3729: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3730:
3731: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3732: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3733: fprintf(fichtm,"\
3734: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3735: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3736:
3737: fprintf(fichtm,"\
3738: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3739: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3740: fprintf(fichtm,"\
3741: - 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): \
3742: <a href=\"%s\">%s</a> <br>\n</li>",
3743: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3744: fprintf(fichtm,"\
3745: - (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): \
3746: <a href=\"%s\">%s</a> <br>\n</li>",
3747: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3748: fprintf(fichtm,"\
3749: - 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",
3750: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3751: fprintf(fichtm,"\
3752: - 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",
3753: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3754: fprintf(fichtm,"\
3755: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3756: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3757:
3758: /* if(popforecast==1) fprintf(fichtm,"\n */
3759: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3760: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3761: /* <br>",fileres,fileres,fileres,fileres); */
3762: /* else */
3763: /* 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); */
3764: fflush(fichtm);
3765: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3766:
3767: m=cptcoveff;
3768: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3769:
3770: jj1=0;
3771: for(k1=1; k1<=m;k1++){
3772: for(i1=1; i1<=ncodemax[k1];i1++){
3773: jj1++;
3774: if (cptcovn > 0) {
3775: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3776: for (cpt=1; cpt<=cptcoveff;cpt++)
3777: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3778: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3779: }
3780: for(cpt=1; cpt<=nlstate;cpt++) {
3781: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3782: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3783: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3784: }
3785: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3786: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3787: true period expectancies (those weighted with period prevalences are also\
3788: drawn in addition to the population based expectancies computed using\
3789: observed and cahotic prevalences: %s%d.png<br>\
3790: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3791: } /* end i1 */
3792: }/* End k1 */
3793: fprintf(fichtm,"</ul>");
3794: fflush(fichtm);
3795: }
3796:
3797: /******************* Gnuplot file **************/
3798: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3799:
3800: char dirfileres[132],optfileres[132];
3801: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3802: int ng=0;
3803: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3804: /* printf("Problem with file %s",optionfilegnuplot); */
3805: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3806: /* } */
3807:
3808: /*#ifdef windows */
3809: fprintf(ficgp,"cd \"%s\" \n",pathc);
3810: /*#endif */
3811: m=pow(2,cptcoveff);
3812:
3813: strcpy(dirfileres,optionfilefiname);
3814: strcpy(optfileres,"vpl");
3815: /* 1eme*/
3816: for (cpt=1; cpt<= nlstate ; cpt ++) {
3817: for (k1=1; k1<= m ; k1 ++) {
3818: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3819: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3820: fprintf(ficgp,"set xlabel \"Age\" \n\
3821: set ylabel \"Probability\" \n\
3822: set ter png small\n\
3823: set size 0.65,0.65\n\
3824: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3825:
3826: for (i=1; i<= nlstate ; i ++) {
3827: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3828: else fprintf(ficgp," \%%*lf (\%%*lf)");
3829: }
3830: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3831: for (i=1; i<= nlstate ; i ++) {
3832: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3833: else fprintf(ficgp," \%%*lf (\%%*lf)");
3834: }
3835: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3836: for (i=1; i<= nlstate ; i ++) {
3837: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3838: else fprintf(ficgp," \%%*lf (\%%*lf)");
3839: }
3840: fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3841: }
3842: }
3843: /*2 eme*/
3844:
3845: for (k1=1; k1<= m ; k1 ++) {
3846: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3847: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3848:
3849: for (i=1; i<= nlstate+1 ; i ++) {
3850: k=2*i;
3851: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3852: for (j=1; j<= nlstate+1 ; j ++) {
3853: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3854: else fprintf(ficgp," \%%*lf (\%%*lf)");
3855: }
3856: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3857: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3858: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3859: for (j=1; j<= nlstate+1 ; j ++) {
3860: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3861: else fprintf(ficgp," \%%*lf (\%%*lf)");
3862: }
3863: fprintf(ficgp,"\" t\"\" w l lt 1,");
3864: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3865: for (j=1; j<= nlstate+1 ; j ++) {
3866: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3867: else fprintf(ficgp," \%%*lf (\%%*lf)");
3868: }
3869: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
3870: else fprintf(ficgp,"\" t\"\" w l lt 1,");
3871: }
3872: }
3873:
3874: /*3eme*/
3875:
3876: for (k1=1; k1<= m ; k1 ++) {
3877: for (cpt=1; cpt<= nlstate ; cpt ++) {
3878: /* k=2+nlstate*(2*cpt-2); */
3879: k=2+(nlstate+1)*(cpt-1);
3880: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3881: fprintf(ficgp,"set ter png small\n\
3882: set size 0.65,0.65\n\
3883: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3884: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3885: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3886: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3887: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3888: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3889: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3890:
3891: */
3892: for (i=1; i< nlstate ; i ++) {
3893: 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);
3894: /* 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);*/
3895:
3896: }
3897: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3898: }
3899: }
3900:
3901: /* CV preval stable (period) */
3902: for (k1=1; k1<= m ; k1 ++) {
3903: for (cpt=1; cpt<=nlstate ; cpt ++) {
3904: k=3;
3905: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3906: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3907: set ter png small\nset size 0.65,0.65\n\
3908: unset log y\n\
3909: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3910:
3911: for (i=1; i< nlstate ; i ++)
3912: fprintf(ficgp,"+$%d",k+i+1);
3913: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3914:
3915: l=3+(nlstate+ndeath)*cpt;
3916: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3917: for (i=1; i< nlstate ; i ++) {
3918: l=3+(nlstate+ndeath)*cpt;
3919: fprintf(ficgp,"+$%d",l+i+1);
3920: }
3921: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3922: }
3923: }
3924:
3925: /* proba elementaires */
3926: for(i=1,jk=1; i <=nlstate; i++){
3927: for(k=1; k <=(nlstate+ndeath); k++){
3928: if (k != i) {
3929: for(j=1; j <=ncovmodel; j++){
3930: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3931: jk++;
3932: fprintf(ficgp,"\n");
3933: }
3934: }
3935: }
3936: }
3937:
3938: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3939: for(jk=1; jk <=m; jk++) {
3940: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3941: if (ng==2)
3942: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3943: else
3944: fprintf(ficgp,"\nset title \"Probability\"\n");
3945: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3946: i=1;
3947: for(k2=1; k2<=nlstate; k2++) {
3948: k3=i;
3949: for(k=1; k<=(nlstate+ndeath); k++) {
3950: if (k != k2){
3951: if(ng==2)
3952: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3953: else
3954: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3955: ij=1;/* To be checked else nbcode[0][0] wrong */
3956: for(j=3; j <=ncovmodel; j++) {
3957: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
3958: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3959: ij++;
3960: }
3961: else
3962: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3963: }
3964: fprintf(ficgp,")/(1");
3965:
3966: for(k1=1; k1 <=nlstate; k1++){
3967: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3968: ij=1;
3969: for(j=3; j <=ncovmodel; j++){
3970: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3971: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3972: ij++;
3973: }
3974: else
3975: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3976: }
3977: fprintf(ficgp,")");
3978: }
3979: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3980: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3981: i=i+ncovmodel;
3982: }
3983: } /* end k */
3984: } /* end k2 */
3985: } /* end jk */
3986: } /* end ng */
3987: fflush(ficgp);
3988: } /* end gnuplot */
3989:
3990:
3991: /*************** Moving average **************/
3992: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3993:
3994: int i, cpt, cptcod;
3995: int modcovmax =1;
3996: int mobilavrange, mob;
3997: double age;
3998:
3999: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4000: a covariate has 2 modalities */
4001: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4002:
4003: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4004: if(mobilav==1) mobilavrange=5; /* default */
4005: else mobilavrange=mobilav;
4006: for (age=bage; age<=fage; age++)
4007: for (i=1; i<=nlstate;i++)
4008: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4009: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4010: /* We keep the original values on the extreme ages bage, fage and for
4011: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4012: we use a 5 terms etc. until the borders are no more concerned.
4013: */
4014: for (mob=3;mob <=mobilavrange;mob=mob+2){
4015: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4016: for (i=1; i<=nlstate;i++){
4017: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4018: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4019: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4020: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4021: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4022: }
4023: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4024: }
4025: }
4026: }/* end age */
4027: }/* end mob */
4028: }else return -1;
4029: return 0;
4030: }/* End movingaverage */
4031:
4032:
4033: /************** Forecasting ******************/
4034: 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){
4035: /* proj1, year, month, day of starting projection
4036: agemin, agemax range of age
4037: dateprev1 dateprev2 range of dates during which prevalence is computed
4038: anproj2 year of en of projection (same day and month as proj1).
4039: */
4040: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4041: int *popage;
4042: double agec; /* generic age */
4043: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4044: double *popeffectif,*popcount;
4045: double ***p3mat;
4046: double ***mobaverage;
4047: char fileresf[FILENAMELENGTH];
4048:
4049: agelim=AGESUP;
4050: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4051:
4052: strcpy(fileresf,"f");
4053: strcat(fileresf,fileres);
4054: if((ficresf=fopen(fileresf,"w"))==NULL) {
4055: printf("Problem with forecast resultfile: %s\n", fileresf);
4056: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4057: }
4058: printf("Computing forecasting: result on file '%s' \n", fileresf);
4059: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4060:
4061: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4062:
4063: if (mobilav!=0) {
4064: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4065: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4066: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4067: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4068: }
4069: }
4070:
4071: stepsize=(int) (stepm+YEARM-1)/YEARM;
4072: if (stepm<=12) stepsize=1;
4073: if(estepm < stepm){
4074: printf ("Problem %d lower than %d\n",estepm, stepm);
4075: }
4076: else hstepm=estepm;
4077:
4078: hstepm=hstepm/stepm;
4079: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4080: fractional in yp1 */
4081: anprojmean=yp;
4082: yp2=modf((yp1*12),&yp);
4083: mprojmean=yp;
4084: yp1=modf((yp2*30.5),&yp);
4085: jprojmean=yp;
4086: if(jprojmean==0) jprojmean=1;
4087: if(mprojmean==0) jprojmean=1;
4088:
4089: i1=cptcoveff;
4090: if (cptcovn < 1){i1=1;}
4091:
4092: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4093:
4094: fprintf(ficresf,"#****** Routine prevforecast **\n");
4095:
4096: /* if (h==(int)(YEARM*yearp)){ */
4097: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4098: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4099: k=k+1;
4100: fprintf(ficresf,"\n#******");
4101: for(j=1;j<=cptcoveff;j++) {
4102: 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]]);
4103: }
4104: fprintf(ficresf,"******\n");
4105: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4106: for(j=1; j<=nlstate+ndeath;j++){
4107: for(i=1; i<=nlstate;i++)
4108: fprintf(ficresf," p%d%d",i,j);
4109: fprintf(ficresf," p.%d",j);
4110: }
4111: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4112: fprintf(ficresf,"\n");
4113: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4114:
4115: for (agec=fage; agec>=(ageminpar-1); agec--){
4116: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4117: nhstepm = nhstepm/hstepm;
4118: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4119: oldm=oldms;savm=savms;
4120: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4121:
4122: for (h=0; h<=nhstepm; h++){
4123: if (h*hstepm/YEARM*stepm ==yearp) {
4124: fprintf(ficresf,"\n");
4125: for(j=1;j<=cptcoveff;j++)
4126: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4127: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4128: }
4129: for(j=1; j<=nlstate+ndeath;j++) {
4130: ppij=0.;
4131: for(i=1; i<=nlstate;i++) {
4132: if (mobilav==1)
4133: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4134: else {
4135: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4136: }
4137: if (h*hstepm/YEARM*stepm== yearp) {
4138: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4139: }
4140: } /* end i */
4141: if (h*hstepm/YEARM*stepm==yearp) {
4142: fprintf(ficresf," %.3f", ppij);
4143: }
4144: }/* end j */
4145: } /* end h */
4146: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4147: } /* end agec */
4148: } /* end yearp */
4149: } /* end cptcod */
4150: } /* end cptcov */
4151:
4152: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4153:
4154: fclose(ficresf);
4155: }
4156:
4157: /************** Forecasting *****not tested NB*************/
4158: 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){
4159:
4160: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4161: int *popage;
4162: double calagedatem, agelim, kk1, kk2;
4163: double *popeffectif,*popcount;
4164: double ***p3mat,***tabpop,***tabpopprev;
4165: double ***mobaverage;
4166: char filerespop[FILENAMELENGTH];
4167:
4168: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4169: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4170: agelim=AGESUP;
4171: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4172:
4173: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4174:
4175:
4176: strcpy(filerespop,"pop");
4177: strcat(filerespop,fileres);
4178: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4179: printf("Problem with forecast resultfile: %s\n", filerespop);
4180: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4181: }
4182: printf("Computing forecasting: result on file '%s' \n", filerespop);
4183: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4184:
4185: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4186:
4187: if (mobilav!=0) {
4188: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4189: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4190: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4191: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4192: }
4193: }
4194:
4195: stepsize=(int) (stepm+YEARM-1)/YEARM;
4196: if (stepm<=12) stepsize=1;
4197:
4198: agelim=AGESUP;
4199:
4200: hstepm=1;
4201: hstepm=hstepm/stepm;
4202:
4203: if (popforecast==1) {
4204: if((ficpop=fopen(popfile,"r"))==NULL) {
4205: printf("Problem with population file : %s\n",popfile);exit(0);
4206: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4207: }
4208: popage=ivector(0,AGESUP);
4209: popeffectif=vector(0,AGESUP);
4210: popcount=vector(0,AGESUP);
4211:
4212: i=1;
4213: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4214:
4215: imx=i;
4216: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4217: }
4218:
4219: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4220: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4221: k=k+1;
4222: fprintf(ficrespop,"\n#******");
4223: for(j=1;j<=cptcoveff;j++) {
4224: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4225: }
4226: fprintf(ficrespop,"******\n");
4227: fprintf(ficrespop,"# Age");
4228: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4229: if (popforecast==1) fprintf(ficrespop," [Population]");
4230:
4231: for (cpt=0; cpt<=0;cpt++) {
4232: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4233:
4234: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4235: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4236: nhstepm = nhstepm/hstepm;
4237:
4238: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4239: oldm=oldms;savm=savms;
4240: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4241:
4242: for (h=0; h<=nhstepm; h++){
4243: if (h==(int) (calagedatem+YEARM*cpt)) {
4244: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4245: }
4246: for(j=1; j<=nlstate+ndeath;j++) {
4247: kk1=0.;kk2=0;
4248: for(i=1; i<=nlstate;i++) {
4249: if (mobilav==1)
4250: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4251: else {
4252: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4253: }
4254: }
4255: if (h==(int)(calagedatem+12*cpt)){
4256: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4257: /*fprintf(ficrespop," %.3f", kk1);
4258: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4259: }
4260: }
4261: for(i=1; i<=nlstate;i++){
4262: kk1=0.;
4263: for(j=1; j<=nlstate;j++){
4264: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4265: }
4266: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4267: }
4268:
4269: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4270: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4271: }
4272: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4273: }
4274: }
4275:
4276: /******/
4277:
4278: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4279: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4280: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4281: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4282: nhstepm = nhstepm/hstepm;
4283:
4284: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4285: oldm=oldms;savm=savms;
4286: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4287: for (h=0; h<=nhstepm; h++){
4288: if (h==(int) (calagedatem+YEARM*cpt)) {
4289: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4290: }
4291: for(j=1; j<=nlstate+ndeath;j++) {
4292: kk1=0.;kk2=0;
4293: for(i=1; i<=nlstate;i++) {
4294: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4295: }
4296: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4297: }
4298: }
4299: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4300: }
4301: }
4302: }
4303: }
4304:
4305: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4306:
4307: if (popforecast==1) {
4308: free_ivector(popage,0,AGESUP);
4309: free_vector(popeffectif,0,AGESUP);
4310: free_vector(popcount,0,AGESUP);
4311: }
4312: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4313: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4314: fclose(ficrespop);
4315: } /* End of popforecast */
4316:
4317: int fileappend(FILE *fichier, char *optionfich)
4318: {
4319: if((fichier=fopen(optionfich,"a"))==NULL) {
4320: printf("Problem with file: %s\n", optionfich);
4321: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4322: return (0);
4323: }
4324: fflush(fichier);
4325: return (1);
4326: }
4327:
4328:
4329: /**************** function prwizard **********************/
4330: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4331: {
4332:
4333: /* Wizard to print covariance matrix template */
4334:
4335: char ca[32], cb[32], cc[32];
4336: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4337: int numlinepar;
4338:
4339: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4340: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4341: for(i=1; i <=nlstate; i++){
4342: jj=0;
4343: for(j=1; j <=nlstate+ndeath; j++){
4344: if(j==i) continue;
4345: jj++;
4346: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4347: printf("%1d%1d",i,j);
4348: fprintf(ficparo,"%1d%1d",i,j);
4349: for(k=1; k<=ncovmodel;k++){
4350: /* printf(" %lf",param[i][j][k]); */
4351: /* fprintf(ficparo," %lf",param[i][j][k]); */
4352: printf(" 0.");
4353: fprintf(ficparo," 0.");
4354: }
4355: printf("\n");
4356: fprintf(ficparo,"\n");
4357: }
4358: }
4359: printf("# Scales (for hessian or gradient estimation)\n");
4360: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4361: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4362: for(i=1; i <=nlstate; i++){
4363: jj=0;
4364: for(j=1; j <=nlstate+ndeath; j++){
4365: if(j==i) continue;
4366: jj++;
4367: fprintf(ficparo,"%1d%1d",i,j);
4368: printf("%1d%1d",i,j);
4369: fflush(stdout);
4370: for(k=1; k<=ncovmodel;k++){
4371: /* printf(" %le",delti3[i][j][k]); */
4372: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4373: printf(" 0.");
4374: fprintf(ficparo," 0.");
4375: }
4376: numlinepar++;
4377: printf("\n");
4378: fprintf(ficparo,"\n");
4379: }
4380: }
4381: printf("# Covariance matrix\n");
4382: /* # 121 Var(a12)\n\ */
4383: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4384: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4385: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4386: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4387: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4388: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4389: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4390: fflush(stdout);
4391: fprintf(ficparo,"# Covariance matrix\n");
4392: /* # 121 Var(a12)\n\ */
4393: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4394: /* # ...\n\ */
4395: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4396:
4397: for(itimes=1;itimes<=2;itimes++){
4398: jj=0;
4399: for(i=1; i <=nlstate; i++){
4400: for(j=1; j <=nlstate+ndeath; j++){
4401: if(j==i) continue;
4402: for(k=1; k<=ncovmodel;k++){
4403: jj++;
4404: ca[0]= k+'a'-1;ca[1]='\0';
4405: if(itimes==1){
4406: printf("#%1d%1d%d",i,j,k);
4407: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4408: }else{
4409: printf("%1d%1d%d",i,j,k);
4410: fprintf(ficparo,"%1d%1d%d",i,j,k);
4411: /* printf(" %.5le",matcov[i][j]); */
4412: }
4413: ll=0;
4414: for(li=1;li <=nlstate; li++){
4415: for(lj=1;lj <=nlstate+ndeath; lj++){
4416: if(lj==li) continue;
4417: for(lk=1;lk<=ncovmodel;lk++){
4418: ll++;
4419: if(ll<=jj){
4420: cb[0]= lk +'a'-1;cb[1]='\0';
4421: if(ll<jj){
4422: if(itimes==1){
4423: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4424: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4425: }else{
4426: printf(" 0.");
4427: fprintf(ficparo," 0.");
4428: }
4429: }else{
4430: if(itimes==1){
4431: printf(" Var(%s%1d%1d)",ca,i,j);
4432: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4433: }else{
4434: printf(" 0.");
4435: fprintf(ficparo," 0.");
4436: }
4437: }
4438: }
4439: } /* end lk */
4440: } /* end lj */
4441: } /* end li */
4442: printf("\n");
4443: fprintf(ficparo,"\n");
4444: numlinepar++;
4445: } /* end k*/
4446: } /*end j */
4447: } /* end i */
4448: } /* end itimes */
4449:
4450: } /* end of prwizard */
4451: /******************* Gompertz Likelihood ******************************/
4452: double gompertz(double x[])
4453: {
4454: double A,B,L=0.0,sump=0.,num=0.;
4455: int i,n=0; /* n is the size of the sample */
4456:
4457: for (i=0;i<=imx-1 ; i++) {
4458: sump=sump+weight[i];
4459: /* sump=sump+1;*/
4460: num=num+1;
4461: }
4462:
4463:
4464: /* for (i=0; i<=imx; i++)
4465: 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]);*/
4466:
4467: for (i=1;i<=imx ; i++)
4468: {
4469: if (cens[i] == 1 && wav[i]>1)
4470: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4471:
4472: if (cens[i] == 0 && wav[i]>1)
4473: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4474: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4475:
4476: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4477: if (wav[i] > 1 ) { /* ??? */
4478: L=L+A*weight[i];
4479: /* 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]);*/
4480: }
4481: }
4482:
4483: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4484:
4485: return -2*L*num/sump;
4486: }
4487:
4488: #ifdef GSL
4489: /******************* Gompertz_f Likelihood ******************************/
4490: double gompertz_f(const gsl_vector *v, void *params)
4491: {
4492: double A,B,LL=0.0,sump=0.,num=0.;
4493: double *x= (double *) v->data;
4494: int i,n=0; /* n is the size of the sample */
4495:
4496: for (i=0;i<=imx-1 ; i++) {
4497: sump=sump+weight[i];
4498: /* sump=sump+1;*/
4499: num=num+1;
4500: }
4501:
4502:
4503: /* for (i=0; i<=imx; i++)
4504: 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]);*/
4505: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4506: for (i=1;i<=imx ; i++)
4507: {
4508: if (cens[i] == 1 && wav[i]>1)
4509: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4510:
4511: if (cens[i] == 0 && wav[i]>1)
4512: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4513: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4514:
4515: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4516: if (wav[i] > 1 ) { /* ??? */
4517: LL=LL+A*weight[i];
4518: /* 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]);*/
4519: }
4520: }
4521:
4522: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4523: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4524:
4525: return -2*LL*num/sump;
4526: }
4527: #endif
4528:
4529: /******************* Printing html file ***********/
4530: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4531: int lastpass, int stepm, int weightopt, char model[],\
4532: int imx, double p[],double **matcov,double agemortsup){
4533: int i,k;
4534:
4535: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4536: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4537: for (i=1;i<=2;i++)
4538: 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]));
4539: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4540: fprintf(fichtm,"</ul>");
4541:
4542: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4543:
4544: 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>");
4545:
4546: for (k=agegomp;k<(agemortsup-2);k++)
4547: 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]);
4548:
4549:
4550: fflush(fichtm);
4551: }
4552:
4553: /******************* Gnuplot file **************/
4554: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4555:
4556: char dirfileres[132],optfileres[132];
4557: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4558: int ng;
4559:
4560:
4561: /*#ifdef windows */
4562: fprintf(ficgp,"cd \"%s\" \n",pathc);
4563: /*#endif */
4564:
4565:
4566: strcpy(dirfileres,optionfilefiname);
4567: strcpy(optfileres,"vpl");
4568: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4569: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4570: fprintf(ficgp, "set ter png small\n set log y\n");
4571: fprintf(ficgp, "set size 0.65,0.65\n");
4572: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4573:
4574: }
4575:
4576: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4577: {
4578:
4579: /*-------- data file ----------*/
4580: FILE *fic;
4581: char dummy[]=" ";
4582: int i, j, n;
4583: int linei, month, year,iout;
4584: char line[MAXLINE], linetmp[MAXLINE];
4585: char stra[80], strb[80];
4586: char *stratrunc;
4587: int lstra;
4588:
4589:
4590: if((fic=fopen(datafile,"r"))==NULL) {
4591: printf("Problem while opening datafile: %s\n", datafile);return 1;
4592: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4593: }
4594:
4595: i=1;
4596: linei=0;
4597: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4598: linei=linei+1;
4599: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4600: if(line[j] == '\t')
4601: line[j] = ' ';
4602: }
4603: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4604: ;
4605: };
4606: line[j+1]=0; /* Trims blanks at end of line */
4607: if(line[0]=='#'){
4608: fprintf(ficlog,"Comment line\n%s\n",line);
4609: printf("Comment line\n%s\n",line);
4610: continue;
4611: }
4612: trimbb(linetmp,line); /* Trims multiple blanks in line */
4613: for (j=0; line[j]!='\0';j++){
4614: line[j]=linetmp[j];
4615: }
4616:
4617:
4618: for (j=maxwav;j>=1;j--){
4619: cutv(stra, strb, line, ' ');
4620: if(strb[0]=='.') { /* Missing status */
4621: lval=-1;
4622: }else{
4623: errno=0;
4624: lval=strtol(strb,&endptr,10);
4625: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4626: if( strb[0]=='\0' || (*endptr != '\0')){
4627: printf("Error reading data around '%s' at line number %d 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);
4628: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);fflush(ficlog);
4629: return 1;
4630: }
4631: }
4632: s[j][i]=lval;
4633:
4634: strcpy(line,stra);
4635: cutv(stra, strb,line,' ');
4636: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4637: }
4638: else if(iout=sscanf(strb,"%s.") != 0){
4639: month=99;
4640: year=9999;
4641: }else{
4642: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4643: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
4644: return 1;
4645: }
4646: anint[j][i]= (double) year;
4647: mint[j][i]= (double)month;
4648: strcpy(line,stra);
4649: } /* ENd Waves */
4650:
4651: cutv(stra, strb,line,' ');
4652: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4653: }
4654: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4655: month=99;
4656: year=9999;
4657: }else{
4658: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4659: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4660: return 1;
4661: }
4662: andc[i]=(double) year;
4663: moisdc[i]=(double) month;
4664: strcpy(line,stra);
4665:
4666: cutv(stra, strb,line,' ');
4667: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4668: }
4669: else if(iout=sscanf(strb,"%s.") != 0){
4670: month=99;
4671: year=9999;
4672: }else{
4673: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4674: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4675: return 1;
4676: }
4677: if (year==9999) {
4678: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
4679: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
4680: return 1;
4681:
4682: }
4683: annais[i]=(double)(year);
4684: moisnais[i]=(double)(month);
4685: strcpy(line,stra);
4686:
4687: cutv(stra, strb,line,' ');
4688: errno=0;
4689: dval=strtod(strb,&endptr);
4690: if( strb[0]=='\0' || (*endptr != '\0')){
4691: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4692: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4693: fflush(ficlog);
4694: return 1;
4695: }
4696: weight[i]=dval;
4697: strcpy(line,stra);
4698:
4699: for (j=ncovcol;j>=1;j--){
4700: cutv(stra, strb,line,' ');
4701: if(strb[0]=='.') { /* Missing status */
4702: lval=-1;
4703: }else{
4704: errno=0;
4705: lval=strtol(strb,&endptr,10);
4706: if( strb[0]=='\0' || (*endptr != '\0')){
4707: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
4708: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
4709: return 1;
4710: }
4711: }
4712: if(lval <-1 || lval >1){
4713: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4714: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4715: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4716: For example, for multinomial values like 1, 2 and 3,\n \
4717: build V1=0 V2=0 for the reference value (1),\n \
4718: V1=1 V2=0 for (2) \n \
4719: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4720: output of IMaCh is often meaningless.\n \
4721: Exiting.\n",lval,linei, i,line,j);
4722: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4723: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4724: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4725: For example, for multinomial values like 1, 2 and 3,\n \
4726: build V1=0 V2=0 for the reference value (1),\n \
4727: V1=1 V2=0 for (2) \n \
4728: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4729: output of IMaCh is often meaningless.\n \
4730: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4731: return 1;
4732: }
4733: covar[j][i]=(double)(lval);
4734: strcpy(line,stra);
4735: }
4736: lstra=strlen(stra);
4737:
4738: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4739: stratrunc = &(stra[lstra-9]);
4740: num[i]=atol(stratrunc);
4741: }
4742: else
4743: num[i]=atol(stra);
4744: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4745: 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;}*/
4746:
4747: i=i+1;
4748: } /* End loop reading data */
4749:
4750: *imax=i-1; /* Number of individuals */
4751: fclose(fic);
4752:
4753: return (0);
4754: endread:
4755: printf("Exiting readdata: ");
4756: fclose(fic);
4757: return (1);
4758:
4759:
4760:
4761: }
4762:
4763: int decodemodel ( char model[], int lastobs)
4764: {
4765: int i, j, k;
4766: int i1, j1, k1, k2;
4767: char modelsav[80];
4768: char stra[80], strb[80], strc[80], strd[80],stre[80];
4769:
4770: if (strlen(model) >1){ /* If there is at least 1 covariate */
4771: j=0, j1=0, k1=1, k2=1;
4772: j=nbocc(model,'+'); /* j=Number of '+' */
4773: j1=nbocc(model,'*'); /* j1=Number of '*' */
4774: cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
4775: but the covariates which are product must be computed and stored. */
4776: cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
4777:
4778: strcpy(modelsav,model);
4779: if (strstr(model,"AGE") !=0){
4780: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4781: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
4782: return 1;
4783: }
4784: if (strstr(model,"v") !=0){
4785: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4786: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4787: return 1;
4788: }
4789:
4790: /* This loop fills the array Tvar from the string 'model'.*/
4791: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
4792: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
4793: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
4794: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
4795: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
4796: /* k=1 Tvar[1]=2 (from V2) */
4797: /* k=5 Tvar[5] */
4798: /* for (k=1; k<=cptcovn;k++) { */
4799: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
4800: /* } */
4801: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4802: for(k=cptcovn; k>=1;k--){
4803: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
4804: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
4805: */
4806: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4807: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4808: /*scanf("%d",i);*/
4809: if (strchr(strb,'*')) { /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
4810: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
4811: if (strcmp(strc,"age")==0) { /* Vn*age */
4812: cptcovprod--;
4813: cutv(strb,stre,strd,'V'); /* stre="V3" */
4814: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
4815: cptcovage++; /* Sums the number of covariates which include age as a product */
4816: Tage[cptcovage]=k; /* Tage[1] = 4 */
4817: /*printf("stre=%s ", stre);*/
4818: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
4819: cptcovprod--;
4820: cutv(strb,stre,strc,'V');
4821: Tvar[k]=atoi(stre);
4822: cptcovage++;
4823: Tage[cptcovage]=k;
4824: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
4825: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
4826: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
4827: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
4828: because this model-covariate is a construction we invent a new column
4829: ncovcol + k1
4830: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
4831: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
4832: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4833: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
4834: Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
4835: Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
4836: Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
4837: Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
4838: for (i=1; i<=lastobs;i++){
4839: /* Computes the new covariate which is a product of
4840: covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
4841: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
4842: }
4843: k1++;
4844: k2=k2+2;
4845: } /* End age is not in the model */
4846: } /* End if model includes a product */
4847: else { /* no more sum */
4848: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4849: /* scanf("%d",i);*/
4850: cutv(strd,strc,strb,'V');
4851: Tvar[k]=atoi(strc);
4852: }
4853: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
4854: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4855: scanf("%d",i);*/
4856: } /* end of loop + */
4857: } /* end model */
4858:
4859: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4860: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4861:
4862: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4863: printf("cptcovprod=%d ", cptcovprod);
4864: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4865:
4866: scanf("%d ",i);*/
4867:
4868:
4869: return (0); /* with covar[new additional covariate if product] and Tage if age */
4870: endread:
4871: printf("Exiting decodemodel: ");
4872: return (1);
4873: }
4874:
4875: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
4876: {
4877: int i, m;
4878:
4879: for (i=1; i<=imx; i++) {
4880: for(m=2; (m<= maxwav); m++) {
4881: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4882: anint[m][i]=9999;
4883: s[m][i]=-1;
4884: }
4885: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4886: *nberr++;
4887: 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);
4888: 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);
4889: s[m][i]=-1;
4890: }
4891: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4892: *nberr++;
4893: 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]);
4894: 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]);
4895: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4896: }
4897: }
4898: }
4899:
4900: for (i=1; i<=imx; i++) {
4901: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4902: for(m=firstpass; (m<= lastpass); m++){
4903: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4904: if (s[m][i] >= nlstate+1) {
4905: if(agedc[i]>0)
4906: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4907: agev[m][i]=agedc[i];
4908: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4909: else {
4910: if ((int)andc[i]!=9999){
4911: nbwarn++;
4912: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4913: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4914: agev[m][i]=-1;
4915: }
4916: }
4917: }
4918: else if(s[m][i] !=9){ /* Standard case, age in fractional
4919: years but with the precision of a month */
4920: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4921: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4922: agev[m][i]=1;
4923: else if(agev[m][i] < *agemin){
4924: *agemin=agev[m][i];
4925: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
4926: }
4927: else if(agev[m][i] >*agemax){
4928: *agemax=agev[m][i];
4929: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
4930: }
4931: /*agev[m][i]=anint[m][i]-annais[i];*/
4932: /* agev[m][i] = age[i]+2*m;*/
4933: }
4934: else { /* =9 */
4935: agev[m][i]=1;
4936: s[m][i]=-1;
4937: }
4938: }
4939: else /*= 0 Unknown */
4940: agev[m][i]=1;
4941: }
4942:
4943: }
4944: for (i=1; i<=imx; i++) {
4945: for(m=firstpass; (m<=lastpass); m++){
4946: if (s[m][i] > (nlstate+ndeath)) {
4947: *nberr++;
4948: 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);
4949: 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);
4950: return 1;
4951: }
4952: }
4953: }
4954:
4955: /*for (i=1; i<=imx; i++){
4956: for (m=firstpass; (m<lastpass); m++){
4957: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4958: }
4959:
4960: }*/
4961:
4962:
4963: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
4964: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
4965:
4966: return (0);
4967: endread:
4968: printf("Exiting calandcheckages: ");
4969: return (1);
4970: }
4971:
4972:
4973: /***********************************************/
4974: /**************** Main Program *****************/
4975: /***********************************************/
4976:
4977: int main(int argc, char *argv[])
4978: {
4979: #ifdef GSL
4980: const gsl_multimin_fminimizer_type *T;
4981: size_t iteri = 0, it;
4982: int rval = GSL_CONTINUE;
4983: int status = GSL_SUCCESS;
4984: double ssval;
4985: #endif
4986: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4987: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4988: int linei, month, year,iout;
4989: int jj, ll, li, lj, lk, imk;
4990: int numlinepar=0; /* Current linenumber of parameter file */
4991: int itimes;
4992: int NDIM=2;
4993: int vpopbased=0;
4994:
4995: char ca[32], cb[32], cc[32];
4996: /* FILE *fichtm; *//* Html File */
4997: /* FILE *ficgp;*/ /*Gnuplot File */
4998: struct stat info;
4999: double agedeb, agefin,hf;
5000: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5001:
5002: double fret;
5003: double **xi,tmp,delta;
5004:
5005: double dum; /* Dummy variable */
5006: double ***p3mat;
5007: double ***mobaverage;
5008: int *indx;
5009: char line[MAXLINE], linepar[MAXLINE];
5010: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5011: char pathr[MAXLINE], pathimach[MAXLINE];
5012: char **bp, *tok, *val; /* pathtot */
5013: int firstobs=1, lastobs=10;
5014: int sdeb, sfin; /* Status at beginning and end */
5015: int c, h , cpt,l;
5016: int ju,jl, mi;
5017: int i1,j1, jk,aa,bb, stepsize, ij;
5018: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5019: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5020: int mobilav=0,popforecast=0;
5021: int hstepm, nhstepm;
5022: int agemortsup;
5023: float sumlpop=0.;
5024: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5025: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5026:
5027: double bage, fage, age, agelim, agebase;
5028: double ftolpl=FTOL;
5029: double **prlim;
5030: double ***param; /* Matrix of parameters */
5031: double *p;
5032: double **matcov; /* Matrix of covariance */
5033: double ***delti3; /* Scale */
5034: double *delti; /* Scale */
5035: double ***eij, ***vareij;
5036: double **varpl; /* Variances of prevalence limits by age */
5037: double *epj, vepp;
5038: double kk1, kk2;
5039: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5040: double **ximort;
5041: char *alph[]={"a","a","b","c","d","e"}, str[4];
5042: int *dcwave;
5043:
5044: char z[1]="c", occ;
5045:
5046: /*char *strt;*/
5047: char strtend[80];
5048:
5049: long total_usecs;
5050:
5051: /* setlocale (LC_ALL, ""); */
5052: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5053: /* textdomain (PACKAGE); */
5054: /* setlocale (LC_CTYPE, ""); */
5055: /* setlocale (LC_MESSAGES, ""); */
5056:
5057: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5058: (void) gettimeofday(&start_time,&tzp);
5059: curr_time=start_time;
5060: tm = *localtime(&start_time.tv_sec);
5061: tmg = *gmtime(&start_time.tv_sec);
5062: strcpy(strstart,asctime(&tm));
5063:
5064: /* printf("Localtime (at start)=%s",strstart); */
5065: /* tp.tv_sec = tp.tv_sec +86400; */
5066: /* tm = *localtime(&start_time.tv_sec); */
5067: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5068: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5069: /* tmg.tm_hour=tmg.tm_hour + 1; */
5070: /* tp.tv_sec = mktime(&tmg); */
5071: /* strt=asctime(&tmg); */
5072: /* printf("Time(after) =%s",strstart); */
5073: /* (void) time (&time_value);
5074: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5075: * tm = *localtime(&time_value);
5076: * strstart=asctime(&tm);
5077: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5078: */
5079:
5080: nberr=0; /* Number of errors and warnings */
5081: nbwarn=0;
5082: getcwd(pathcd, size);
5083:
5084: printf("\n%s\n%s",version,fullversion);
5085: if(argc <=1){
5086: printf("\nEnter the parameter file name: ");
5087: fgets(pathr,FILENAMELENGTH,stdin);
5088: i=strlen(pathr);
5089: if(pathr[i-1]=='\n')
5090: pathr[i-1]='\0';
5091: for (tok = pathr; tok != NULL; ){
5092: printf("Pathr |%s|\n",pathr);
5093: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5094: printf("val= |%s| pathr=%s\n",val,pathr);
5095: strcpy (pathtot, val);
5096: if(pathr[0] == '\0') break; /* Dirty */
5097: }
5098: }
5099: else{
5100: strcpy(pathtot,argv[1]);
5101: }
5102: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5103: /*cygwin_split_path(pathtot,path,optionfile);
5104: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5105: /* cutv(path,optionfile,pathtot,'\\');*/
5106:
5107: /* Split argv[0], imach program to get pathimach */
5108: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5109: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5110: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5111: /* strcpy(pathimach,argv[0]); */
5112: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5113: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5114: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5115: chdir(path); /* Can be a relative path */
5116: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5117: printf("Current directory %s!\n",pathcd);
5118: strcpy(command,"mkdir ");
5119: strcat(command,optionfilefiname);
5120: if((outcmd=system(command)) != 0){
5121: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5122: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5123: /* fclose(ficlog); */
5124: /* exit(1); */
5125: }
5126: /* if((imk=mkdir(optionfilefiname))<0){ */
5127: /* perror("mkdir"); */
5128: /* } */
5129:
5130: /*-------- arguments in the command line --------*/
5131:
5132: /* Log file */
5133: strcat(filelog, optionfilefiname);
5134: strcat(filelog,".log"); /* */
5135: if((ficlog=fopen(filelog,"w"))==NULL) {
5136: printf("Problem with logfile %s\n",filelog);
5137: goto end;
5138: }
5139: fprintf(ficlog,"Log filename:%s\n",filelog);
5140: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5141: fprintf(ficlog,"\nEnter the parameter file name: \n");
5142: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5143: path=%s \n\
5144: optionfile=%s\n\
5145: optionfilext=%s\n\
5146: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5147:
5148: printf("Local time (at start):%s",strstart);
5149: fprintf(ficlog,"Local time (at start): %s",strstart);
5150: fflush(ficlog);
5151: /* (void) gettimeofday(&curr_time,&tzp); */
5152: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5153:
5154: /* */
5155: strcpy(fileres,"r");
5156: strcat(fileres, optionfilefiname);
5157: strcat(fileres,".txt"); /* Other files have txt extension */
5158:
5159: /*---------arguments file --------*/
5160:
5161: if((ficpar=fopen(optionfile,"r"))==NULL) {
5162: printf("Problem with optionfile %s\n",optionfile);
5163: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5164: fflush(ficlog);
5165: goto end;
5166: }
5167:
5168:
5169:
5170: strcpy(filereso,"o");
5171: strcat(filereso,fileres);
5172: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5173: printf("Problem with Output resultfile: %s\n", filereso);
5174: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5175: fflush(ficlog);
5176: goto end;
5177: }
5178:
5179: /* Reads comments: lines beginning with '#' */
5180: numlinepar=0;
5181: while((c=getc(ficpar))=='#' && c!= EOF){
5182: ungetc(c,ficpar);
5183: fgets(line, MAXLINE, ficpar);
5184: numlinepar++;
5185: fputs(line,stdout);
5186: fputs(line,ficparo);
5187: fputs(line,ficlog);
5188: }
5189: ungetc(c,ficpar);
5190:
5191: 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);
5192: numlinepar++;
5193: 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);
5194: 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);
5195: 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);
5196: fflush(ficlog);
5197: while((c=getc(ficpar))=='#' && c!= EOF){
5198: ungetc(c,ficpar);
5199: fgets(line, MAXLINE, ficpar);
5200: numlinepar++;
5201: fputs(line, stdout);
5202: //puts(line);
5203: fputs(line,ficparo);
5204: fputs(line,ficlog);
5205: }
5206: ungetc(c,ficpar);
5207:
5208:
5209: covar=matrix(0,NCOVMAX,1,n);
5210: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5211: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5212: v1+v2*age+v2*v3 makes cptcovn = 3
5213: */
5214: if (strlen(model)>1)
5215: cptcovn=nbocc(model,'+')+1;
5216: /* ncovprod */
5217: ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5218: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5219: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5220: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5221: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5222: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
5223: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
5224: fflush(stdout);
5225: fclose (ficlog);
5226: goto end;
5227: }
5228: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5229: delti=delti3[1][1];
5230: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5231: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5232: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5233: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5234: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5235: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5236: fclose (ficparo);
5237: fclose (ficlog);
5238: goto end;
5239: exit(0);
5240: }
5241: else if(mle==-3) {
5242: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5243: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5244: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5245: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5246: matcov=matrix(1,npar,1,npar);
5247: }
5248: else{
5249: /* Read guess parameters */
5250: /* Reads comments: lines beginning with '#' */
5251: while((c=getc(ficpar))=='#' && c!= EOF){
5252: ungetc(c,ficpar);
5253: fgets(line, MAXLINE, ficpar);
5254: numlinepar++;
5255: fputs(line,stdout);
5256: fputs(line,ficparo);
5257: fputs(line,ficlog);
5258: }
5259: ungetc(c,ficpar);
5260:
5261: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5262: for(i=1; i <=nlstate; i++){
5263: j=0;
5264: for(jj=1; jj <=nlstate+ndeath; jj++){
5265: if(jj==i) continue;
5266: j++;
5267: fscanf(ficpar,"%1d%1d",&i1,&j1);
5268: if ((i1 != i) && (j1 != j)){
5269: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5270: It might be a problem of design; if ncovcol and the model are correct\n \
5271: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5272: exit(1);
5273: }
5274: fprintf(ficparo,"%1d%1d",i1,j1);
5275: if(mle==1)
5276: printf("%1d%1d",i,j);
5277: fprintf(ficlog,"%1d%1d",i,j);
5278: for(k=1; k<=ncovmodel;k++){
5279: fscanf(ficpar," %lf",¶m[i][j][k]);
5280: if(mle==1){
5281: printf(" %lf",param[i][j][k]);
5282: fprintf(ficlog," %lf",param[i][j][k]);
5283: }
5284: else
5285: fprintf(ficlog," %lf",param[i][j][k]);
5286: fprintf(ficparo," %lf",param[i][j][k]);
5287: }
5288: fscanf(ficpar,"\n");
5289: numlinepar++;
5290: if(mle==1)
5291: printf("\n");
5292: fprintf(ficlog,"\n");
5293: fprintf(ficparo,"\n");
5294: }
5295: }
5296: fflush(ficlog);
5297:
5298: p=param[1][1];
5299:
5300: /* Reads comments: lines beginning with '#' */
5301: while((c=getc(ficpar))=='#' && c!= EOF){
5302: ungetc(c,ficpar);
5303: fgets(line, MAXLINE, ficpar);
5304: numlinepar++;
5305: fputs(line,stdout);
5306: fputs(line,ficparo);
5307: fputs(line,ficlog);
5308: }
5309: ungetc(c,ficpar);
5310:
5311: for(i=1; i <=nlstate; i++){
5312: for(j=1; j <=nlstate+ndeath-1; j++){
5313: fscanf(ficpar,"%1d%1d",&i1,&j1);
5314: if ((i1-i)*(j1-j)!=0){
5315: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5316: exit(1);
5317: }
5318: printf("%1d%1d",i,j);
5319: fprintf(ficparo,"%1d%1d",i1,j1);
5320: fprintf(ficlog,"%1d%1d",i1,j1);
5321: for(k=1; k<=ncovmodel;k++){
5322: fscanf(ficpar,"%le",&delti3[i][j][k]);
5323: printf(" %le",delti3[i][j][k]);
5324: fprintf(ficparo," %le",delti3[i][j][k]);
5325: fprintf(ficlog," %le",delti3[i][j][k]);
5326: }
5327: fscanf(ficpar,"\n");
5328: numlinepar++;
5329: printf("\n");
5330: fprintf(ficparo,"\n");
5331: fprintf(ficlog,"\n");
5332: }
5333: }
5334: fflush(ficlog);
5335:
5336: delti=delti3[1][1];
5337:
5338:
5339: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5340:
5341: /* Reads comments: lines beginning with '#' */
5342: while((c=getc(ficpar))=='#' && c!= EOF){
5343: ungetc(c,ficpar);
5344: fgets(line, MAXLINE, ficpar);
5345: numlinepar++;
5346: fputs(line,stdout);
5347: fputs(line,ficparo);
5348: fputs(line,ficlog);
5349: }
5350: ungetc(c,ficpar);
5351:
5352: matcov=matrix(1,npar,1,npar);
5353: for(i=1; i <=npar; i++)
5354: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5355:
5356: for(i=1; i <=npar; i++){
5357: fscanf(ficpar,"%s",&str);
5358: if(mle==1)
5359: printf("%s",str);
5360: fprintf(ficlog,"%s",str);
5361: fprintf(ficparo,"%s",str);
5362: for(j=1; j <=i; j++){
5363: fscanf(ficpar," %le",&matcov[i][j]);
5364: if(mle==1){
5365: printf(" %.5le",matcov[i][j]);
5366: }
5367: fprintf(ficlog," %.5le",matcov[i][j]);
5368: fprintf(ficparo," %.5le",matcov[i][j]);
5369: }
5370: fscanf(ficpar,"\n");
5371: numlinepar++;
5372: if(mle==1)
5373: printf("\n");
5374: fprintf(ficlog,"\n");
5375: fprintf(ficparo,"\n");
5376: }
5377: for(i=1; i <=npar; i++)
5378: for(j=i+1;j<=npar;j++)
5379: matcov[i][j]=matcov[j][i];
5380:
5381: if(mle==1)
5382: printf("\n");
5383: fprintf(ficlog,"\n");
5384:
5385: fflush(ficlog);
5386:
5387: /*-------- Rewriting parameter file ----------*/
5388: strcpy(rfileres,"r"); /* "Rparameterfile */
5389: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5390: strcat(rfileres,"."); /* */
5391: strcat(rfileres,optionfilext); /* Other files have txt extension */
5392: if((ficres =fopen(rfileres,"w"))==NULL) {
5393: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5394: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5395: }
5396: fprintf(ficres,"#%s\n",version);
5397: } /* End of mle != -3 */
5398:
5399:
5400: n= lastobs;
5401: num=lvector(1,n);
5402: moisnais=vector(1,n);
5403: annais=vector(1,n);
5404: moisdc=vector(1,n);
5405: andc=vector(1,n);
5406: agedc=vector(1,n);
5407: cod=ivector(1,n);
5408: weight=vector(1,n);
5409: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5410: mint=matrix(1,maxwav,1,n);
5411: anint=matrix(1,maxwav,1,n);
5412: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5413: tab=ivector(1,NCOVMAX);
5414: ncodemax=ivector(1,8); /* hard coded ? */
5415:
5416: /* Reads data from file datafile */
5417: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5418: goto end;
5419:
5420: /* Calculation of the number of parameters from char model */
5421: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5422: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5423: k=3 V4 Tvar[k=3]= 4 (from V4)
5424: k=2 V1 Tvar[k=2]= 1 (from V1)
5425: k=1 Tvar[1]=2 (from V2)
5426: */
5427: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5428: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5429: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5430: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5431: */
5432: /* For model-covariate k tells which data-covariate to use but
5433: because this model-covariate is a construction we invent a new column
5434: ncovcol + k1
5435: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5436: Tvar[3=V1*V4]=4+1 etc */
5437: Tprod=ivector(1,15); /* Gives the position of a product */
5438: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5439: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5440: */
5441: Tvaraff=ivector(1,15);
5442: Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
5443: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5444: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5445: Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5446: 4 covariates (3 plus signs)
5447: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5448: */
5449:
5450: if(decodemodel(model, lastobs) == 1)
5451: goto end;
5452:
5453: if((double)(lastobs-imx)/(double)imx > 1.10){
5454: nbwarn++;
5455: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5456: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5457: }
5458: /* if(mle==1){*/
5459: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5460: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5461: }
5462:
5463: /*-calculation of age at interview from date of interview and age at death -*/
5464: agev=matrix(1,maxwav,1,imx);
5465:
5466: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5467: goto end;
5468:
5469:
5470: agegomp=(int)agemin;
5471: free_vector(moisnais,1,n);
5472: free_vector(annais,1,n);
5473: /* free_matrix(mint,1,maxwav,1,n);
5474: free_matrix(anint,1,maxwav,1,n);*/
5475: free_vector(moisdc,1,n);
5476: free_vector(andc,1,n);
5477:
5478:
5479: wav=ivector(1,imx);
5480: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5481: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5482: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5483:
5484: /* Concatenates waves */
5485: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5486:
5487: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5488:
5489: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5490: ncodemax[1]=1;
5491: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5492:
5493: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5494: the estimations*/
5495: h=0;
5496: m=pow(2,cptcoveff);
5497:
5498: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5499: for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5500: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5501: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5502: h++;
5503: if (h>m)
5504: h=1;
5505: codtab[h][k]=j;
5506: codtab[h][Tvar[k]]=j;
5507: 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]]);
5508: }
5509: }
5510: }
5511: }
5512: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5513: codtab[1][2]=1;codtab[2][2]=2; */
5514: /* for(i=1; i <=m ;i++){
5515: for(k=1; k <=cptcovn; k++){
5516: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5517: }
5518: printf("\n");
5519: }
5520: scanf("%d",i);*/
5521:
5522: /*------------ gnuplot -------------*/
5523: strcpy(optionfilegnuplot,optionfilefiname);
5524: if(mle==-3)
5525: strcat(optionfilegnuplot,"-mort");
5526: strcat(optionfilegnuplot,".gp");
5527:
5528: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5529: printf("Problem with file %s",optionfilegnuplot);
5530: }
5531: else{
5532: fprintf(ficgp,"\n# %s\n", version);
5533: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5534: //fprintf(ficgp,"set missing 'NaNq'\n");
5535: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5536: }
5537: /* fclose(ficgp);*/
5538: /*--------- index.htm --------*/
5539:
5540: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5541: if(mle==-3)
5542: strcat(optionfilehtm,"-mort");
5543: strcat(optionfilehtm,".htm");
5544: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5545: printf("Problem with %s \n",optionfilehtm);
5546: exit(0);
5547: }
5548:
5549: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5550: strcat(optionfilehtmcov,"-cov.htm");
5551: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5552: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5553: }
5554: else{
5555: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5556: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5557: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5558: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5559: }
5560:
5561: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5562: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5563: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5564: \n\
5565: <hr size=\"2\" color=\"#EC5E5E\">\
5566: <ul><li><h4>Parameter files</h4>\n\
5567: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5568: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5569: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5570: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5571: - Date and time at start: %s</ul>\n",\
5572: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5573: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5574: fileres,fileres,\
5575: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5576: fflush(fichtm);
5577:
5578: strcpy(pathr,path);
5579: strcat(pathr,optionfilefiname);
5580: chdir(optionfilefiname); /* Move to directory named optionfile */
5581:
5582: /* Calculates basic frequencies. Computes observed prevalence at single age
5583: and prints on file fileres'p'. */
5584: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5585:
5586: fprintf(fichtm,"\n");
5587: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5588: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5589: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5590: imx,agemin,agemax,jmin,jmax,jmean);
5591: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5592: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5593: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5594: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5595: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5596:
5597:
5598: /* For Powell, parameters are in a vector p[] starting at p[1]
5599: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5600: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5601:
5602: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5603:
5604: if (mle==-3){
5605: ximort=matrix(1,NDIM,1,NDIM);
5606: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5607: cens=ivector(1,n);
5608: ageexmed=vector(1,n);
5609: agecens=vector(1,n);
5610: dcwave=ivector(1,n);
5611:
5612: for (i=1; i<=imx; i++){
5613: dcwave[i]=-1;
5614: for (m=firstpass; m<=lastpass; m++)
5615: if (s[m][i]>nlstate) {
5616: dcwave[i]=m;
5617: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5618: break;
5619: }
5620: }
5621:
5622: for (i=1; i<=imx; i++) {
5623: if (wav[i]>0){
5624: ageexmed[i]=agev[mw[1][i]][i];
5625: j=wav[i];
5626: agecens[i]=1.;
5627:
5628: if (ageexmed[i]> 1 && wav[i] > 0){
5629: agecens[i]=agev[mw[j][i]][i];
5630: cens[i]= 1;
5631: }else if (ageexmed[i]< 1)
5632: cens[i]= -1;
5633: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5634: cens[i]=0 ;
5635: }
5636: else cens[i]=-1;
5637: }
5638:
5639: for (i=1;i<=NDIM;i++) {
5640: for (j=1;j<=NDIM;j++)
5641: ximort[i][j]=(i == j ? 1.0 : 0.0);
5642: }
5643:
5644: p[1]=0.0268; p[NDIM]=0.083;
5645: /*printf("%lf %lf", p[1], p[2]);*/
5646:
5647:
5648: #ifdef GSL
5649: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5650: #elsedef
5651: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5652: #endif
5653: strcpy(filerespow,"pow-mort");
5654: strcat(filerespow,fileres);
5655: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5656: printf("Problem with resultfile: %s\n", filerespow);
5657: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5658: }
5659: #ifdef GSL
5660: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5661: #elsedef
5662: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5663: #endif
5664: /* for (i=1;i<=nlstate;i++)
5665: for(j=1;j<=nlstate+ndeath;j++)
5666: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5667: */
5668: fprintf(ficrespow,"\n");
5669: #ifdef GSL
5670: /* gsl starts here */
5671: T = gsl_multimin_fminimizer_nmsimplex;
5672: gsl_multimin_fminimizer *sfm = NULL;
5673: gsl_vector *ss, *x;
5674: gsl_multimin_function minex_func;
5675:
5676: /* Initial vertex size vector */
5677: ss = gsl_vector_alloc (NDIM);
5678:
5679: if (ss == NULL){
5680: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5681: }
5682: /* Set all step sizes to 1 */
5683: gsl_vector_set_all (ss, 0.001);
5684:
5685: /* Starting point */
5686:
5687: x = gsl_vector_alloc (NDIM);
5688:
5689: if (x == NULL){
5690: gsl_vector_free(ss);
5691: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5692: }
5693:
5694: /* Initialize method and iterate */
5695: /* p[1]=0.0268; p[NDIM]=0.083; */
5696: /* gsl_vector_set(x, 0, 0.0268); */
5697: /* gsl_vector_set(x, 1, 0.083); */
5698: gsl_vector_set(x, 0, p[1]);
5699: gsl_vector_set(x, 1, p[2]);
5700:
5701: minex_func.f = &gompertz_f;
5702: minex_func.n = NDIM;
5703: minex_func.params = (void *)&p; /* ??? */
5704:
5705: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5706: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5707:
5708: printf("Iterations beginning .....\n\n");
5709: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5710:
5711: iteri=0;
5712: while (rval == GSL_CONTINUE){
5713: iteri++;
5714: status = gsl_multimin_fminimizer_iterate(sfm);
5715:
5716: if (status) printf("error: %s\n", gsl_strerror (status));
5717: fflush(0);
5718:
5719: if (status)
5720: break;
5721:
5722: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5723: ssval = gsl_multimin_fminimizer_size (sfm);
5724:
5725: if (rval == GSL_SUCCESS)
5726: printf ("converged to a local maximum at\n");
5727:
5728: printf("%5d ", iteri);
5729: for (it = 0; it < NDIM; it++){
5730: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
5731: }
5732: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
5733: }
5734:
5735: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
5736:
5737: gsl_vector_free(x); /* initial values */
5738: gsl_vector_free(ss); /* inital step size */
5739: for (it=0; it<NDIM; it++){
5740: p[it+1]=gsl_vector_get(sfm->x,it);
5741: fprintf(ficrespow," %.12lf", p[it]);
5742: }
5743: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
5744: #endif
5745: #ifdef POWELL
5746: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5747: #endif
5748: fclose(ficrespow);
5749:
5750: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5751:
5752: for(i=1; i <=NDIM; i++)
5753: for(j=i+1;j<=NDIM;j++)
5754: matcov[i][j]=matcov[j][i];
5755:
5756: printf("\nCovariance matrix\n ");
5757: for(i=1; i <=NDIM; i++) {
5758: for(j=1;j<=NDIM;j++){
5759: printf("%f ",matcov[i][j]);
5760: }
5761: printf("\n ");
5762: }
5763:
5764: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5765: for (i=1;i<=NDIM;i++)
5766: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5767:
5768: lsurv=vector(1,AGESUP);
5769: lpop=vector(1,AGESUP);
5770: tpop=vector(1,AGESUP);
5771: lsurv[agegomp]=100000;
5772:
5773: for (k=agegomp;k<=AGESUP;k++) {
5774: agemortsup=k;
5775: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5776: }
5777:
5778: for (k=agegomp;k<agemortsup;k++)
5779: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5780:
5781: for (k=agegomp;k<agemortsup;k++){
5782: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5783: sumlpop=sumlpop+lpop[k];
5784: }
5785:
5786: tpop[agegomp]=sumlpop;
5787: for (k=agegomp;k<(agemortsup-3);k++){
5788: /* tpop[k+1]=2;*/
5789: tpop[k+1]=tpop[k]-lpop[k];
5790: }
5791:
5792:
5793: printf("\nAge lx qx dx Lx Tx e(x)\n");
5794: for (k=agegomp;k<(agemortsup-2);k++)
5795: 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]);
5796:
5797:
5798: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5799: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5800:
5801: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5802: stepm, weightopt,\
5803: model,imx,p,matcov,agemortsup);
5804:
5805: free_vector(lsurv,1,AGESUP);
5806: free_vector(lpop,1,AGESUP);
5807: free_vector(tpop,1,AGESUP);
5808: #ifdef GSL
5809: free_ivector(cens,1,n);
5810: free_vector(agecens,1,n);
5811: free_ivector(dcwave,1,n);
5812: free_matrix(ximort,1,NDIM,1,NDIM);
5813: #endif
5814: } /* Endof if mle==-3 */
5815:
5816: else{ /* For mle >=1 */
5817: globpr=0;/* debug */
5818: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5819: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5820: for (k=1; k<=npar;k++)
5821: printf(" %d %8.5f",k,p[k]);
5822: printf("\n");
5823: globpr=1; /* to print the contributions */
5824: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5825: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5826: for (k=1; k<=npar;k++)
5827: printf(" %d %8.5f",k,p[k]);
5828: printf("\n");
5829: if(mle>=1){ /* Could be 1 or 2 */
5830: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5831: }
5832:
5833: /*--------- results files --------------*/
5834: 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);
5835:
5836:
5837: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5838: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5839: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5840: for(i=1,jk=1; i <=nlstate; i++){
5841: for(k=1; k <=(nlstate+ndeath); k++){
5842: if (k != i) {
5843: printf("%d%d ",i,k);
5844: fprintf(ficlog,"%d%d ",i,k);
5845: fprintf(ficres,"%1d%1d ",i,k);
5846: for(j=1; j <=ncovmodel; j++){
5847: printf("%lf ",p[jk]);
5848: fprintf(ficlog,"%lf ",p[jk]);
5849: fprintf(ficres,"%lf ",p[jk]);
5850: jk++;
5851: }
5852: printf("\n");
5853: fprintf(ficlog,"\n");
5854: fprintf(ficres,"\n");
5855: }
5856: }
5857: }
5858: if(mle!=0){
5859: /* Computing hessian and covariance matrix */
5860: ftolhess=ftol; /* Usually correct */
5861: hesscov(matcov, p, npar, delti, ftolhess, func);
5862: }
5863: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5864: printf("# Scales (for hessian or gradient estimation)\n");
5865: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5866: for(i=1,jk=1; i <=nlstate; i++){
5867: for(j=1; j <=nlstate+ndeath; j++){
5868: if (j!=i) {
5869: fprintf(ficres,"%1d%1d",i,j);
5870: printf("%1d%1d",i,j);
5871: fprintf(ficlog,"%1d%1d",i,j);
5872: for(k=1; k<=ncovmodel;k++){
5873: printf(" %.5e",delti[jk]);
5874: fprintf(ficlog," %.5e",delti[jk]);
5875: fprintf(ficres," %.5e",delti[jk]);
5876: jk++;
5877: }
5878: printf("\n");
5879: fprintf(ficlog,"\n");
5880: fprintf(ficres,"\n");
5881: }
5882: }
5883: }
5884:
5885: 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");
5886: if(mle>=1)
5887: 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");
5888: 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");
5889: /* # 121 Var(a12)\n\ */
5890: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5891: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5892: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5893: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5894: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5895: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5896: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5897:
5898:
5899: /* Just to have a covariance matrix which will be more understandable
5900: even is we still don't want to manage dictionary of variables
5901: */
5902: for(itimes=1;itimes<=2;itimes++){
5903: jj=0;
5904: for(i=1; i <=nlstate; i++){
5905: for(j=1; j <=nlstate+ndeath; j++){
5906: if(j==i) continue;
5907: for(k=1; k<=ncovmodel;k++){
5908: jj++;
5909: ca[0]= k+'a'-1;ca[1]='\0';
5910: if(itimes==1){
5911: if(mle>=1)
5912: printf("#%1d%1d%d",i,j,k);
5913: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5914: fprintf(ficres,"#%1d%1d%d",i,j,k);
5915: }else{
5916: if(mle>=1)
5917: printf("%1d%1d%d",i,j,k);
5918: fprintf(ficlog,"%1d%1d%d",i,j,k);
5919: fprintf(ficres,"%1d%1d%d",i,j,k);
5920: }
5921: ll=0;
5922: for(li=1;li <=nlstate; li++){
5923: for(lj=1;lj <=nlstate+ndeath; lj++){
5924: if(lj==li) continue;
5925: for(lk=1;lk<=ncovmodel;lk++){
5926: ll++;
5927: if(ll<=jj){
5928: cb[0]= lk +'a'-1;cb[1]='\0';
5929: if(ll<jj){
5930: if(itimes==1){
5931: if(mle>=1)
5932: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5933: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5934: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5935: }else{
5936: if(mle>=1)
5937: printf(" %.5e",matcov[jj][ll]);
5938: fprintf(ficlog," %.5e",matcov[jj][ll]);
5939: fprintf(ficres," %.5e",matcov[jj][ll]);
5940: }
5941: }else{
5942: if(itimes==1){
5943: if(mle>=1)
5944: printf(" Var(%s%1d%1d)",ca,i,j);
5945: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5946: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5947: }else{
5948: if(mle>=1)
5949: printf(" %.5e",matcov[jj][ll]);
5950: fprintf(ficlog," %.5e",matcov[jj][ll]);
5951: fprintf(ficres," %.5e",matcov[jj][ll]);
5952: }
5953: }
5954: }
5955: } /* end lk */
5956: } /* end lj */
5957: } /* end li */
5958: if(mle>=1)
5959: printf("\n");
5960: fprintf(ficlog,"\n");
5961: fprintf(ficres,"\n");
5962: numlinepar++;
5963: } /* end k*/
5964: } /*end j */
5965: } /* end i */
5966: } /* end itimes */
5967:
5968: fflush(ficlog);
5969: fflush(ficres);
5970:
5971: while((c=getc(ficpar))=='#' && c!= EOF){
5972: ungetc(c,ficpar);
5973: fgets(line, MAXLINE, ficpar);
5974: fputs(line,stdout);
5975: fputs(line,ficparo);
5976: }
5977: ungetc(c,ficpar);
5978:
5979: estepm=0;
5980: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5981: if (estepm==0 || estepm < stepm) estepm=stepm;
5982: if (fage <= 2) {
5983: bage = ageminpar;
5984: fage = agemaxpar;
5985: }
5986:
5987: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5988: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5989: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5990:
5991: while((c=getc(ficpar))=='#' && c!= EOF){
5992: ungetc(c,ficpar);
5993: fgets(line, MAXLINE, ficpar);
5994: fputs(line,stdout);
5995: fputs(line,ficparo);
5996: }
5997: ungetc(c,ficpar);
5998:
5999: 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);
6000: 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);
6001: 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);
6002: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6003: 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);
6004:
6005: while((c=getc(ficpar))=='#' && c!= EOF){
6006: ungetc(c,ficpar);
6007: fgets(line, MAXLINE, ficpar);
6008: fputs(line,stdout);
6009: fputs(line,ficparo);
6010: }
6011: ungetc(c,ficpar);
6012:
6013:
6014: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6015: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6016:
6017: fscanf(ficpar,"pop_based=%d\n",&popbased);
6018: fprintf(ficparo,"pop_based=%d\n",popbased);
6019: fprintf(ficres,"pop_based=%d\n",popbased);
6020:
6021: while((c=getc(ficpar))=='#' && c!= EOF){
6022: ungetc(c,ficpar);
6023: fgets(line, MAXLINE, ficpar);
6024: fputs(line,stdout);
6025: fputs(line,ficparo);
6026: }
6027: ungetc(c,ficpar);
6028:
6029: 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);
6030: 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);
6031: 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);
6032: 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);
6033: 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);
6034: /* day and month of proj2 are not used but only year anproj2.*/
6035:
6036:
6037:
6038: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
6039: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
6040:
6041: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6042: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6043:
6044: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6045: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6046: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6047:
6048: /*------------ free_vector -------------*/
6049: /* chdir(path); */
6050:
6051: free_ivector(wav,1,imx);
6052: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6053: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6054: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6055: free_lvector(num,1,n);
6056: free_vector(agedc,1,n);
6057: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6058: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6059: fclose(ficparo);
6060: fclose(ficres);
6061:
6062:
6063: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6064:
6065: strcpy(filerespl,"pl");
6066: strcat(filerespl,fileres);
6067: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6068: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6069: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6070: }
6071: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6072: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6073: pstamp(ficrespl);
6074: fprintf(ficrespl,"# Period (stable) prevalence \n");
6075: fprintf(ficrespl,"#Age ");
6076: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6077: fprintf(ficrespl,"\n");
6078:
6079: prlim=matrix(1,nlstate,1,nlstate);
6080:
6081: agebase=ageminpar;
6082: agelim=agemaxpar;
6083: ftolpl=1.e-10;
6084: i1=cptcoveff;
6085: if (cptcovn < 1){i1=1;}
6086:
6087: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6088: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6089: k=k+1;
6090: /* to clean */
6091: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
6092: fprintf(ficrespl,"\n#******");
6093: printf("\n#******");
6094: fprintf(ficlog,"\n#******");
6095: for(j=1;j<=cptcoveff;j++) {
6096: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6097: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6098: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6099: }
6100: fprintf(ficrespl,"******\n");
6101: printf("******\n");
6102: fprintf(ficlog,"******\n");
6103:
6104: for (age=agebase; age<=agelim; age++){
6105: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6106: fprintf(ficrespl,"%.0f ",age );
6107: for(j=1;j<=cptcoveff;j++)
6108: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6109: for(i=1; i<=nlstate;i++)
6110: fprintf(ficrespl," %.5f", prlim[i][i]);
6111: fprintf(ficrespl,"\n");
6112: }
6113: }
6114: }
6115: fclose(ficrespl);
6116:
6117: /*------------- h Pij x at various ages ------------*/
6118:
6119: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6120: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6121: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
6122: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
6123: }
6124: printf("Computing pij: result on file '%s' \n", filerespij);
6125: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6126:
6127: stepsize=(int) (stepm+YEARM-1)/YEARM;
6128: /*if (stepm<=24) stepsize=2;*/
6129:
6130: agelim=AGESUP;
6131: hstepm=stepsize*YEARM; /* Every year of age */
6132: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6133:
6134: /* hstepm=1; aff par mois*/
6135: pstamp(ficrespij);
6136: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6137: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6138: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6139: k=k+1;
6140: fprintf(ficrespij,"\n#****** ");
6141: for(j=1;j<=cptcoveff;j++)
6142: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6143: fprintf(ficrespij,"******\n");
6144:
6145: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6146: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6147: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6148:
6149: /* nhstepm=nhstepm*YEARM; aff par mois*/
6150:
6151: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6152: oldm=oldms;savm=savms;
6153: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6154: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6155: for(i=1; i<=nlstate;i++)
6156: for(j=1; j<=nlstate+ndeath;j++)
6157: fprintf(ficrespij," %1d-%1d",i,j);
6158: fprintf(ficrespij,"\n");
6159: for (h=0; h<=nhstepm; h++){
6160: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
6161: for(i=1; i<=nlstate;i++)
6162: for(j=1; j<=nlstate+ndeath;j++)
6163: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6164: fprintf(ficrespij,"\n");
6165: }
6166: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6167: fprintf(ficrespij,"\n");
6168: }
6169: }
6170: }
6171:
6172: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6173:
6174: fclose(ficrespij);
6175:
6176: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6177: for(i=1;i<=AGESUP;i++)
6178: for(j=1;j<=NCOVMAX;j++)
6179: for(k=1;k<=NCOVMAX;k++)
6180: probs[i][j][k]=0.;
6181:
6182: /*---------- Forecasting ------------------*/
6183: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6184: if(prevfcast==1){
6185: /* if(stepm ==1){*/
6186: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6187: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6188: /* } */
6189: /* else{ */
6190: /* erreur=108; */
6191: /* 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); */
6192: /* 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); */
6193: /* } */
6194: }
6195:
6196:
6197: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6198:
6199: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6200: /* 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",\
6201: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6202: */
6203:
6204: if (mobilav!=0) {
6205: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6206: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6207: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6208: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6209: }
6210: }
6211:
6212:
6213: /*---------- Health expectancies, no variances ------------*/
6214:
6215: strcpy(filerese,"e");
6216: strcat(filerese,fileres);
6217: if((ficreseij=fopen(filerese,"w"))==NULL) {
6218: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6219: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6220: }
6221: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6222: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6223: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6224: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6225: k=k+1;
6226: fprintf(ficreseij,"\n#****** ");
6227: for(j=1;j<=cptcoveff;j++) {
6228: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6229: }
6230: fprintf(ficreseij,"******\n");
6231:
6232: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6233: oldm=oldms;savm=savms;
6234: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6235:
6236: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6237: }
6238: }
6239: fclose(ficreseij);
6240:
6241:
6242: /*---------- Health expectancies and variances ------------*/
6243:
6244:
6245: strcpy(filerest,"t");
6246: strcat(filerest,fileres);
6247: if((ficrest=fopen(filerest,"w"))==NULL) {
6248: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6249: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6250: }
6251: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6252: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6253:
6254:
6255: strcpy(fileresstde,"stde");
6256: strcat(fileresstde,fileres);
6257: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6258: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6259: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6260: }
6261: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6262: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6263:
6264: strcpy(filerescve,"cve");
6265: strcat(filerescve,fileres);
6266: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6267: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6268: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6269: }
6270: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6271: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6272:
6273: strcpy(fileresv,"v");
6274: strcat(fileresv,fileres);
6275: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6276: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6277: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6278: }
6279: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6280: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6281:
6282: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6283: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6284: k=k+1;
6285: fprintf(ficrest,"\n#****** ");
6286: for(j=1;j<=cptcoveff;j++)
6287: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6288: fprintf(ficrest,"******\n");
6289:
6290: fprintf(ficresstdeij,"\n#****** ");
6291: fprintf(ficrescveij,"\n#****** ");
6292: for(j=1;j<=cptcoveff;j++) {
6293: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6294: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6295: }
6296: fprintf(ficresstdeij,"******\n");
6297: fprintf(ficrescveij,"******\n");
6298:
6299: fprintf(ficresvij,"\n#****** ");
6300: for(j=1;j<=cptcoveff;j++)
6301: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6302: fprintf(ficresvij,"******\n");
6303:
6304: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6305: oldm=oldms;savm=savms;
6306: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6307:
6308: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6309: pstamp(ficrest);
6310: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6311: oldm=oldms;savm=savms;
6312: 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 ");
6313: if(vpopbased==1)
6314: 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);
6315: else
6316: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6317: fprintf(ficrest,"# Age e.. (std) ");
6318: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6319: fprintf(ficrest,"\n");
6320:
6321: epj=vector(1,nlstate+1);
6322: for(age=bage; age <=fage ;age++){
6323: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6324: if (vpopbased==1) {
6325: if(mobilav ==0){
6326: for(i=1; i<=nlstate;i++)
6327: prlim[i][i]=probs[(int)age][i][k];
6328: }else{ /* mobilav */
6329: for(i=1; i<=nlstate;i++)
6330: prlim[i][i]=mobaverage[(int)age][i][k];
6331: }
6332: }
6333:
6334: fprintf(ficrest," %4.0f",age);
6335: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6336: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6337: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6338: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6339: }
6340: epj[nlstate+1] +=epj[j];
6341: }
6342:
6343: for(i=1, vepp=0.;i <=nlstate;i++)
6344: for(j=1;j <=nlstate;j++)
6345: vepp += vareij[i][j][(int)age];
6346: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6347: for(j=1;j <=nlstate;j++){
6348: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6349: }
6350: fprintf(ficrest,"\n");
6351: }
6352: }
6353: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6354: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6355: free_vector(epj,1,nlstate+1);
6356: }
6357: }
6358: free_vector(weight,1,n);
6359: free_imatrix(Tvard,1,15,1,2);
6360: free_imatrix(s,1,maxwav+1,1,n);
6361: free_matrix(anint,1,maxwav,1,n);
6362: free_matrix(mint,1,maxwav,1,n);
6363: free_ivector(cod,1,n);
6364: free_ivector(tab,1,NCOVMAX);
6365: fclose(ficresstdeij);
6366: fclose(ficrescveij);
6367: fclose(ficresvij);
6368: fclose(ficrest);
6369: fclose(ficpar);
6370:
6371: /*------- Variance of period (stable) prevalence------*/
6372:
6373: strcpy(fileresvpl,"vpl");
6374: strcat(fileresvpl,fileres);
6375: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6376: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6377: exit(0);
6378: }
6379: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6380:
6381: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6382: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6383: k=k+1;
6384: fprintf(ficresvpl,"\n#****** ");
6385: for(j=1;j<=cptcoveff;j++)
6386: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6387: fprintf(ficresvpl,"******\n");
6388:
6389: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6390: oldm=oldms;savm=savms;
6391: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6392: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6393: }
6394: }
6395:
6396: fclose(ficresvpl);
6397:
6398: /*---------- End : free ----------------*/
6399: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6400: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6401: } /* mle==-3 arrives here for freeing */
6402: endfree:
6403: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6404: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6405: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6406: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6407: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6408: free_matrix(covar,0,NCOVMAX,1,n);
6409: free_matrix(matcov,1,npar,1,npar);
6410: /*free_vector(delti,1,npar);*/
6411: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6412: free_matrix(agev,1,maxwav,1,imx);
6413: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6414:
6415: free_ivector(ncodemax,1,8);
6416: free_ivector(Tvar,1,15);
6417: free_ivector(Tprod,1,15);
6418: free_ivector(Tvaraff,1,15);
6419: free_ivector(Tage,1,15);
6420:
6421: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6422: free_imatrix(codtab,1,100,1,10);
6423: fflush(fichtm);
6424: fflush(ficgp);
6425:
6426:
6427: if((nberr >0) || (nbwarn>0)){
6428: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6429: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6430: }else{
6431: printf("End of Imach\n");
6432: fprintf(ficlog,"End of Imach\n");
6433: }
6434: printf("See log file on %s\n",filelog);
6435: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6436: (void) gettimeofday(&end_time,&tzp);
6437: tm = *localtime(&end_time.tv_sec);
6438: tmg = *gmtime(&end_time.tv_sec);
6439: strcpy(strtend,asctime(&tm));
6440: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6441: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6442: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6443:
6444: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6445: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6446: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6447: /* printf("Total time was %d uSec.\n", total_usecs);*/
6448: /* if(fileappend(fichtm,optionfilehtm)){ */
6449: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6450: fclose(fichtm);
6451: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6452: fclose(fichtmcov);
6453: fclose(ficgp);
6454: fclose(ficlog);
6455: /*------ End -----------*/
6456:
6457:
6458: printf("Before Current directory %s!\n",pathcd);
6459: if(chdir(pathcd) != 0)
6460: printf("Can't move to directory %s!\n",path);
6461: if(getcwd(pathcd,MAXLINE) > 0)
6462: printf("Current directory %s!\n",pathcd);
6463: /*strcat(plotcmd,CHARSEPARATOR);*/
6464: sprintf(plotcmd,"gnuplot");
6465: #ifndef UNIX
6466: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6467: #endif
6468: if(!stat(plotcmd,&info)){
6469: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6470: if(!stat(getenv("GNUPLOTBIN"),&info)){
6471: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6472: }else
6473: strcpy(pplotcmd,plotcmd);
6474: #ifdef UNIX
6475: strcpy(plotcmd,GNUPLOTPROGRAM);
6476: if(!stat(plotcmd,&info)){
6477: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6478: }else
6479: strcpy(pplotcmd,plotcmd);
6480: #endif
6481: }else
6482: strcpy(pplotcmd,plotcmd);
6483:
6484: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6485: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6486:
6487: if((outcmd=system(plotcmd)) != 0){
6488: printf("\n Problem with gnuplot\n");
6489: }
6490: printf(" Wait...");
6491: while (z[0] != 'q') {
6492: /* chdir(path); */
6493: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6494: scanf("%s",z);
6495: /* if (z[0] == 'c') system("./imach"); */
6496: if (z[0] == 'e') {
6497: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6498: system(optionfilehtm);
6499: }
6500: else if (z[0] == 'g') system(plotcmd);
6501: else if (z[0] == 'q') exit(0);
6502: }
6503: end:
6504: while (z[0] != 'q') {
6505: printf("\nType q for exiting: ");
6506: scanf("%s",z);
6507: }
6508: }
6509:
6510:
6511:
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