1: /* $Id: imach.c,v 1.144 2014/02/10 22:17:31 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.144 2014/02/10 22:17:31 brouard
5: *** empty log message ***
6:
7: Revision 1.143 2014/01/26 09:45:38 brouard
8: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
9:
10: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
11: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
12:
13: Revision 1.142 2014/01/26 03:57:36 brouard
14: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
15:
16: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
17:
18: Revision 1.141 2014/01/26 02:42:01 brouard
19: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
20:
21: Revision 1.140 2011/09/02 10:37:54 brouard
22: Summary: times.h is ok with mingw32 now.
23:
24: Revision 1.139 2010/06/14 07:50:17 brouard
25: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
26: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
27:
28: Revision 1.138 2010/04/30 18:19:40 brouard
29: *** empty log message ***
30:
31: Revision 1.137 2010/04/29 18:11:38 brouard
32: (Module): Checking covariates for more complex models
33: than V1+V2. A lot of change to be done. Unstable.
34:
35: Revision 1.136 2010/04/26 20:30:53 brouard
36: (Module): merging some libgsl code. Fixing computation
37: of likelione (using inter/intrapolation if mle = 0) in order to
38: get same likelihood as if mle=1.
39: Some cleaning of code and comments added.
40:
41: Revision 1.135 2009/10/29 15:33:14 brouard
42: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
43:
44: Revision 1.134 2009/10/29 13:18:53 brouard
45: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
46:
47: Revision 1.133 2009/07/06 10:21:25 brouard
48: just nforces
49:
50: Revision 1.132 2009/07/06 08:22:05 brouard
51: Many tings
52:
53: Revision 1.131 2009/06/20 16:22:47 brouard
54: Some dimensions resccaled
55:
56: Revision 1.130 2009/05/26 06:44:34 brouard
57: (Module): Max Covariate is now set to 20 instead of 8. A
58: lot of cleaning with variables initialized to 0. Trying to make
59: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
60:
61: Revision 1.129 2007/08/31 13:49:27 lievre
62: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
63:
64: Revision 1.128 2006/06/30 13:02:05 brouard
65: (Module): Clarifications on computing e.j
66:
67: Revision 1.127 2006/04/28 18:11:50 brouard
68: (Module): Yes the sum of survivors was wrong since
69: imach-114 because nhstepm was no more computed in the age
70: loop. Now we define nhstepma in the age loop.
71: (Module): In order to speed up (in case of numerous covariates) we
72: compute health expectancies (without variances) in a first step
73: and then all the health expectancies with variances or standard
74: deviation (needs data from the Hessian matrices) which slows the
75: computation.
76: In the future we should be able to stop the program is only health
77: expectancies and graph are needed without standard deviations.
78:
79: Revision 1.126 2006/04/28 17:23:28 brouard
80: (Module): Yes the sum of survivors was wrong since
81: imach-114 because nhstepm was no more computed in the age
82: loop. Now we define nhstepma in the age loop.
83: Version 0.98h
84:
85: Revision 1.125 2006/04/04 15:20:31 lievre
86: Errors in calculation of health expectancies. Age was not initialized.
87: Forecasting file added.
88:
89: Revision 1.124 2006/03/22 17:13:53 lievre
90: Parameters are printed with %lf instead of %f (more numbers after the comma).
91: The log-likelihood is printed in the log file
92:
93: Revision 1.123 2006/03/20 10:52:43 brouard
94: * imach.c (Module): <title> changed, corresponds to .htm file
95: name. <head> headers where missing.
96:
97: * imach.c (Module): Weights can have a decimal point as for
98: English (a comma might work with a correct LC_NUMERIC environment,
99: otherwise the weight is truncated).
100: Modification of warning when the covariates values are not 0 or
101: 1.
102: Version 0.98g
103:
104: Revision 1.122 2006/03/20 09:45:41 brouard
105: (Module): Weights can have a decimal point as for
106: English (a comma might work with a correct LC_NUMERIC environment,
107: otherwise the weight is truncated).
108: Modification of warning when the covariates values are not 0 or
109: 1.
110: Version 0.98g
111:
112: Revision 1.121 2006/03/16 17:45:01 lievre
113: * imach.c (Module): Comments concerning covariates added
114:
115: * imach.c (Module): refinements in the computation of lli if
116: status=-2 in order to have more reliable computation if stepm is
117: not 1 month. Version 0.98f
118:
119: Revision 1.120 2006/03/16 15:10:38 lievre
120: (Module): refinements in the computation of lli if
121: status=-2 in order to have more reliable computation if stepm is
122: not 1 month. Version 0.98f
123:
124: Revision 1.119 2006/03/15 17:42:26 brouard
125: (Module): Bug if status = -2, the loglikelihood was
126: computed as likelihood omitting the logarithm. Version O.98e
127:
128: Revision 1.118 2006/03/14 18:20:07 brouard
129: (Module): varevsij Comments added explaining the second
130: table of variances if popbased=1 .
131: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
132: (Module): Function pstamp added
133: (Module): Version 0.98d
134:
135: Revision 1.117 2006/03/14 17:16:22 brouard
136: (Module): varevsij Comments added explaining the second
137: table of variances if popbased=1 .
138: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
139: (Module): Function pstamp added
140: (Module): Version 0.98d
141:
142: Revision 1.116 2006/03/06 10:29:27 brouard
143: (Module): Variance-covariance wrong links and
144: varian-covariance of ej. is needed (Saito).
145:
146: Revision 1.115 2006/02/27 12:17:45 brouard
147: (Module): One freematrix added in mlikeli! 0.98c
148:
149: Revision 1.114 2006/02/26 12:57:58 brouard
150: (Module): Some improvements in processing parameter
151: filename with strsep.
152:
153: Revision 1.113 2006/02/24 14:20:24 brouard
154: (Module): Memory leaks checks with valgrind and:
155: datafile was not closed, some imatrix were not freed and on matrix
156: allocation too.
157:
158: Revision 1.112 2006/01/30 09:55:26 brouard
159: (Module): Back to gnuplot.exe instead of wgnuplot.exe
160:
161: Revision 1.111 2006/01/25 20:38:18 brouard
162: (Module): Lots of cleaning and bugs added (Gompertz)
163: (Module): Comments can be added in data file. Missing date values
164: can be a simple dot '.'.
165:
166: Revision 1.110 2006/01/25 00:51:50 brouard
167: (Module): Lots of cleaning and bugs added (Gompertz)
168:
169: Revision 1.109 2006/01/24 19:37:15 brouard
170: (Module): Comments (lines starting with a #) are allowed in data.
171:
172: Revision 1.108 2006/01/19 18:05:42 lievre
173: Gnuplot problem appeared...
174: To be fixed
175:
176: Revision 1.107 2006/01/19 16:20:37 brouard
177: Test existence of gnuplot in imach path
178:
179: Revision 1.106 2006/01/19 13:24:36 brouard
180: Some cleaning and links added in html output
181:
182: Revision 1.105 2006/01/05 20:23:19 lievre
183: *** empty log message ***
184:
185: Revision 1.104 2005/09/30 16:11:43 lievre
186: (Module): sump fixed, loop imx fixed, and simplifications.
187: (Module): If the status is missing at the last wave but we know
188: that the person is alive, then we can code his/her status as -2
189: (instead of missing=-1 in earlier versions) and his/her
190: contributions to the likelihood is 1 - Prob of dying from last
191: health status (= 1-p13= p11+p12 in the easiest case of somebody in
192: the healthy state at last known wave). Version is 0.98
193:
194: Revision 1.103 2005/09/30 15:54:49 lievre
195: (Module): sump fixed, loop imx fixed, and simplifications.
196:
197: Revision 1.102 2004/09/15 17:31:30 brouard
198: Add the possibility to read data file including tab characters.
199:
200: Revision 1.101 2004/09/15 10:38:38 brouard
201: Fix on curr_time
202:
203: Revision 1.100 2004/07/12 18:29:06 brouard
204: Add version for Mac OS X. Just define UNIX in Makefile
205:
206: Revision 1.99 2004/06/05 08:57:40 brouard
207: *** empty log message ***
208:
209: Revision 1.98 2004/05/16 15:05:56 brouard
210: New version 0.97 . First attempt to estimate force of mortality
211: directly from the data i.e. without the need of knowing the health
212: state at each age, but using a Gompertz model: log u =a + b*age .
213: This is the basic analysis of mortality and should be done before any
214: other analysis, in order to test if the mortality estimated from the
215: cross-longitudinal survey is different from the mortality estimated
216: from other sources like vital statistic data.
217:
218: The same imach parameter file can be used but the option for mle should be -3.
219:
220: Agnès, who wrote this part of the code, tried to keep most of the
221: former routines in order to include the new code within the former code.
222:
223: The output is very simple: only an estimate of the intercept and of
224: the slope with 95% confident intervals.
225:
226: Current limitations:
227: A) Even if you enter covariates, i.e. with the
228: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
229: B) There is no computation of Life Expectancy nor Life Table.
230:
231: Revision 1.97 2004/02/20 13:25:42 lievre
232: Version 0.96d. Population forecasting command line is (temporarily)
233: suppressed.
234:
235: Revision 1.96 2003/07/15 15:38:55 brouard
236: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
237: rewritten within the same printf. Workaround: many printfs.
238:
239: Revision 1.95 2003/07/08 07:54:34 brouard
240: * imach.c (Repository):
241: (Repository): Using imachwizard code to output a more meaningful covariance
242: matrix (cov(a12,c31) instead of numbers.
243:
244: Revision 1.94 2003/06/27 13:00:02 brouard
245: Just cleaning
246:
247: Revision 1.93 2003/06/25 16:33:55 brouard
248: (Module): On windows (cygwin) function asctime_r doesn't
249: exist so I changed back to asctime which exists.
250: (Module): Version 0.96b
251:
252: Revision 1.92 2003/06/25 16:30:45 brouard
253: (Module): On windows (cygwin) function asctime_r doesn't
254: exist so I changed back to asctime which exists.
255:
256: Revision 1.91 2003/06/25 15:30:29 brouard
257: * imach.c (Repository): Duplicated warning errors corrected.
258: (Repository): Elapsed time after each iteration is now output. It
259: helps to forecast when convergence will be reached. Elapsed time
260: is stamped in powell. We created a new html file for the graphs
261: concerning matrix of covariance. It has extension -cov.htm.
262:
263: Revision 1.90 2003/06/24 12:34:15 brouard
264: (Module): Some bugs corrected for windows. Also, when
265: mle=-1 a template is output in file "or"mypar.txt with the design
266: of the covariance matrix to be input.
267:
268: Revision 1.89 2003/06/24 12:30:52 brouard
269: (Module): Some bugs corrected for windows. Also, when
270: mle=-1 a template is output in file "or"mypar.txt with the design
271: of the covariance matrix to be input.
272:
273: Revision 1.88 2003/06/23 17:54:56 brouard
274: * 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.
275:
276: Revision 1.87 2003/06/18 12:26:01 brouard
277: Version 0.96
278:
279: Revision 1.86 2003/06/17 20:04:08 brouard
280: (Module): Change position of html and gnuplot routines and added
281: routine fileappend.
282:
283: Revision 1.85 2003/06/17 13:12:43 brouard
284: * imach.c (Repository): Check when date of death was earlier that
285: current date of interview. It may happen when the death was just
286: prior to the death. In this case, dh was negative and likelihood
287: was wrong (infinity). We still send an "Error" but patch by
288: assuming that the date of death was just one stepm after the
289: interview.
290: (Repository): Because some people have very long ID (first column)
291: we changed int to long in num[] and we added a new lvector for
292: memory allocation. But we also truncated to 8 characters (left
293: truncation)
294: (Repository): No more line truncation errors.
295:
296: Revision 1.84 2003/06/13 21:44:43 brouard
297: * imach.c (Repository): Replace "freqsummary" at a correct
298: place. It differs from routine "prevalence" which may be called
299: many times. Probs is memory consuming and must be used with
300: parcimony.
301: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
302:
303: Revision 1.83 2003/06/10 13:39:11 lievre
304: *** empty log message ***
305:
306: Revision 1.82 2003/06/05 15:57:20 brouard
307: Add log in imach.c and fullversion number is now printed.
308:
309: */
310: /*
311: Interpolated Markov Chain
312:
313: Short summary of the programme:
314:
315: This program computes Healthy Life Expectancies from
316: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
317: first survey ("cross") where individuals from different ages are
318: interviewed on their health status or degree of disability (in the
319: case of a health survey which is our main interest) -2- at least a
320: second wave of interviews ("longitudinal") which measure each change
321: (if any) in individual health status. Health expectancies are
322: computed from the time spent in each health state according to a
323: model. More health states you consider, more time is necessary to reach the
324: Maximum Likelihood of the parameters involved in the model. The
325: simplest model is the multinomial logistic model where pij is the
326: probability to be observed in state j at the second wave
327: conditional to be observed in state i at the first wave. Therefore
328: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
329: 'age' is age and 'sex' is a covariate. If you want to have a more
330: complex model than "constant and age", you should modify the program
331: where the markup *Covariates have to be included here again* invites
332: you to do it. More covariates you add, slower the
333: convergence.
334:
335: The advantage of this computer programme, compared to a simple
336: multinomial logistic model, is clear when the delay between waves is not
337: identical for each individual. Also, if a individual missed an
338: intermediate interview, the information is lost, but taken into
339: account using an interpolation or extrapolation.
340:
341: hPijx is the probability to be observed in state i at age x+h
342: conditional to the observed state i at age x. The delay 'h' can be
343: split into an exact number (nh*stepm) of unobserved intermediate
344: states. This elementary transition (by month, quarter,
345: semester or year) is modelled as a multinomial logistic. The hPx
346: matrix is simply the matrix product of nh*stepm elementary matrices
347: and the contribution of each individual to the likelihood is simply
348: hPijx.
349:
350: Also this programme outputs the covariance matrix of the parameters but also
351: of the life expectancies. It also computes the period (stable) prevalence.
352:
353: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
354: Institut national d'études démographiques, Paris.
355: This software have been partly granted by Euro-REVES, a concerted action
356: from the European Union.
357: It is copyrighted identically to a GNU software product, ie programme and
358: software can be distributed freely for non commercial use. Latest version
359: can be accessed at http://euroreves.ined.fr/imach .
360:
361: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
362: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
363:
364: **********************************************************************/
365: /*
366: main
367: read parameterfile
368: read datafile
369: concatwav
370: freqsummary
371: if (mle >= 1)
372: mlikeli
373: print results files
374: if mle==1
375: computes hessian
376: read end of parameter file: agemin, agemax, bage, fage, estepm
377: begin-prev-date,...
378: open gnuplot file
379: open html file
380: period (stable) prevalence
381: for age prevalim()
382: h Pij x
383: variance of p varprob
384: forecasting if prevfcast==1 prevforecast call prevalence()
385: health expectancies
386: Variance-covariance of DFLE
387: prevalence()
388: movingaverage()
389: varevsij()
390: if popbased==1 varevsij(,popbased)
391: total life expectancies
392: Variance of period (stable) prevalence
393: end
394: */
395:
396:
397:
398:
399: #include <math.h>
400: #include <stdio.h>
401: #include <stdlib.h>
402: #include <string.h>
403: #include <unistd.h>
404:
405: #include <limits.h>
406: #include <sys/types.h>
407: #include <sys/stat.h>
408: #include <errno.h>
409: extern int errno;
410:
411: #ifdef LINUX
412: #include <time.h>
413: #include "timeval.h"
414: #else
415: #include <sys/time.h>
416: #endif
417:
418: #ifdef GSL
419: #include <gsl/gsl_errno.h>
420: #include <gsl/gsl_multimin.h>
421: #endif
422:
423: /* #include <libintl.h> */
424: /* #define _(String) gettext (String) */
425:
426: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
427:
428: #define GNUPLOTPROGRAM "gnuplot"
429: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
430: #define FILENAMELENGTH 132
431:
432: #define GLOCK_ERROR_NOPATH -1 /* empty path */
433: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
434:
435: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
436: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
437:
438: #define NINTERVMAX 8
439: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
440: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
441: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
442: #define MAXN 20000
443: #define YEARM 12. /**< Number of months per year */
444: #define AGESUP 130
445: #define AGEBASE 40
446: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
447: #ifdef UNIX
448: #define DIRSEPARATOR '/'
449: #define CHARSEPARATOR "/"
450: #define ODIRSEPARATOR '\\'
451: #else
452: #define DIRSEPARATOR '\\'
453: #define CHARSEPARATOR "\\"
454: #define ODIRSEPARATOR '/'
455: #endif
456:
457: /* $Id: imach.c,v 1.144 2014/02/10 22:17:31 brouard Exp $ */
458: /* $State: Exp $ */
459:
460: char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
461: char fullversion[]="$Revision: 1.144 $ $Date: 2014/02/10 22:17:31 $";
462: char strstart[80];
463: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
464: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
465: int nvar=0, nforce=0; /* Number of variables, number of forces */
466: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
467: int npar=NPARMAX;
468: int nlstate=2; /* Number of live states */
469: int ndeath=1; /* Number of dead states */
470: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
471: int popbased=0;
472:
473: int *wav; /* Number of waves for this individuual 0 is possible */
474: int maxwav=0; /* Maxim number of waves */
475: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
476: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
477: int gipmx=0, gsw=0; /* Global variables on the number of contributions
478: to the likelihood and the sum of weights (done by funcone)*/
479: int mle=1, weightopt=0;
480: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
481: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
482: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
483: * wave mi and wave mi+1 is not an exact multiple of stepm. */
484: double jmean=1; /* Mean space between 2 waves */
485: double **oldm, **newm, **savm; /* Working pointers to matrices */
486: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
487: /*FILE *fic ; */ /* Used in readdata only */
488: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
489: FILE *ficlog, *ficrespow;
490: int globpr=0; /* Global variable for printing or not */
491: double fretone; /* Only one call to likelihood */
492: long ipmx=0; /* Number of contributions */
493: double sw; /* Sum of weights */
494: char filerespow[FILENAMELENGTH];
495: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
496: FILE *ficresilk;
497: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
498: FILE *ficresprobmorprev;
499: FILE *fichtm, *fichtmcov; /* Html File */
500: FILE *ficreseij;
501: char filerese[FILENAMELENGTH];
502: FILE *ficresstdeij;
503: char fileresstde[FILENAMELENGTH];
504: FILE *ficrescveij;
505: char filerescve[FILENAMELENGTH];
506: FILE *ficresvij;
507: char fileresv[FILENAMELENGTH];
508: FILE *ficresvpl;
509: char fileresvpl[FILENAMELENGTH];
510: char title[MAXLINE];
511: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
512: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
513: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
514: char command[FILENAMELENGTH];
515: int outcmd=0;
516:
517: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
518:
519: char filelog[FILENAMELENGTH]; /* Log file */
520: char filerest[FILENAMELENGTH];
521: char fileregp[FILENAMELENGTH];
522: char popfile[FILENAMELENGTH];
523:
524: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
525:
526: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
527: struct timezone tzp;
528: extern int gettimeofday();
529: struct tm tmg, tm, tmf, *gmtime(), *localtime();
530: long time_value;
531: extern long time();
532: char strcurr[80], strfor[80];
533:
534: char *endptr;
535: long lval;
536: double dval;
537:
538: #define NR_END 1
539: #define FREE_ARG char*
540: #define FTOL 1.0e-10
541:
542: #define NRANSI
543: #define ITMAX 200
544:
545: #define TOL 2.0e-4
546:
547: #define CGOLD 0.3819660
548: #define ZEPS 1.0e-10
549: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
550:
551: #define GOLD 1.618034
552: #define GLIMIT 100.0
553: #define TINY 1.0e-20
554:
555: static double maxarg1,maxarg2;
556: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
557: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
558:
559: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
560: #define rint(a) floor(a+0.5)
561:
562: static double sqrarg;
563: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
564: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
565: int agegomp= AGEGOMP;
566:
567: int imx;
568: int stepm=1;
569: /* Stepm, step in month: minimum step interpolation*/
570:
571: int estepm;
572: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
573:
574: int m,nb;
575: long *num;
576: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
577: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
578: double **pmmij, ***probs;
579: double *ageexmed,*agecens;
580: double dateintmean=0;
581:
582: double *weight;
583: int **s; /* Status */
584: double *agedc;
585: double **covar; /**< covar[i,j], value of jth covariate for individual i,
586: * covar=matrix(0,NCOVMAX,1,n);
587: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
588: double idx;
589: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
590: int **codtab; /**< codtab=imatrix(1,100,1,10); */
591: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
592: double *lsurv, *lpop, *tpop;
593:
594: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
595: double ftolhess; /**< Tolerance for computing hessian */
596:
597: /**************** split *************************/
598: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
599: {
600: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
601: the name of the file (name), its extension only (ext) and its first part of the name (finame)
602: */
603: char *ss; /* pointer */
604: int l1, l2; /* length counters */
605:
606: l1 = strlen(path ); /* length of path */
607: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
608: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
609: if ( ss == NULL ) { /* no directory, so determine current directory */
610: strcpy( name, path ); /* we got the fullname name because no directory */
611: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
612: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
613: /* get current working directory */
614: /* extern char* getcwd ( char *buf , int len);*/
615: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
616: return( GLOCK_ERROR_GETCWD );
617: }
618: /* got dirc from getcwd*/
619: printf(" DIRC = %s \n",dirc);
620: } else { /* strip direcotry from path */
621: ss++; /* after this, the filename */
622: l2 = strlen( ss ); /* length of filename */
623: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
624: strcpy( name, ss ); /* save file name */
625: strncpy( dirc, path, l1 - l2 ); /* now the directory */
626: dirc[l1-l2] = 0; /* add zero */
627: printf(" DIRC2 = %s \n",dirc);
628: }
629: /* We add a separator at the end of dirc if not exists */
630: l1 = strlen( dirc ); /* length of directory */
631: if( dirc[l1-1] != DIRSEPARATOR ){
632: dirc[l1] = DIRSEPARATOR;
633: dirc[l1+1] = 0;
634: printf(" DIRC3 = %s \n",dirc);
635: }
636: ss = strrchr( name, '.' ); /* find last / */
637: if (ss >0){
638: ss++;
639: strcpy(ext,ss); /* save extension */
640: l1= strlen( name);
641: l2= strlen(ss)+1;
642: strncpy( finame, name, l1-l2);
643: finame[l1-l2]= 0;
644: }
645:
646: return( 0 ); /* we're done */
647: }
648:
649:
650: /******************************************/
651:
652: void replace_back_to_slash(char *s, char*t)
653: {
654: int i;
655: int lg=0;
656: i=0;
657: lg=strlen(t);
658: for(i=0; i<= lg; i++) {
659: (s[i] = t[i]);
660: if (t[i]== '\\') s[i]='/';
661: }
662: }
663:
664: char *trimbb(char *out, char *in)
665: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
666: char *s;
667: s=out;
668: while (*in != '\0'){
669: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
670: in++;
671: }
672: *out++ = *in++;
673: }
674: *out='\0';
675: return s;
676: }
677:
678: char *cutv(char *blocc, char *alocc, char *in, char occ)
679: {
680: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
681: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
682: gives blocc="abcdef2ghi" and alocc="j".
683: If occ is not found blocc is null and alocc is equal to in. Returns alocc
684: */
685: char *s, *t;
686: t=in;s=in;
687: while (*in != '\0'){
688: while( *in == occ){
689: *blocc++ = *in++;
690: s=in;
691: }
692: *blocc++ = *in++;
693: }
694: if (s == t) /* occ not found */
695: *(blocc-(in-s))='\0';
696: else
697: *(blocc-(in-s)-1)='\0';
698: in=s;
699: while ( *in != '\0'){
700: *alocc++ = *in++;
701: }
702:
703: *alocc='\0';
704: return s;
705: }
706:
707: int nbocc(char *s, char occ)
708: {
709: int i,j=0;
710: int lg=20;
711: i=0;
712: lg=strlen(s);
713: for(i=0; i<= lg; i++) {
714: if (s[i] == occ ) j++;
715: }
716: return j;
717: }
718:
719: /* void cutv(char *u,char *v, char*t, char occ) */
720: /* { */
721: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
722: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
723: /* gives u="abcdef2ghi" and v="j" *\/ */
724: /* int i,lg,j,p=0; */
725: /* i=0; */
726: /* lg=strlen(t); */
727: /* for(j=0; j<=lg-1; j++) { */
728: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
729: /* } */
730:
731: /* for(j=0; j<p; j++) { */
732: /* (u[j] = t[j]); */
733: /* } */
734: /* u[p]='\0'; */
735:
736: /* for(j=0; j<= lg; j++) { */
737: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
738: /* } */
739: /* } */
740:
741: /********************** nrerror ********************/
742:
743: void nrerror(char error_text[])
744: {
745: fprintf(stderr,"ERREUR ...\n");
746: fprintf(stderr,"%s\n",error_text);
747: exit(EXIT_FAILURE);
748: }
749: /*********************** vector *******************/
750: double *vector(int nl, int nh)
751: {
752: double *v;
753: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
754: if (!v) nrerror("allocation failure in vector");
755: return v-nl+NR_END;
756: }
757:
758: /************************ free vector ******************/
759: void free_vector(double*v, int nl, int nh)
760: {
761: free((FREE_ARG)(v+nl-NR_END));
762: }
763:
764: /************************ivector *******************************/
765: int *ivector(long nl,long nh)
766: {
767: int *v;
768: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
769: if (!v) nrerror("allocation failure in ivector");
770: return v-nl+NR_END;
771: }
772:
773: /******************free ivector **************************/
774: void free_ivector(int *v, long nl, long nh)
775: {
776: free((FREE_ARG)(v+nl-NR_END));
777: }
778:
779: /************************lvector *******************************/
780: long *lvector(long nl,long nh)
781: {
782: long *v;
783: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
784: if (!v) nrerror("allocation failure in ivector");
785: return v-nl+NR_END;
786: }
787:
788: /******************free lvector **************************/
789: void free_lvector(long *v, long nl, long nh)
790: {
791: free((FREE_ARG)(v+nl-NR_END));
792: }
793:
794: /******************* imatrix *******************************/
795: int **imatrix(long nrl, long nrh, long ncl, long nch)
796: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
797: {
798: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
799: int **m;
800:
801: /* allocate pointers to rows */
802: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
803: if (!m) nrerror("allocation failure 1 in matrix()");
804: m += NR_END;
805: m -= nrl;
806:
807:
808: /* allocate rows and set pointers to them */
809: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
810: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
811: m[nrl] += NR_END;
812: m[nrl] -= ncl;
813:
814: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
815:
816: /* return pointer to array of pointers to rows */
817: return m;
818: }
819:
820: /****************** free_imatrix *************************/
821: void free_imatrix(m,nrl,nrh,ncl,nch)
822: int **m;
823: long nch,ncl,nrh,nrl;
824: /* free an int matrix allocated by imatrix() */
825: {
826: free((FREE_ARG) (m[nrl]+ncl-NR_END));
827: free((FREE_ARG) (m+nrl-NR_END));
828: }
829:
830: /******************* matrix *******************************/
831: double **matrix(long nrl, long nrh, long ncl, long nch)
832: {
833: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
834: double **m;
835:
836: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
837: if (!m) nrerror("allocation failure 1 in matrix()");
838: m += NR_END;
839: m -= nrl;
840:
841: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
842: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
843: m[nrl] += NR_END;
844: m[nrl] -= ncl;
845:
846: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
847: return m;
848: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
849: */
850: }
851:
852: /*************************free matrix ************************/
853: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
854: {
855: free((FREE_ARG)(m[nrl]+ncl-NR_END));
856: free((FREE_ARG)(m+nrl-NR_END));
857: }
858:
859: /******************* ma3x *******************************/
860: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
861: {
862: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
863: double ***m;
864:
865: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
866: if (!m) nrerror("allocation failure 1 in matrix()");
867: m += NR_END;
868: m -= nrl;
869:
870: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
871: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
872: m[nrl] += NR_END;
873: m[nrl] -= ncl;
874:
875: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
876:
877: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
878: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
879: m[nrl][ncl] += NR_END;
880: m[nrl][ncl] -= nll;
881: for (j=ncl+1; j<=nch; j++)
882: m[nrl][j]=m[nrl][j-1]+nlay;
883:
884: for (i=nrl+1; i<=nrh; i++) {
885: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
886: for (j=ncl+1; j<=nch; j++)
887: m[i][j]=m[i][j-1]+nlay;
888: }
889: return m;
890: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
891: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
892: */
893: }
894:
895: /*************************free ma3x ************************/
896: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
897: {
898: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
899: free((FREE_ARG)(m[nrl]+ncl-NR_END));
900: free((FREE_ARG)(m+nrl-NR_END));
901: }
902:
903: /*************** function subdirf ***********/
904: char *subdirf(char fileres[])
905: {
906: /* Caution optionfilefiname is hidden */
907: strcpy(tmpout,optionfilefiname);
908: strcat(tmpout,"/"); /* Add to the right */
909: strcat(tmpout,fileres);
910: return tmpout;
911: }
912:
913: /*************** function subdirf2 ***********/
914: char *subdirf2(char fileres[], char *preop)
915: {
916:
917: /* Caution optionfilefiname is hidden */
918: strcpy(tmpout,optionfilefiname);
919: strcat(tmpout,"/");
920: strcat(tmpout,preop);
921: strcat(tmpout,fileres);
922: return tmpout;
923: }
924:
925: /*************** function subdirf3 ***********/
926: char *subdirf3(char fileres[], char *preop, char *preop2)
927: {
928:
929: /* Caution optionfilefiname is hidden */
930: strcpy(tmpout,optionfilefiname);
931: strcat(tmpout,"/");
932: strcat(tmpout,preop);
933: strcat(tmpout,preop2);
934: strcat(tmpout,fileres);
935: return tmpout;
936: }
937:
938: /***************** f1dim *************************/
939: extern int ncom;
940: extern double *pcom,*xicom;
941: extern double (*nrfunc)(double []);
942:
943: double f1dim(double x)
944: {
945: int j;
946: double f;
947: double *xt;
948:
949: xt=vector(1,ncom);
950: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
951: f=(*nrfunc)(xt);
952: free_vector(xt,1,ncom);
953: return f;
954: }
955:
956: /*****************brent *************************/
957: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
958: {
959: int iter;
960: double a,b,d,etemp;
961: double fu,fv,fw,fx;
962: double ftemp;
963: double p,q,r,tol1,tol2,u,v,w,x,xm;
964: double e=0.0;
965:
966: a=(ax < cx ? ax : cx);
967: b=(ax > cx ? ax : cx);
968: x=w=v=bx;
969: fw=fv=fx=(*f)(x);
970: for (iter=1;iter<=ITMAX;iter++) {
971: xm=0.5*(a+b);
972: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
973: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
974: printf(".");fflush(stdout);
975: fprintf(ficlog,".");fflush(ficlog);
976: #ifdef DEBUG
977: 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);
978: 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);
979: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
980: #endif
981: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
982: *xmin=x;
983: return fx;
984: }
985: ftemp=fu;
986: if (fabs(e) > tol1) {
987: r=(x-w)*(fx-fv);
988: q=(x-v)*(fx-fw);
989: p=(x-v)*q-(x-w)*r;
990: q=2.0*(q-r);
991: if (q > 0.0) p = -p;
992: q=fabs(q);
993: etemp=e;
994: e=d;
995: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
996: d=CGOLD*(e=(x >= xm ? a-x : b-x));
997: else {
998: d=p/q;
999: u=x+d;
1000: if (u-a < tol2 || b-u < tol2)
1001: d=SIGN(tol1,xm-x);
1002: }
1003: } else {
1004: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1005: }
1006: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1007: fu=(*f)(u);
1008: if (fu <= fx) {
1009: if (u >= x) a=x; else b=x;
1010: SHFT(v,w,x,u)
1011: SHFT(fv,fw,fx,fu)
1012: } else {
1013: if (u < x) a=u; else b=u;
1014: if (fu <= fw || w == x) {
1015: v=w;
1016: w=u;
1017: fv=fw;
1018: fw=fu;
1019: } else if (fu <= fv || v == x || v == w) {
1020: v=u;
1021: fv=fu;
1022: }
1023: }
1024: }
1025: nrerror("Too many iterations in brent");
1026: *xmin=x;
1027: return fx;
1028: }
1029:
1030: /****************** mnbrak ***********************/
1031:
1032: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1033: double (*func)(double))
1034: {
1035: double ulim,u,r,q, dum;
1036: double fu;
1037:
1038: *fa=(*func)(*ax);
1039: *fb=(*func)(*bx);
1040: if (*fb > *fa) {
1041: SHFT(dum,*ax,*bx,dum)
1042: SHFT(dum,*fb,*fa,dum)
1043: }
1044: *cx=(*bx)+GOLD*(*bx-*ax);
1045: *fc=(*func)(*cx);
1046: while (*fb > *fc) {
1047: r=(*bx-*ax)*(*fb-*fc);
1048: q=(*bx-*cx)*(*fb-*fa);
1049: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1050: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1051: ulim=(*bx)+GLIMIT*(*cx-*bx);
1052: if ((*bx-u)*(u-*cx) > 0.0) {
1053: fu=(*func)(u);
1054: } else if ((*cx-u)*(u-ulim) > 0.0) {
1055: fu=(*func)(u);
1056: if (fu < *fc) {
1057: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1058: SHFT(*fb,*fc,fu,(*func)(u))
1059: }
1060: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1061: u=ulim;
1062: fu=(*func)(u);
1063: } else {
1064: u=(*cx)+GOLD*(*cx-*bx);
1065: fu=(*func)(u);
1066: }
1067: SHFT(*ax,*bx,*cx,u)
1068: SHFT(*fa,*fb,*fc,fu)
1069: }
1070: }
1071:
1072: /*************** linmin ************************/
1073:
1074: int ncom;
1075: double *pcom,*xicom;
1076: double (*nrfunc)(double []);
1077:
1078: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1079: {
1080: double brent(double ax, double bx, double cx,
1081: double (*f)(double), double tol, double *xmin);
1082: double f1dim(double x);
1083: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1084: double *fc, double (*func)(double));
1085: int j;
1086: double xx,xmin,bx,ax;
1087: double fx,fb,fa;
1088:
1089: ncom=n;
1090: pcom=vector(1,n);
1091: xicom=vector(1,n);
1092: nrfunc=func;
1093: for (j=1;j<=n;j++) {
1094: pcom[j]=p[j];
1095: xicom[j]=xi[j];
1096: }
1097: ax=0.0;
1098: xx=1.0;
1099: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1100: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1101: #ifdef DEBUG
1102: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1103: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1104: #endif
1105: for (j=1;j<=n;j++) {
1106: xi[j] *= xmin;
1107: p[j] += xi[j];
1108: }
1109: free_vector(xicom,1,n);
1110: free_vector(pcom,1,n);
1111: }
1112:
1113: char *asc_diff_time(long time_sec, char ascdiff[])
1114: {
1115: long sec_left, days, hours, minutes;
1116: days = (time_sec) / (60*60*24);
1117: sec_left = (time_sec) % (60*60*24);
1118: hours = (sec_left) / (60*60) ;
1119: sec_left = (sec_left) %(60*60);
1120: minutes = (sec_left) /60;
1121: sec_left = (sec_left) % (60);
1122: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1123: return ascdiff;
1124: }
1125:
1126: /*************** powell ************************/
1127: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1128: double (*func)(double []))
1129: {
1130: void linmin(double p[], double xi[], int n, double *fret,
1131: double (*func)(double []));
1132: int i,ibig,j;
1133: double del,t,*pt,*ptt,*xit;
1134: double fp,fptt;
1135: double *xits;
1136: int niterf, itmp;
1137:
1138: pt=vector(1,n);
1139: ptt=vector(1,n);
1140: xit=vector(1,n);
1141: xits=vector(1,n);
1142: *fret=(*func)(p);
1143: for (j=1;j<=n;j++) pt[j]=p[j];
1144: for (*iter=1;;++(*iter)) {
1145: fp=(*fret);
1146: ibig=0;
1147: del=0.0;
1148: last_time=curr_time;
1149: (void) gettimeofday(&curr_time,&tzp);
1150: 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);
1151: 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);
1152: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1153: for (i=1;i<=n;i++) {
1154: printf(" %d %.12f",i, p[i]);
1155: fprintf(ficlog," %d %.12lf",i, p[i]);
1156: fprintf(ficrespow," %.12lf", p[i]);
1157: }
1158: printf("\n");
1159: fprintf(ficlog,"\n");
1160: fprintf(ficrespow,"\n");fflush(ficrespow);
1161: if(*iter <=3){
1162: tm = *localtime(&curr_time.tv_sec);
1163: strcpy(strcurr,asctime(&tm));
1164: /* asctime_r(&tm,strcurr); */
1165: forecast_time=curr_time;
1166: itmp = strlen(strcurr);
1167: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1168: strcurr[itmp-1]='\0';
1169: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1170: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1171: for(niterf=10;niterf<=30;niterf+=10){
1172: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1173: tmf = *localtime(&forecast_time.tv_sec);
1174: /* asctime_r(&tmf,strfor); */
1175: strcpy(strfor,asctime(&tmf));
1176: itmp = strlen(strfor);
1177: if(strfor[itmp-1]=='\n')
1178: strfor[itmp-1]='\0';
1179: 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);
1180: 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);
1181: }
1182: }
1183: for (i=1;i<=n;i++) {
1184: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1185: fptt=(*fret);
1186: #ifdef DEBUG
1187: printf("fret=%lf \n",*fret);
1188: fprintf(ficlog,"fret=%lf \n",*fret);
1189: #endif
1190: printf("%d",i);fflush(stdout);
1191: fprintf(ficlog,"%d",i);fflush(ficlog);
1192: linmin(p,xit,n,fret,func);
1193: if (fabs(fptt-(*fret)) > del) {
1194: del=fabs(fptt-(*fret));
1195: ibig=i;
1196: }
1197: #ifdef DEBUG
1198: printf("%d %.12e",i,(*fret));
1199: fprintf(ficlog,"%d %.12e",i,(*fret));
1200: for (j=1;j<=n;j++) {
1201: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1202: printf(" x(%d)=%.12e",j,xit[j]);
1203: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1204: }
1205: for(j=1;j<=n;j++) {
1206: printf(" p=%.12e",p[j]);
1207: fprintf(ficlog," p=%.12e",p[j]);
1208: }
1209: printf("\n");
1210: fprintf(ficlog,"\n");
1211: #endif
1212: }
1213: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1214: #ifdef DEBUG
1215: int k[2],l;
1216: k[0]=1;
1217: k[1]=-1;
1218: printf("Max: %.12e",(*func)(p));
1219: fprintf(ficlog,"Max: %.12e",(*func)(p));
1220: for (j=1;j<=n;j++) {
1221: printf(" %.12e",p[j]);
1222: fprintf(ficlog," %.12e",p[j]);
1223: }
1224: printf("\n");
1225: fprintf(ficlog,"\n");
1226: for(l=0;l<=1;l++) {
1227: for (j=1;j<=n;j++) {
1228: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1229: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1230: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1231: }
1232: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1233: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1234: }
1235: #endif
1236:
1237:
1238: free_vector(xit,1,n);
1239: free_vector(xits,1,n);
1240: free_vector(ptt,1,n);
1241: free_vector(pt,1,n);
1242: return;
1243: }
1244: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1245: for (j=1;j<=n;j++) {
1246: ptt[j]=2.0*p[j]-pt[j];
1247: xit[j]=p[j]-pt[j];
1248: pt[j]=p[j];
1249: }
1250: fptt=(*func)(ptt);
1251: if (fptt < fp) {
1252: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1253: if (t < 0.0) {
1254: linmin(p,xit,n,fret,func);
1255: for (j=1;j<=n;j++) {
1256: xi[j][ibig]=xi[j][n];
1257: xi[j][n]=xit[j];
1258: }
1259: #ifdef DEBUG
1260: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1261: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1262: for(j=1;j<=n;j++){
1263: printf(" %.12e",xit[j]);
1264: fprintf(ficlog," %.12e",xit[j]);
1265: }
1266: printf("\n");
1267: fprintf(ficlog,"\n");
1268: #endif
1269: }
1270: }
1271: }
1272: }
1273:
1274: /**** Prevalence limit (stable or period prevalence) ****************/
1275:
1276: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1277: {
1278: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1279: matrix by transitions matrix until convergence is reached */
1280:
1281: int i, ii,j,k;
1282: double min, max, maxmin, maxmax,sumnew=0.;
1283: double **matprod2();
1284: double **out, cov[NCOVMAX+1], **pmij();
1285: double **newm;
1286: double agefin, delaymax=50 ; /* Max number of years to converge */
1287:
1288: for (ii=1;ii<=nlstate+ndeath;ii++)
1289: for (j=1;j<=nlstate+ndeath;j++){
1290: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1291: }
1292:
1293: cov[1]=1.;
1294:
1295: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1296: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1297: newm=savm;
1298: /* Covariates have to be included here again */
1299: cov[2]=agefin;
1300:
1301: for (k=1; k<=cptcovn;k++) {
1302: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1303: /* 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]]);*/
1304: }
1305: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1306: for (k=1; k<=cptcovprod;k++)
1307: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1308:
1309: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1310: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1311: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1312: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1313:
1314: savm=oldm;
1315: oldm=newm;
1316: maxmax=0.;
1317: for(j=1;j<=nlstate;j++){
1318: min=1.;
1319: max=0.;
1320: for(i=1; i<=nlstate; i++) {
1321: sumnew=0;
1322: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1323: prlim[i][j]= newm[i][j]/(1-sumnew);
1324: max=FMAX(max,prlim[i][j]);
1325: min=FMIN(min,prlim[i][j]);
1326: }
1327: maxmin=max-min;
1328: maxmax=FMAX(maxmax,maxmin);
1329: }
1330: if(maxmax < ftolpl){
1331: return prlim;
1332: }
1333: }
1334: }
1335:
1336: /*************** transition probabilities ***************/
1337:
1338: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1339: {
1340: /* According to parameters values stored in x and the covariate's values stored in cov,
1341: computes the probability to be observed in state j being in state i by appying the
1342: model to the ncovmodel covariates (including constant and age).
1343: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1344: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1345: ncth covariate in the global vector x is given by the formula:
1346: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1347: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1348: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1349: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1350: Outputs ps[i][j] the probability to be observed in j being in j according to
1351: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1352: */
1353: double s1, lnpijopii;
1354: /*double t34;*/
1355: int i,j,j1, nc, ii, jj;
1356:
1357: for(i=1; i<= nlstate; i++){
1358: for(j=1; j<i;j++){
1359: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1360: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1361: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1362: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1363: }
1364: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1365: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1366: }
1367: for(j=i+1; j<=nlstate+ndeath;j++){
1368: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1369: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1370: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1371: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1372: }
1373: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1374: }
1375: }
1376:
1377: for(i=1; i<= nlstate; i++){
1378: s1=0;
1379: for(j=1; j<i; j++){
1380: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1381: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1382: }
1383: for(j=i+1; j<=nlstate+ndeath; j++){
1384: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1385: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1386: }
1387: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1388: ps[i][i]=1./(s1+1.);
1389: /* Computing other pijs */
1390: for(j=1; j<i; j++)
1391: ps[i][j]= exp(ps[i][j])*ps[i][i];
1392: for(j=i+1; j<=nlstate+ndeath; j++)
1393: ps[i][j]= exp(ps[i][j])*ps[i][i];
1394: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1395: } /* end i */
1396:
1397: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1398: for(jj=1; jj<= nlstate+ndeath; jj++){
1399: ps[ii][jj]=0;
1400: ps[ii][ii]=1;
1401: }
1402: }
1403:
1404:
1405: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1406: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1407: /* printf("ddd %lf ",ps[ii][jj]); */
1408: /* } */
1409: /* printf("\n "); */
1410: /* } */
1411: /* printf("\n ");printf("%lf ",cov[2]); */
1412: /*
1413: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1414: goto end;*/
1415: return ps;
1416: }
1417:
1418: /**************** Product of 2 matrices ******************/
1419:
1420: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1421: {
1422: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1423: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1424: /* in, b, out are matrice of pointers which should have been initialized
1425: before: only the contents of out is modified. The function returns
1426: a pointer to pointers identical to out */
1427: long i, j, k;
1428: for(i=nrl; i<= nrh; i++)
1429: for(k=ncolol; k<=ncoloh; k++)
1430: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1431: out[i][k] +=in[i][j]*b[j][k];
1432:
1433: return out;
1434: }
1435:
1436:
1437: /************* Higher Matrix Product ***************/
1438:
1439: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1440: {
1441: /* Computes the transition matrix starting at age 'age' over
1442: 'nhstepm*hstepm*stepm' months (i.e. until
1443: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1444: nhstepm*hstepm matrices.
1445: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1446: (typically every 2 years instead of every month which is too big
1447: for the memory).
1448: Model is determined by parameters x and covariates have to be
1449: included manually here.
1450:
1451: */
1452:
1453: int i, j, d, h, k;
1454: double **out, cov[NCOVMAX+1];
1455: double **newm;
1456:
1457: /* Hstepm could be zero and should return the unit matrix */
1458: for (i=1;i<=nlstate+ndeath;i++)
1459: for (j=1;j<=nlstate+ndeath;j++){
1460: oldm[i][j]=(i==j ? 1.0 : 0.0);
1461: po[i][j][0]=(i==j ? 1.0 : 0.0);
1462: }
1463: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1464: for(h=1; h <=nhstepm; h++){
1465: for(d=1; d <=hstepm; d++){
1466: newm=savm;
1467: /* Covariates have to be included here again */
1468: cov[1]=1.;
1469: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1470: for (k=1; k<=cptcovn;k++)
1471: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1472: for (k=1; k<=cptcovage;k++)
1473: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1474: for (k=1; k<=cptcovprod;k++)
1475: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1476:
1477:
1478: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1479: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1480: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1481: pmij(pmmij,cov,ncovmodel,x,nlstate));
1482: savm=oldm;
1483: oldm=newm;
1484: }
1485: for(i=1; i<=nlstate+ndeath; i++)
1486: for(j=1;j<=nlstate+ndeath;j++) {
1487: po[i][j][h]=newm[i][j];
1488: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1489: }
1490: /*printf("h=%d ",h);*/
1491: } /* end h */
1492: /* printf("\n H=%d \n",h); */
1493: return po;
1494: }
1495:
1496:
1497: /*************** log-likelihood *************/
1498: double func( double *x)
1499: {
1500: int i, ii, j, k, mi, d, kk;
1501: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1502: double **out;
1503: double sw; /* Sum of weights */
1504: double lli; /* Individual log likelihood */
1505: int s1, s2;
1506: double bbh, survp;
1507: long ipmx;
1508: /*extern weight */
1509: /* We are differentiating ll according to initial status */
1510: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1511: /*for(i=1;i<imx;i++)
1512: printf(" %d\n",s[4][i]);
1513: */
1514: cov[1]=1.;
1515:
1516: for(k=1; k<=nlstate; k++) ll[k]=0.;
1517:
1518: if(mle==1){
1519: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1520: /* Computes the values of the ncovmodel covariates of the model
1521: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1522: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1523: to be observed in j being in i according to the model.
1524: */
1525: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1526: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1527: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1528: has been calculated etc */
1529: for(mi=1; mi<= wav[i]-1; mi++){
1530: for (ii=1;ii<=nlstate+ndeath;ii++)
1531: for (j=1;j<=nlstate+ndeath;j++){
1532: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1533: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1534: }
1535: for(d=0; d<dh[mi][i]; d++){
1536: newm=savm;
1537: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1538: for (kk=1; kk<=cptcovage;kk++) {
1539: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1540: }
1541: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1542: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1543: savm=oldm;
1544: oldm=newm;
1545: } /* end mult */
1546:
1547: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1548: /* But now since version 0.9 we anticipate for bias at large stepm.
1549: * If stepm is larger than one month (smallest stepm) and if the exact delay
1550: * (in months) between two waves is not a multiple of stepm, we rounded to
1551: * the nearest (and in case of equal distance, to the lowest) interval but now
1552: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1553: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1554: * probability in order to take into account the bias as a fraction of the way
1555: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1556: * -stepm/2 to stepm/2 .
1557: * For stepm=1 the results are the same as for previous versions of Imach.
1558: * For stepm > 1 the results are less biased than in previous versions.
1559: */
1560: s1=s[mw[mi][i]][i];
1561: s2=s[mw[mi+1][i]][i];
1562: bbh=(double)bh[mi][i]/(double)stepm;
1563: /* bias bh is positive if real duration
1564: * is higher than the multiple of stepm and negative otherwise.
1565: */
1566: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1567: if( s2 > nlstate){
1568: /* i.e. if s2 is a death state and if the date of death is known
1569: then the contribution to the likelihood is the probability to
1570: die between last step unit time and current step unit time,
1571: which is also equal to probability to die before dh
1572: minus probability to die before dh-stepm .
1573: In version up to 0.92 likelihood was computed
1574: as if date of death was unknown. Death was treated as any other
1575: health state: the date of the interview describes the actual state
1576: and not the date of a change in health state. The former idea was
1577: to consider that at each interview the state was recorded
1578: (healthy, disable or death) and IMaCh was corrected; but when we
1579: introduced the exact date of death then we should have modified
1580: the contribution of an exact death to the likelihood. This new
1581: contribution is smaller and very dependent of the step unit
1582: stepm. It is no more the probability to die between last interview
1583: and month of death but the probability to survive from last
1584: interview up to one month before death multiplied by the
1585: probability to die within a month. Thanks to Chris
1586: Jackson for correcting this bug. Former versions increased
1587: mortality artificially. The bad side is that we add another loop
1588: which slows down the processing. The difference can be up to 10%
1589: lower mortality.
1590: */
1591: lli=log(out[s1][s2] - savm[s1][s2]);
1592:
1593:
1594: } else if (s2==-2) {
1595: for (j=1,survp=0. ; j<=nlstate; j++)
1596: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1597: /*survp += out[s1][j]; */
1598: lli= log(survp);
1599: }
1600:
1601: else if (s2==-4) {
1602: for (j=3,survp=0. ; j<=nlstate; j++)
1603: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1604: lli= log(survp);
1605: }
1606:
1607: else if (s2==-5) {
1608: for (j=1,survp=0. ; j<=2; j++)
1609: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1610: lli= log(survp);
1611: }
1612:
1613: else{
1614: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1615: /* 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 */
1616: }
1617: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1618: /*if(lli ==000.0)*/
1619: /*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); */
1620: ipmx +=1;
1621: sw += weight[i];
1622: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1623: } /* end of wave */
1624: } /* end of individual */
1625: } else if(mle==2){
1626: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1627: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1628: for(mi=1; mi<= wav[i]-1; mi++){
1629: for (ii=1;ii<=nlstate+ndeath;ii++)
1630: for (j=1;j<=nlstate+ndeath;j++){
1631: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1632: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1633: }
1634: for(d=0; d<=dh[mi][i]; d++){
1635: newm=savm;
1636: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1637: for (kk=1; kk<=cptcovage;kk++) {
1638: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1639: }
1640: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1641: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1642: savm=oldm;
1643: oldm=newm;
1644: } /* end mult */
1645:
1646: s1=s[mw[mi][i]][i];
1647: s2=s[mw[mi+1][i]][i];
1648: bbh=(double)bh[mi][i]/(double)stepm;
1649: 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 */
1650: ipmx +=1;
1651: sw += weight[i];
1652: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1653: } /* end of wave */
1654: } /* end of individual */
1655: } else if(mle==3){ /* exponential inter-extrapolation */
1656: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1657: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1658: for(mi=1; mi<= wav[i]-1; mi++){
1659: for (ii=1;ii<=nlstate+ndeath;ii++)
1660: for (j=1;j<=nlstate+ndeath;j++){
1661: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1662: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1663: }
1664: for(d=0; d<dh[mi][i]; d++){
1665: newm=savm;
1666: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1667: for (kk=1; kk<=cptcovage;kk++) {
1668: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1669: }
1670: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1671: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1672: savm=oldm;
1673: oldm=newm;
1674: } /* end mult */
1675:
1676: s1=s[mw[mi][i]][i];
1677: s2=s[mw[mi+1][i]][i];
1678: bbh=(double)bh[mi][i]/(double)stepm;
1679: 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 */
1680: ipmx +=1;
1681: sw += weight[i];
1682: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1683: } /* end of wave */
1684: } /* end of individual */
1685: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1686: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1687: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1688: for(mi=1; mi<= wav[i]-1; mi++){
1689: for (ii=1;ii<=nlstate+ndeath;ii++)
1690: for (j=1;j<=nlstate+ndeath;j++){
1691: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1692: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1693: }
1694: for(d=0; d<dh[mi][i]; d++){
1695: newm=savm;
1696: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1697: for (kk=1; kk<=cptcovage;kk++) {
1698: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1699: }
1700:
1701: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1702: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1703: savm=oldm;
1704: oldm=newm;
1705: } /* end mult */
1706:
1707: s1=s[mw[mi][i]][i];
1708: s2=s[mw[mi+1][i]][i];
1709: if( s2 > nlstate){
1710: lli=log(out[s1][s2] - savm[s1][s2]);
1711: }else{
1712: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1713: }
1714: ipmx +=1;
1715: sw += weight[i];
1716: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1717: /* 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]); */
1718: } /* end of wave */
1719: } /* end of individual */
1720: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1721: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1722: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1723: for(mi=1; mi<= wav[i]-1; mi++){
1724: for (ii=1;ii<=nlstate+ndeath;ii++)
1725: for (j=1;j<=nlstate+ndeath;j++){
1726: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1727: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1728: }
1729: for(d=0; d<dh[mi][i]; d++){
1730: newm=savm;
1731: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1732: for (kk=1; kk<=cptcovage;kk++) {
1733: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1734: }
1735:
1736: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1737: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1738: savm=oldm;
1739: oldm=newm;
1740: } /* end mult */
1741:
1742: s1=s[mw[mi][i]][i];
1743: s2=s[mw[mi+1][i]][i];
1744: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1745: ipmx +=1;
1746: sw += weight[i];
1747: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1748: /*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]);*/
1749: } /* end of wave */
1750: } /* end of individual */
1751: } /* End of if */
1752: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1753: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1754: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1755: return -l;
1756: }
1757:
1758: /*************** log-likelihood *************/
1759: double funcone( double *x)
1760: {
1761: /* Same as likeli but slower because of a lot of printf and if */
1762: int i, ii, j, k, mi, d, kk;
1763: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1764: double **out;
1765: double lli; /* Individual log likelihood */
1766: double llt;
1767: int s1, s2;
1768: double bbh, survp;
1769: /*extern weight */
1770: /* We are differentiating ll according to initial status */
1771: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1772: /*for(i=1;i<imx;i++)
1773: printf(" %d\n",s[4][i]);
1774: */
1775: cov[1]=1.;
1776:
1777: for(k=1; k<=nlstate; k++) ll[k]=0.;
1778:
1779: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1780: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1781: for(mi=1; mi<= wav[i]-1; mi++){
1782: for (ii=1;ii<=nlstate+ndeath;ii++)
1783: for (j=1;j<=nlstate+ndeath;j++){
1784: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1785: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1786: }
1787: for(d=0; d<dh[mi][i]; d++){
1788: newm=savm;
1789: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1790: for (kk=1; kk<=cptcovage;kk++) {
1791: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1792: }
1793: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1794: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1795: savm=oldm;
1796: oldm=newm;
1797: } /* end mult */
1798:
1799: s1=s[mw[mi][i]][i];
1800: s2=s[mw[mi+1][i]][i];
1801: bbh=(double)bh[mi][i]/(double)stepm;
1802: /* bias is positive if real duration
1803: * is higher than the multiple of stepm and negative otherwise.
1804: */
1805: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1806: lli=log(out[s1][s2] - savm[s1][s2]);
1807: } else if (s2==-2) {
1808: for (j=1,survp=0. ; j<=nlstate; j++)
1809: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1810: lli= log(survp);
1811: }else if (mle==1){
1812: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1813: } else if(mle==2){
1814: 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 */
1815: } else if(mle==3){ /* exponential inter-extrapolation */
1816: 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 */
1817: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1818: lli=log(out[s1][s2]); /* Original formula */
1819: } else{ /* mle=0 back to 1 */
1820: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1821: /*lli=log(out[s1][s2]); */ /* Original formula */
1822: } /* End of if */
1823: ipmx +=1;
1824: sw += weight[i];
1825: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1826: /*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]); */
1827: if(globpr){
1828: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1829: %11.6f %11.6f %11.6f ", \
1830: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1831: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1832: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1833: llt +=ll[k]*gipmx/gsw;
1834: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1835: }
1836: fprintf(ficresilk," %10.6f\n", -llt);
1837: }
1838: } /* end of wave */
1839: } /* end of individual */
1840: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1841: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1842: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1843: if(globpr==0){ /* First time we count the contributions and weights */
1844: gipmx=ipmx;
1845: gsw=sw;
1846: }
1847: return -l;
1848: }
1849:
1850:
1851: /*************** function likelione ***********/
1852: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1853: {
1854: /* This routine should help understanding what is done with
1855: the selection of individuals/waves and
1856: to check the exact contribution to the likelihood.
1857: Plotting could be done.
1858: */
1859: int k;
1860:
1861: if(*globpri !=0){ /* Just counts and sums, no printings */
1862: strcpy(fileresilk,"ilk");
1863: strcat(fileresilk,fileres);
1864: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1865: printf("Problem with resultfile: %s\n", fileresilk);
1866: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1867: }
1868: 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");
1869: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1870: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1871: for(k=1; k<=nlstate; k++)
1872: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1873: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1874: }
1875:
1876: *fretone=(*funcone)(p);
1877: if(*globpri !=0){
1878: fclose(ficresilk);
1879: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1880: fflush(fichtm);
1881: }
1882: return;
1883: }
1884:
1885:
1886: /*********** Maximum Likelihood Estimation ***************/
1887:
1888: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1889: {
1890: int i,j, iter;
1891: double **xi;
1892: double fret;
1893: double fretone; /* Only one call to likelihood */
1894: /* char filerespow[FILENAMELENGTH];*/
1895: xi=matrix(1,npar,1,npar);
1896: for (i=1;i<=npar;i++)
1897: for (j=1;j<=npar;j++)
1898: xi[i][j]=(i==j ? 1.0 : 0.0);
1899: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1900: strcpy(filerespow,"pow");
1901: strcat(filerespow,fileres);
1902: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1903: printf("Problem with resultfile: %s\n", filerespow);
1904: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1905: }
1906: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1907: for (i=1;i<=nlstate;i++)
1908: for(j=1;j<=nlstate+ndeath;j++)
1909: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1910: fprintf(ficrespow,"\n");
1911:
1912: powell(p,xi,npar,ftol,&iter,&fret,func);
1913:
1914: free_matrix(xi,1,npar,1,npar);
1915: fclose(ficrespow);
1916: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1917: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1918: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1919:
1920: }
1921:
1922: /**** Computes Hessian and covariance matrix ***/
1923: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1924: {
1925: double **a,**y,*x,pd;
1926: double **hess;
1927: int i, j,jk;
1928: int *indx;
1929:
1930: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1931: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1932: void lubksb(double **a, int npar, int *indx, double b[]) ;
1933: void ludcmp(double **a, int npar, int *indx, double *d) ;
1934: double gompertz(double p[]);
1935: hess=matrix(1,npar,1,npar);
1936:
1937: printf("\nCalculation of the hessian matrix. Wait...\n");
1938: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1939: for (i=1;i<=npar;i++){
1940: printf("%d",i);fflush(stdout);
1941: fprintf(ficlog,"%d",i);fflush(ficlog);
1942:
1943: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1944:
1945: /* printf(" %f ",p[i]);
1946: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1947: }
1948:
1949: for (i=1;i<=npar;i++) {
1950: for (j=1;j<=npar;j++) {
1951: if (j>i) {
1952: printf(".%d%d",i,j);fflush(stdout);
1953: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1954: hess[i][j]=hessij(p,delti,i,j,func,npar);
1955:
1956: hess[j][i]=hess[i][j];
1957: /*printf(" %lf ",hess[i][j]);*/
1958: }
1959: }
1960: }
1961: printf("\n");
1962: fprintf(ficlog,"\n");
1963:
1964: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1965: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1966:
1967: a=matrix(1,npar,1,npar);
1968: y=matrix(1,npar,1,npar);
1969: x=vector(1,npar);
1970: indx=ivector(1,npar);
1971: for (i=1;i<=npar;i++)
1972: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1973: ludcmp(a,npar,indx,&pd);
1974:
1975: for (j=1;j<=npar;j++) {
1976: for (i=1;i<=npar;i++) x[i]=0;
1977: x[j]=1;
1978: lubksb(a,npar,indx,x);
1979: for (i=1;i<=npar;i++){
1980: matcov[i][j]=x[i];
1981: }
1982: }
1983:
1984: printf("\n#Hessian matrix#\n");
1985: fprintf(ficlog,"\n#Hessian matrix#\n");
1986: for (i=1;i<=npar;i++) {
1987: for (j=1;j<=npar;j++) {
1988: printf("%.3e ",hess[i][j]);
1989: fprintf(ficlog,"%.3e ",hess[i][j]);
1990: }
1991: printf("\n");
1992: fprintf(ficlog,"\n");
1993: }
1994:
1995: /* Recompute Inverse */
1996: for (i=1;i<=npar;i++)
1997: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1998: ludcmp(a,npar,indx,&pd);
1999:
2000: /* printf("\n#Hessian matrix recomputed#\n");
2001:
2002: for (j=1;j<=npar;j++) {
2003: for (i=1;i<=npar;i++) x[i]=0;
2004: x[j]=1;
2005: lubksb(a,npar,indx,x);
2006: for (i=1;i<=npar;i++){
2007: y[i][j]=x[i];
2008: printf("%.3e ",y[i][j]);
2009: fprintf(ficlog,"%.3e ",y[i][j]);
2010: }
2011: printf("\n");
2012: fprintf(ficlog,"\n");
2013: }
2014: */
2015:
2016: free_matrix(a,1,npar,1,npar);
2017: free_matrix(y,1,npar,1,npar);
2018: free_vector(x,1,npar);
2019: free_ivector(indx,1,npar);
2020: free_matrix(hess,1,npar,1,npar);
2021:
2022:
2023: }
2024:
2025: /*************** hessian matrix ****************/
2026: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2027: {
2028: int i;
2029: int l=1, lmax=20;
2030: double k1,k2;
2031: double p2[MAXPARM+1]; /* identical to x */
2032: double res;
2033: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2034: double fx;
2035: int k=0,kmax=10;
2036: double l1;
2037:
2038: fx=func(x);
2039: for (i=1;i<=npar;i++) p2[i]=x[i];
2040: for(l=0 ; l <=lmax; l++){
2041: l1=pow(10,l);
2042: delts=delt;
2043: for(k=1 ; k <kmax; k=k+1){
2044: delt = delta*(l1*k);
2045: p2[theta]=x[theta] +delt;
2046: k1=func(p2)-fx;
2047: p2[theta]=x[theta]-delt;
2048: k2=func(p2)-fx;
2049: /*res= (k1-2.0*fx+k2)/delt/delt; */
2050: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2051:
2052: #ifdef DEBUGHESS
2053: 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);
2054: 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);
2055: #endif
2056: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2057: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2058: k=kmax;
2059: }
2060: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2061: k=kmax; l=lmax*10.;
2062: }
2063: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2064: delts=delt;
2065: }
2066: }
2067: }
2068: delti[theta]=delts;
2069: return res;
2070:
2071: }
2072:
2073: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2074: {
2075: int i;
2076: int l=1, l1, lmax=20;
2077: double k1,k2,k3,k4,res,fx;
2078: double p2[MAXPARM+1];
2079: int k;
2080:
2081: fx=func(x);
2082: for (k=1; k<=2; k++) {
2083: for (i=1;i<=npar;i++) p2[i]=x[i];
2084: p2[thetai]=x[thetai]+delti[thetai]/k;
2085: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2086: k1=func(p2)-fx;
2087:
2088: p2[thetai]=x[thetai]+delti[thetai]/k;
2089: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2090: k2=func(p2)-fx;
2091:
2092: p2[thetai]=x[thetai]-delti[thetai]/k;
2093: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2094: k3=func(p2)-fx;
2095:
2096: p2[thetai]=x[thetai]-delti[thetai]/k;
2097: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2098: k4=func(p2)-fx;
2099: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2100: #ifdef DEBUG
2101: 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);
2102: 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);
2103: #endif
2104: }
2105: return res;
2106: }
2107:
2108: /************** Inverse of matrix **************/
2109: void ludcmp(double **a, int n, int *indx, double *d)
2110: {
2111: int i,imax,j,k;
2112: double big,dum,sum,temp;
2113: double *vv;
2114:
2115: vv=vector(1,n);
2116: *d=1.0;
2117: for (i=1;i<=n;i++) {
2118: big=0.0;
2119: for (j=1;j<=n;j++)
2120: if ((temp=fabs(a[i][j])) > big) big=temp;
2121: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2122: vv[i]=1.0/big;
2123: }
2124: for (j=1;j<=n;j++) {
2125: for (i=1;i<j;i++) {
2126: sum=a[i][j];
2127: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2128: a[i][j]=sum;
2129: }
2130: big=0.0;
2131: for (i=j;i<=n;i++) {
2132: sum=a[i][j];
2133: for (k=1;k<j;k++)
2134: sum -= a[i][k]*a[k][j];
2135: a[i][j]=sum;
2136: if ( (dum=vv[i]*fabs(sum)) >= big) {
2137: big=dum;
2138: imax=i;
2139: }
2140: }
2141: if (j != imax) {
2142: for (k=1;k<=n;k++) {
2143: dum=a[imax][k];
2144: a[imax][k]=a[j][k];
2145: a[j][k]=dum;
2146: }
2147: *d = -(*d);
2148: vv[imax]=vv[j];
2149: }
2150: indx[j]=imax;
2151: if (a[j][j] == 0.0) a[j][j]=TINY;
2152: if (j != n) {
2153: dum=1.0/(a[j][j]);
2154: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2155: }
2156: }
2157: free_vector(vv,1,n); /* Doesn't work */
2158: ;
2159: }
2160:
2161: void lubksb(double **a, int n, int *indx, double b[])
2162: {
2163: int i,ii=0,ip,j;
2164: double sum;
2165:
2166: for (i=1;i<=n;i++) {
2167: ip=indx[i];
2168: sum=b[ip];
2169: b[ip]=b[i];
2170: if (ii)
2171: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2172: else if (sum) ii=i;
2173: b[i]=sum;
2174: }
2175: for (i=n;i>=1;i--) {
2176: sum=b[i];
2177: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2178: b[i]=sum/a[i][i];
2179: }
2180: }
2181:
2182: void pstamp(FILE *fichier)
2183: {
2184: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2185: }
2186:
2187: /************ Frequencies ********************/
2188: 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[])
2189: { /* Some frequencies */
2190:
2191: int i, m, jk, k1,i1, j1, bool, z1,j;
2192: int first;
2193: double ***freq; /* Frequencies */
2194: double *pp, **prop;
2195: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2196: char fileresp[FILENAMELENGTH];
2197:
2198: pp=vector(1,nlstate);
2199: prop=matrix(1,nlstate,iagemin,iagemax+3);
2200: strcpy(fileresp,"p");
2201: strcat(fileresp,fileres);
2202: if((ficresp=fopen(fileresp,"w"))==NULL) {
2203: printf("Problem with prevalence resultfile: %s\n", fileresp);
2204: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2205: exit(0);
2206: }
2207: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2208: j1=0;
2209:
2210: j=cptcoveff;
2211: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2212:
2213: first=1;
2214:
2215: for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2216: for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2217: j1++;
2218: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2219: scanf("%d", i);*/
2220: for (i=-5; i<=nlstate+ndeath; i++)
2221: for (jk=-5; jk<=nlstate+ndeath; jk++)
2222: for(m=iagemin; m <= iagemax+3; m++)
2223: freq[i][jk][m]=0;
2224:
2225: for (i=1; i<=nlstate; i++)
2226: for(m=iagemin; m <= iagemax+3; m++)
2227: prop[i][m]=0;
2228:
2229: dateintsum=0;
2230: k2cpt=0;
2231: for (i=1; i<=imx; i++) {
2232: bool=1;
2233: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2234: for (z1=1; z1<=cptcoveff; z1++)
2235: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2236: bool=0;
2237: printf("bool=%d i=%d, z1=%d, i1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2238: bool,i,z1, i1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2239: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);
2240: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2241: }
2242: }
2243:
2244: if (bool==1){
2245: for(m=firstpass; m<=lastpass; m++){
2246: k2=anint[m][i]+(mint[m][i]/12.);
2247: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2248: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2249: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2250: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2251: if (m<lastpass) {
2252: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2253: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2254: }
2255:
2256: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2257: dateintsum=dateintsum+k2;
2258: k2cpt++;
2259: }
2260: /*}*/
2261: }
2262: }
2263: }
2264:
2265: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2266: pstamp(ficresp);
2267: if (cptcovn>0) {
2268: fprintf(ficresp, "\n#********** Variable ");
2269: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2270: fprintf(ficresp, "**********\n#");
2271: fprintf(ficlog, "\n#********** Variable ");
2272: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2273: fprintf(ficlog, "**********\n#");
2274: }
2275: for(i=1; i<=nlstate;i++)
2276: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2277: fprintf(ficresp, "\n");
2278:
2279: for(i=iagemin; i <= iagemax+3; i++){
2280: if(i==iagemax+3){
2281: fprintf(ficlog,"Total");
2282: }else{
2283: if(first==1){
2284: first=0;
2285: printf("See log file for details...\n");
2286: }
2287: fprintf(ficlog,"Age %d", i);
2288: }
2289: for(jk=1; jk <=nlstate ; jk++){
2290: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2291: pp[jk] += freq[jk][m][i];
2292: }
2293: for(jk=1; jk <=nlstate ; jk++){
2294: for(m=-1, pos=0; m <=0 ; m++)
2295: pos += freq[jk][m][i];
2296: if(pp[jk]>=1.e-10){
2297: if(first==1){
2298: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2299: }
2300: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2301: }else{
2302: if(first==1)
2303: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2304: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2305: }
2306: }
2307:
2308: for(jk=1; jk <=nlstate ; jk++){
2309: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2310: pp[jk] += freq[jk][m][i];
2311: }
2312: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2313: pos += pp[jk];
2314: posprop += prop[jk][i];
2315: }
2316: for(jk=1; jk <=nlstate ; jk++){
2317: if(pos>=1.e-5){
2318: if(first==1)
2319: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2320: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2321: }else{
2322: if(first==1)
2323: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2324: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2325: }
2326: if( i <= iagemax){
2327: if(pos>=1.e-5){
2328: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2329: /*probs[i][jk][j1]= pp[jk]/pos;*/
2330: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2331: }
2332: else
2333: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2334: }
2335: }
2336:
2337: for(jk=-1; jk <=nlstate+ndeath; jk++)
2338: for(m=-1; m <=nlstate+ndeath; m++)
2339: if(freq[jk][m][i] !=0 ) {
2340: if(first==1)
2341: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2342: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2343: }
2344: if(i <= iagemax)
2345: fprintf(ficresp,"\n");
2346: if(first==1)
2347: printf("Others in log...\n");
2348: fprintf(ficlog,"\n");
2349: }
2350: }
2351: }
2352: dateintmean=dateintsum/k2cpt;
2353:
2354: fclose(ficresp);
2355: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2356: free_vector(pp,1,nlstate);
2357: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2358: /* End of Freq */
2359: }
2360:
2361: /************ Prevalence ********************/
2362: 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)
2363: {
2364: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2365: in each health status at the date of interview (if between dateprev1 and dateprev2).
2366: We still use firstpass and lastpass as another selection.
2367: */
2368:
2369: int i, m, jk, k1, i1, j1, bool, z1,j;
2370: double ***freq; /* Frequencies */
2371: double *pp, **prop;
2372: double pos,posprop;
2373: double y2; /* in fractional years */
2374: int iagemin, iagemax;
2375:
2376: iagemin= (int) agemin;
2377: iagemax= (int) agemax;
2378: /*pp=vector(1,nlstate);*/
2379: prop=matrix(1,nlstate,iagemin,iagemax+3);
2380: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2381: j1=0;
2382:
2383: j=cptcoveff;
2384: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2385:
2386: for(k1=1; k1<=j;k1++){
2387: for(i1=1; i1<=ncodemax[k1];i1++){
2388: j1++;
2389:
2390: for (i=1; i<=nlstate; i++)
2391: for(m=iagemin; m <= iagemax+3; m++)
2392: prop[i][m]=0.0;
2393:
2394: for (i=1; i<=imx; i++) { /* Each individual */
2395: bool=1;
2396: if (cptcovn>0) {
2397: for (z1=1; z1<=cptcoveff; z1++)
2398: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2399: bool=0;
2400: }
2401: if (bool==1) {
2402: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2403: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2404: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2405: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2406: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2407: 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);
2408: if (s[m][i]>0 && s[m][i]<=nlstate) {
2409: /*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]]);*/
2410: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2411: prop[s[m][i]][iagemax+3] += weight[i];
2412: }
2413: }
2414: } /* end selection of waves */
2415: }
2416: }
2417: for(i=iagemin; i <= iagemax+3; i++){
2418:
2419: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2420: posprop += prop[jk][i];
2421: }
2422:
2423: for(jk=1; jk <=nlstate ; jk++){
2424: if( i <= iagemax){
2425: if(posprop>=1.e-5){
2426: probs[i][jk][j1]= prop[jk][i]/posprop;
2427: } else
2428: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2429: }
2430: }/* end jk */
2431: }/* end i */
2432: } /* end i1 */
2433: } /* end k1 */
2434:
2435: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2436: /*free_vector(pp,1,nlstate);*/
2437: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2438: } /* End of prevalence */
2439:
2440: /************* Waves Concatenation ***************/
2441:
2442: 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)
2443: {
2444: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2445: Death is a valid wave (if date is known).
2446: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2447: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2448: and mw[mi+1][i]. dh depends on stepm.
2449: */
2450:
2451: int i, mi, m;
2452: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2453: double sum=0., jmean=0.;*/
2454: int first;
2455: int j, k=0,jk, ju, jl;
2456: double sum=0.;
2457: first=0;
2458: jmin=1e+5;
2459: jmax=-1;
2460: jmean=0.;
2461: for(i=1; i<=imx; i++){
2462: mi=0;
2463: m=firstpass;
2464: while(s[m][i] <= nlstate){
2465: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2466: mw[++mi][i]=m;
2467: if(m >=lastpass)
2468: break;
2469: else
2470: m++;
2471: }/* end while */
2472: if (s[m][i] > nlstate){
2473: mi++; /* Death is another wave */
2474: /* if(mi==0) never been interviewed correctly before death */
2475: /* Only death is a correct wave */
2476: mw[mi][i]=m;
2477: }
2478:
2479: wav[i]=mi;
2480: if(mi==0){
2481: nbwarn++;
2482: if(first==0){
2483: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2484: first=1;
2485: }
2486: if(first==1){
2487: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2488: }
2489: } /* end mi==0 */
2490: } /* End individuals */
2491:
2492: for(i=1; i<=imx; i++){
2493: for(mi=1; mi<wav[i];mi++){
2494: if (stepm <=0)
2495: dh[mi][i]=1;
2496: else{
2497: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2498: if (agedc[i] < 2*AGESUP) {
2499: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2500: if(j==0) j=1; /* Survives at least one month after exam */
2501: else if(j<0){
2502: nberr++;
2503: 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]);
2504: j=1; /* Temporary Dangerous patch */
2505: 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);
2506: 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]);
2507: 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);
2508: }
2509: k=k+1;
2510: if (j >= jmax){
2511: jmax=j;
2512: ijmax=i;
2513: }
2514: if (j <= jmin){
2515: jmin=j;
2516: ijmin=i;
2517: }
2518: sum=sum+j;
2519: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2520: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2521: }
2522: }
2523: else{
2524: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2525: /* 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]); */
2526:
2527: k=k+1;
2528: if (j >= jmax) {
2529: jmax=j;
2530: ijmax=i;
2531: }
2532: else if (j <= jmin){
2533: jmin=j;
2534: ijmin=i;
2535: }
2536: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2537: /*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]);*/
2538: if(j<0){
2539: nberr++;
2540: 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]);
2541: 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]);
2542: }
2543: sum=sum+j;
2544: }
2545: jk= j/stepm;
2546: jl= j -jk*stepm;
2547: ju= j -(jk+1)*stepm;
2548: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2549: if(jl==0){
2550: dh[mi][i]=jk;
2551: bh[mi][i]=0;
2552: }else{ /* We want a negative bias in order to only have interpolation ie
2553: * to avoid the price of an extra matrix product in likelihood */
2554: dh[mi][i]=jk+1;
2555: bh[mi][i]=ju;
2556: }
2557: }else{
2558: if(jl <= -ju){
2559: dh[mi][i]=jk;
2560: bh[mi][i]=jl; /* bias is positive if real duration
2561: * is higher than the multiple of stepm and negative otherwise.
2562: */
2563: }
2564: else{
2565: dh[mi][i]=jk+1;
2566: bh[mi][i]=ju;
2567: }
2568: if(dh[mi][i]==0){
2569: dh[mi][i]=1; /* At least one step */
2570: bh[mi][i]=ju; /* At least one step */
2571: /* 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);*/
2572: }
2573: } /* end if mle */
2574: }
2575: } /* end wave */
2576: }
2577: jmean=sum/k;
2578: 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);
2579: 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);
2580: }
2581:
2582: /*********** Tricode ****************************/
2583: void tricode(int *Tvar, int **nbcode, int imx)
2584: {
2585: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2586: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2587: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2588: /* nbcode[Tvar[j][1]=
2589: */
2590:
2591: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2592: int modmaxcovj=0; /* Modality max of covariates j */
2593: cptcoveff=0;
2594:
2595: for (k=0; k < maxncov; k++) Ndum[k]=0;
2596: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2597:
2598: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
2599: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
2600: modality of this covariate Vj*/
2601: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
2602: modality of the nth covariate of individual i. */
2603: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2604: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2605: if (ij > modmaxcovj) modmaxcovj=ij;
2606: /* getting the maximum value of the modality of the covariate
2607: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2608: female is 1, then modmaxcovj=1.*/
2609: }
2610: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2611: for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
2612: if( Ndum[i] != 0 )
2613: ncodemax[j]++;
2614: /* Number of modalities of the j th covariate. In fact
2615: ncodemax[j]=2 (dichotom. variables only) but it could be more for
2616: historical reasons */
2617: } /* Ndum[-1] number of undefined modalities */
2618:
2619: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2620: ij=1;
2621: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
2622: for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
2623: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2624: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2625: k is a modality. If we have model=V1+V1*sex
2626: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2627: ij++;
2628: }
2629: if (ij > ncodemax[j]) break;
2630: } /* end of loop on */
2631: } /* end of loop on modality */
2632: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2633:
2634: for (k=0; k< maxncov; k++) Ndum[k]=0;
2635:
2636: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2637: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2638: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2639: Ndum[ij]++;
2640: }
2641:
2642: ij=1;
2643: for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2644: if((Ndum[i]!=0) && (i<=ncovcol)){
2645: Tvaraff[ij]=i; /*For printing */
2646: ij++;
2647: }
2648: }
2649: ij--;
2650: cptcoveff=ij; /*Number of total covariates*/
2651: }
2652:
2653: /*********** Health Expectancies ****************/
2654:
2655: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2656:
2657: {
2658: /* Health expectancies, no variances */
2659: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2660: int nhstepma, nstepma; /* Decreasing with age */
2661: double age, agelim, hf;
2662: double ***p3mat;
2663: double eip;
2664:
2665: pstamp(ficreseij);
2666: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2667: fprintf(ficreseij,"# Age");
2668: for(i=1; i<=nlstate;i++){
2669: for(j=1; j<=nlstate;j++){
2670: fprintf(ficreseij," e%1d%1d ",i,j);
2671: }
2672: fprintf(ficreseij," e%1d. ",i);
2673: }
2674: fprintf(ficreseij,"\n");
2675:
2676:
2677: if(estepm < stepm){
2678: printf ("Problem %d lower than %d\n",estepm, stepm);
2679: }
2680: else hstepm=estepm;
2681: /* We compute the life expectancy from trapezoids spaced every estepm months
2682: * This is mainly to measure the difference between two models: for example
2683: * if stepm=24 months pijx are given only every 2 years and by summing them
2684: * we are calculating an estimate of the Life Expectancy assuming a linear
2685: * progression in between and thus overestimating or underestimating according
2686: * to the curvature of the survival function. If, for the same date, we
2687: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2688: * to compare the new estimate of Life expectancy with the same linear
2689: * hypothesis. A more precise result, taking into account a more precise
2690: * curvature will be obtained if estepm is as small as stepm. */
2691:
2692: /* For example we decided to compute the life expectancy with the smallest unit */
2693: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2694: nhstepm is the number of hstepm from age to agelim
2695: nstepm is the number of stepm from age to agelin.
2696: Look at hpijx to understand the reason of that which relies in memory size
2697: and note for a fixed period like estepm months */
2698: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2699: survival function given by stepm (the optimization length). Unfortunately it
2700: means that if the survival funtion is printed only each two years of age and if
2701: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2702: results. So we changed our mind and took the option of the best precision.
2703: */
2704: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2705:
2706: agelim=AGESUP;
2707: /* If stepm=6 months */
2708: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2709: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2710:
2711: /* nhstepm age range expressed in number of stepm */
2712: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2713: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2714: /* if (stepm >= YEARM) hstepm=1;*/
2715: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2716: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2717:
2718: for (age=bage; age<=fage; age ++){
2719: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2720: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2721: /* if (stepm >= YEARM) hstepm=1;*/
2722: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2723:
2724: /* If stepm=6 months */
2725: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2726: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2727:
2728: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2729:
2730: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2731:
2732: printf("%d|",(int)age);fflush(stdout);
2733: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2734:
2735: /* Computing expectancies */
2736: for(i=1; i<=nlstate;i++)
2737: for(j=1; j<=nlstate;j++)
2738: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2739: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2740:
2741: /* 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]);*/
2742:
2743: }
2744:
2745: fprintf(ficreseij,"%3.0f",age );
2746: for(i=1; i<=nlstate;i++){
2747: eip=0;
2748: for(j=1; j<=nlstate;j++){
2749: eip +=eij[i][j][(int)age];
2750: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2751: }
2752: fprintf(ficreseij,"%9.4f", eip );
2753: }
2754: fprintf(ficreseij,"\n");
2755:
2756: }
2757: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2758: printf("\n");
2759: fprintf(ficlog,"\n");
2760:
2761: }
2762:
2763: 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[] )
2764:
2765: {
2766: /* Covariances of health expectancies eij and of total life expectancies according
2767: to initial status i, ei. .
2768: */
2769: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2770: int nhstepma, nstepma; /* Decreasing with age */
2771: double age, agelim, hf;
2772: double ***p3matp, ***p3matm, ***varhe;
2773: double **dnewm,**doldm;
2774: double *xp, *xm;
2775: double **gp, **gm;
2776: double ***gradg, ***trgradg;
2777: int theta;
2778:
2779: double eip, vip;
2780:
2781: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2782: xp=vector(1,npar);
2783: xm=vector(1,npar);
2784: dnewm=matrix(1,nlstate*nlstate,1,npar);
2785: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2786:
2787: pstamp(ficresstdeij);
2788: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2789: fprintf(ficresstdeij,"# Age");
2790: for(i=1; i<=nlstate;i++){
2791: for(j=1; j<=nlstate;j++)
2792: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2793: fprintf(ficresstdeij," e%1d. ",i);
2794: }
2795: fprintf(ficresstdeij,"\n");
2796:
2797: pstamp(ficrescveij);
2798: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2799: fprintf(ficrescveij,"# Age");
2800: for(i=1; i<=nlstate;i++)
2801: for(j=1; j<=nlstate;j++){
2802: cptj= (j-1)*nlstate+i;
2803: for(i2=1; i2<=nlstate;i2++)
2804: for(j2=1; j2<=nlstate;j2++){
2805: cptj2= (j2-1)*nlstate+i2;
2806: if(cptj2 <= cptj)
2807: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2808: }
2809: }
2810: fprintf(ficrescveij,"\n");
2811:
2812: if(estepm < stepm){
2813: printf ("Problem %d lower than %d\n",estepm, stepm);
2814: }
2815: else hstepm=estepm;
2816: /* We compute the life expectancy from trapezoids spaced every estepm months
2817: * This is mainly to measure the difference between two models: for example
2818: * if stepm=24 months pijx are given only every 2 years and by summing them
2819: * we are calculating an estimate of the Life Expectancy assuming a linear
2820: * progression in between and thus overestimating or underestimating according
2821: * to the curvature of the survival function. If, for the same date, we
2822: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2823: * to compare the new estimate of Life expectancy with the same linear
2824: * hypothesis. A more precise result, taking into account a more precise
2825: * curvature will be obtained if estepm is as small as stepm. */
2826:
2827: /* For example we decided to compute the life expectancy with the smallest unit */
2828: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2829: nhstepm is the number of hstepm from age to agelim
2830: nstepm is the number of stepm from age to agelin.
2831: Look at hpijx to understand the reason of that which relies in memory size
2832: and note for a fixed period like estepm months */
2833: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2834: survival function given by stepm (the optimization length). Unfortunately it
2835: means that if the survival funtion is printed only each two years of age and if
2836: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2837: results. So we changed our mind and took the option of the best precision.
2838: */
2839: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2840:
2841: /* If stepm=6 months */
2842: /* nhstepm age range expressed in number of stepm */
2843: agelim=AGESUP;
2844: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2845: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2846: /* if (stepm >= YEARM) hstepm=1;*/
2847: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2848:
2849: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2850: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2851: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2852: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2853: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2854: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2855:
2856: for (age=bage; age<=fage; age ++){
2857: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2858: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2859: /* if (stepm >= YEARM) hstepm=1;*/
2860: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2861:
2862: /* If stepm=6 months */
2863: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2864: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2865:
2866: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2867:
2868: /* Computing Variances of health expectancies */
2869: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2870: decrease memory allocation */
2871: for(theta=1; theta <=npar; theta++){
2872: for(i=1; i<=npar; i++){
2873: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2874: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2875: }
2876: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2877: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2878:
2879: for(j=1; j<= nlstate; j++){
2880: for(i=1; i<=nlstate; i++){
2881: for(h=0; h<=nhstepm-1; h++){
2882: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2883: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2884: }
2885: }
2886: }
2887:
2888: for(ij=1; ij<= nlstate*nlstate; ij++)
2889: for(h=0; h<=nhstepm-1; h++){
2890: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2891: }
2892: }/* End theta */
2893:
2894:
2895: for(h=0; h<=nhstepm-1; h++)
2896: for(j=1; j<=nlstate*nlstate;j++)
2897: for(theta=1; theta <=npar; theta++)
2898: trgradg[h][j][theta]=gradg[h][theta][j];
2899:
2900:
2901: for(ij=1;ij<=nlstate*nlstate;ij++)
2902: for(ji=1;ji<=nlstate*nlstate;ji++)
2903: varhe[ij][ji][(int)age] =0.;
2904:
2905: printf("%d|",(int)age);fflush(stdout);
2906: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2907: for(h=0;h<=nhstepm-1;h++){
2908: for(k=0;k<=nhstepm-1;k++){
2909: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2910: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2911: for(ij=1;ij<=nlstate*nlstate;ij++)
2912: for(ji=1;ji<=nlstate*nlstate;ji++)
2913: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2914: }
2915: }
2916:
2917: /* Computing expectancies */
2918: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2919: for(i=1; i<=nlstate;i++)
2920: for(j=1; j<=nlstate;j++)
2921: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2922: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2923:
2924: /* 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]);*/
2925:
2926: }
2927:
2928: fprintf(ficresstdeij,"%3.0f",age );
2929: for(i=1; i<=nlstate;i++){
2930: eip=0.;
2931: vip=0.;
2932: for(j=1; j<=nlstate;j++){
2933: eip += eij[i][j][(int)age];
2934: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2935: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2936: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2937: }
2938: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2939: }
2940: fprintf(ficresstdeij,"\n");
2941:
2942: fprintf(ficrescveij,"%3.0f",age );
2943: for(i=1; i<=nlstate;i++)
2944: for(j=1; j<=nlstate;j++){
2945: cptj= (j-1)*nlstate+i;
2946: for(i2=1; i2<=nlstate;i2++)
2947: for(j2=1; j2<=nlstate;j2++){
2948: cptj2= (j2-1)*nlstate+i2;
2949: if(cptj2 <= cptj)
2950: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2951: }
2952: }
2953: fprintf(ficrescveij,"\n");
2954:
2955: }
2956: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2957: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2958: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2959: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2960: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2961: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2962: printf("\n");
2963: fprintf(ficlog,"\n");
2964:
2965: free_vector(xm,1,npar);
2966: free_vector(xp,1,npar);
2967: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2968: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2969: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2970: }
2971:
2972: /************ Variance ******************/
2973: 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[])
2974: {
2975: /* Variance of health expectancies */
2976: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2977: /* double **newm;*/
2978: double **dnewm,**doldm;
2979: double **dnewmp,**doldmp;
2980: int i, j, nhstepm, hstepm, h, nstepm ;
2981: int k, cptcode;
2982: double *xp;
2983: double **gp, **gm; /* for var eij */
2984: double ***gradg, ***trgradg; /*for var eij */
2985: double **gradgp, **trgradgp; /* for var p point j */
2986: double *gpp, *gmp; /* for var p point j */
2987: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2988: double ***p3mat;
2989: double age,agelim, hf;
2990: double ***mobaverage;
2991: int theta;
2992: char digit[4];
2993: char digitp[25];
2994:
2995: char fileresprobmorprev[FILENAMELENGTH];
2996:
2997: if(popbased==1){
2998: if(mobilav!=0)
2999: strcpy(digitp,"-populbased-mobilav-");
3000: else strcpy(digitp,"-populbased-nomobil-");
3001: }
3002: else
3003: strcpy(digitp,"-stablbased-");
3004:
3005: if (mobilav!=0) {
3006: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3007: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3008: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3009: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3010: }
3011: }
3012:
3013: strcpy(fileresprobmorprev,"prmorprev");
3014: sprintf(digit,"%-d",ij);
3015: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3016: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3017: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3018: strcat(fileresprobmorprev,fileres);
3019: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3020: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3021: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3022: }
3023: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3024:
3025: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3026: pstamp(ficresprobmorprev);
3027: 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);
3028: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3029: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3030: fprintf(ficresprobmorprev," p.%-d SE",j);
3031: for(i=1; i<=nlstate;i++)
3032: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3033: }
3034: fprintf(ficresprobmorprev,"\n");
3035: fprintf(ficgp,"\n# Routine varevsij");
3036: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3037: 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");
3038: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3039: /* } */
3040: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3041: pstamp(ficresvij);
3042: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3043: if(popbased==1)
3044: 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);
3045: else
3046: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3047: fprintf(ficresvij,"# Age");
3048: for(i=1; i<=nlstate;i++)
3049: for(j=1; j<=nlstate;j++)
3050: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3051: fprintf(ficresvij,"\n");
3052:
3053: xp=vector(1,npar);
3054: dnewm=matrix(1,nlstate,1,npar);
3055: doldm=matrix(1,nlstate,1,nlstate);
3056: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3057: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3058:
3059: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3060: gpp=vector(nlstate+1,nlstate+ndeath);
3061: gmp=vector(nlstate+1,nlstate+ndeath);
3062: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3063:
3064: if(estepm < stepm){
3065: printf ("Problem %d lower than %d\n",estepm, stepm);
3066: }
3067: else hstepm=estepm;
3068: /* For example we decided to compute the life expectancy with the smallest unit */
3069: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3070: nhstepm is the number of hstepm from age to agelim
3071: nstepm is the number of stepm from age to agelin.
3072: Look at function hpijx to understand why (it is linked to memory size questions) */
3073: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3074: survival function given by stepm (the optimization length). Unfortunately it
3075: means that if the survival funtion is printed every two years of age and if
3076: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3077: results. So we changed our mind and took the option of the best precision.
3078: */
3079: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3080: agelim = AGESUP;
3081: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3082: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3083: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3084: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3085: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3086: gp=matrix(0,nhstepm,1,nlstate);
3087: gm=matrix(0,nhstepm,1,nlstate);
3088:
3089:
3090: for(theta=1; theta <=npar; theta++){
3091: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3092: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3093: }
3094: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3095: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3096:
3097: if (popbased==1) {
3098: if(mobilav ==0){
3099: for(i=1; i<=nlstate;i++)
3100: prlim[i][i]=probs[(int)age][i][ij];
3101: }else{ /* mobilav */
3102: for(i=1; i<=nlstate;i++)
3103: prlim[i][i]=mobaverage[(int)age][i][ij];
3104: }
3105: }
3106:
3107: for(j=1; j<= nlstate; j++){
3108: for(h=0; h<=nhstepm; h++){
3109: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3110: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3111: }
3112: }
3113: /* This for computing probability of death (h=1 means
3114: computed over hstepm matrices product = hstepm*stepm months)
3115: as a weighted average of prlim.
3116: */
3117: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3118: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3119: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3120: }
3121: /* end probability of death */
3122:
3123: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3124: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3125: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3126: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3127:
3128: if (popbased==1) {
3129: if(mobilav ==0){
3130: for(i=1; i<=nlstate;i++)
3131: prlim[i][i]=probs[(int)age][i][ij];
3132: }else{ /* mobilav */
3133: for(i=1; i<=nlstate;i++)
3134: prlim[i][i]=mobaverage[(int)age][i][ij];
3135: }
3136: }
3137:
3138: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3139: for(h=0; h<=nhstepm; h++){
3140: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3141: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3142: }
3143: }
3144: /* This for computing probability of death (h=1 means
3145: computed over hstepm matrices product = hstepm*stepm months)
3146: as a weighted average of prlim.
3147: */
3148: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3149: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3150: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3151: }
3152: /* end probability of death */
3153:
3154: for(j=1; j<= nlstate; j++) /* vareij */
3155: for(h=0; h<=nhstepm; h++){
3156: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3157: }
3158:
3159: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3160: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3161: }
3162:
3163: } /* End theta */
3164:
3165: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3166:
3167: for(h=0; h<=nhstepm; h++) /* veij */
3168: for(j=1; j<=nlstate;j++)
3169: for(theta=1; theta <=npar; theta++)
3170: trgradg[h][j][theta]=gradg[h][theta][j];
3171:
3172: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3173: for(theta=1; theta <=npar; theta++)
3174: trgradgp[j][theta]=gradgp[theta][j];
3175:
3176:
3177: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3178: for(i=1;i<=nlstate;i++)
3179: for(j=1;j<=nlstate;j++)
3180: vareij[i][j][(int)age] =0.;
3181:
3182: for(h=0;h<=nhstepm;h++){
3183: for(k=0;k<=nhstepm;k++){
3184: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3185: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3186: for(i=1;i<=nlstate;i++)
3187: for(j=1;j<=nlstate;j++)
3188: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3189: }
3190: }
3191:
3192: /* pptj */
3193: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3194: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3195: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3196: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3197: varppt[j][i]=doldmp[j][i];
3198: /* end ppptj */
3199: /* x centered again */
3200: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3201: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3202:
3203: if (popbased==1) {
3204: if(mobilav ==0){
3205: for(i=1; i<=nlstate;i++)
3206: prlim[i][i]=probs[(int)age][i][ij];
3207: }else{ /* mobilav */
3208: for(i=1; i<=nlstate;i++)
3209: prlim[i][i]=mobaverage[(int)age][i][ij];
3210: }
3211: }
3212:
3213: /* This for computing probability of death (h=1 means
3214: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3215: as a weighted average of prlim.
3216: */
3217: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3218: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3219: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3220: }
3221: /* end probability of death */
3222:
3223: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3224: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3225: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3226: for(i=1; i<=nlstate;i++){
3227: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3228: }
3229: }
3230: fprintf(ficresprobmorprev,"\n");
3231:
3232: fprintf(ficresvij,"%.0f ",age );
3233: for(i=1; i<=nlstate;i++)
3234: for(j=1; j<=nlstate;j++){
3235: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3236: }
3237: fprintf(ficresvij,"\n");
3238: free_matrix(gp,0,nhstepm,1,nlstate);
3239: free_matrix(gm,0,nhstepm,1,nlstate);
3240: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3241: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3242: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3243: } /* End age */
3244: free_vector(gpp,nlstate+1,nlstate+ndeath);
3245: free_vector(gmp,nlstate+1,nlstate+ndeath);
3246: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3247: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3248: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
3249: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3250: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3251: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3252: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3253: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3254: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
3255: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
3256: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
3257: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3258: 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);
3259: /* 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);
3260: */
3261: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3262: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3263:
3264: free_vector(xp,1,npar);
3265: free_matrix(doldm,1,nlstate,1,nlstate);
3266: free_matrix(dnewm,1,nlstate,1,npar);
3267: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3268: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3269: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3270: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3271: fclose(ficresprobmorprev);
3272: fflush(ficgp);
3273: fflush(fichtm);
3274: } /* end varevsij */
3275:
3276: /************ Variance of prevlim ******************/
3277: 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[])
3278: {
3279: /* Variance of prevalence limit */
3280: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3281: double **newm;
3282: double **dnewm,**doldm;
3283: int i, j, nhstepm, hstepm;
3284: int k, cptcode;
3285: double *xp;
3286: double *gp, *gm;
3287: double **gradg, **trgradg;
3288: double age,agelim;
3289: int theta;
3290:
3291: pstamp(ficresvpl);
3292: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3293: fprintf(ficresvpl,"# Age");
3294: for(i=1; i<=nlstate;i++)
3295: fprintf(ficresvpl," %1d-%1d",i,i);
3296: fprintf(ficresvpl,"\n");
3297:
3298: xp=vector(1,npar);
3299: dnewm=matrix(1,nlstate,1,npar);
3300: doldm=matrix(1,nlstate,1,nlstate);
3301:
3302: hstepm=1*YEARM; /* Every year of age */
3303: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3304: agelim = AGESUP;
3305: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3306: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3307: if (stepm >= YEARM) hstepm=1;
3308: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3309: gradg=matrix(1,npar,1,nlstate);
3310: gp=vector(1,nlstate);
3311: gm=vector(1,nlstate);
3312:
3313: for(theta=1; theta <=npar; theta++){
3314: for(i=1; i<=npar; i++){ /* Computes gradient */
3315: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3316: }
3317: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3318: for(i=1;i<=nlstate;i++)
3319: gp[i] = prlim[i][i];
3320:
3321: for(i=1; i<=npar; i++) /* Computes gradient */
3322: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3323: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3324: for(i=1;i<=nlstate;i++)
3325: gm[i] = prlim[i][i];
3326:
3327: for(i=1;i<=nlstate;i++)
3328: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3329: } /* End theta */
3330:
3331: trgradg =matrix(1,nlstate,1,npar);
3332:
3333: for(j=1; j<=nlstate;j++)
3334: for(theta=1; theta <=npar; theta++)
3335: trgradg[j][theta]=gradg[theta][j];
3336:
3337: for(i=1;i<=nlstate;i++)
3338: varpl[i][(int)age] =0.;
3339: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3340: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3341: for(i=1;i<=nlstate;i++)
3342: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3343:
3344: fprintf(ficresvpl,"%.0f ",age );
3345: for(i=1; i<=nlstate;i++)
3346: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3347: fprintf(ficresvpl,"\n");
3348: free_vector(gp,1,nlstate);
3349: free_vector(gm,1,nlstate);
3350: free_matrix(gradg,1,npar,1,nlstate);
3351: free_matrix(trgradg,1,nlstate,1,npar);
3352: } /* End age */
3353:
3354: free_vector(xp,1,npar);
3355: free_matrix(doldm,1,nlstate,1,npar);
3356: free_matrix(dnewm,1,nlstate,1,nlstate);
3357:
3358: }
3359:
3360: /************ Variance of one-step probabilities ******************/
3361: 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[])
3362: {
3363: int i, j=0, i1, k1, l1, t, tj;
3364: int k2, l2, j1, z1;
3365: int k=0,l, cptcode;
3366: int first=1, first1;
3367: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3368: double **dnewm,**doldm;
3369: double *xp;
3370: double *gp, *gm;
3371: double **gradg, **trgradg;
3372: double **mu;
3373: double age,agelim, cov[NCOVMAX];
3374: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3375: int theta;
3376: char fileresprob[FILENAMELENGTH];
3377: char fileresprobcov[FILENAMELENGTH];
3378: char fileresprobcor[FILENAMELENGTH];
3379:
3380: double ***varpij;
3381:
3382: strcpy(fileresprob,"prob");
3383: strcat(fileresprob,fileres);
3384: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3385: printf("Problem with resultfile: %s\n", fileresprob);
3386: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3387: }
3388: strcpy(fileresprobcov,"probcov");
3389: strcat(fileresprobcov,fileres);
3390: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3391: printf("Problem with resultfile: %s\n", fileresprobcov);
3392: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3393: }
3394: strcpy(fileresprobcor,"probcor");
3395: strcat(fileresprobcor,fileres);
3396: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3397: printf("Problem with resultfile: %s\n", fileresprobcor);
3398: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3399: }
3400: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3401: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3402: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3403: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3404: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3405: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3406: pstamp(ficresprob);
3407: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3408: fprintf(ficresprob,"# Age");
3409: pstamp(ficresprobcov);
3410: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3411: fprintf(ficresprobcov,"# Age");
3412: pstamp(ficresprobcor);
3413: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3414: fprintf(ficresprobcor,"# Age");
3415:
3416:
3417: for(i=1; i<=nlstate;i++)
3418: for(j=1; j<=(nlstate+ndeath);j++){
3419: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3420: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3421: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3422: }
3423: /* fprintf(ficresprob,"\n");
3424: fprintf(ficresprobcov,"\n");
3425: fprintf(ficresprobcor,"\n");
3426: */
3427: xp=vector(1,npar);
3428: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3429: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3430: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3431: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3432: first=1;
3433: fprintf(ficgp,"\n# Routine varprob");
3434: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3435: fprintf(fichtm,"\n");
3436:
3437: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3438: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3439: file %s<br>\n",optionfilehtmcov);
3440: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3441: and drawn. It helps understanding how is the covariance between two incidences.\
3442: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3443: 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. \
3444: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3445: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3446: standard deviations wide on each axis. <br>\
3447: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3448: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3449: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3450:
3451: cov[1]=1;
3452: tj=cptcoveff;
3453: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3454: j1=0;
3455: for(t=1; t<=tj;t++){
3456: for(i1=1; i1<=ncodemax[t];i1++){
3457: j1++;
3458: if (cptcovn>0) {
3459: fprintf(ficresprob, "\n#********** Variable ");
3460: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3461: fprintf(ficresprob, "**********\n#\n");
3462: fprintf(ficresprobcov, "\n#********** Variable ");
3463: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3464: fprintf(ficresprobcov, "**********\n#\n");
3465:
3466: fprintf(ficgp, "\n#********** Variable ");
3467: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3468: fprintf(ficgp, "**********\n#\n");
3469:
3470:
3471: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3472: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3473: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3474:
3475: fprintf(ficresprobcor, "\n#********** Variable ");
3476: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3477: fprintf(ficresprobcor, "**********\n#");
3478: }
3479:
3480: for (age=bage; age<=fage; age ++){
3481: cov[2]=age;
3482: for (k=1; k<=cptcovn;k++) {
3483: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3484: }
3485: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3486: for (k=1; k<=cptcovprod;k++)
3487: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3488:
3489: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3490: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3491: gp=vector(1,(nlstate)*(nlstate+ndeath));
3492: gm=vector(1,(nlstate)*(nlstate+ndeath));
3493:
3494: for(theta=1; theta <=npar; theta++){
3495: for(i=1; i<=npar; i++)
3496: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3497:
3498: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3499:
3500: k=0;
3501: for(i=1; i<= (nlstate); i++){
3502: for(j=1; j<=(nlstate+ndeath);j++){
3503: k=k+1;
3504: gp[k]=pmmij[i][j];
3505: }
3506: }
3507:
3508: for(i=1; i<=npar; i++)
3509: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3510:
3511: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3512: k=0;
3513: for(i=1; i<=(nlstate); i++){
3514: for(j=1; j<=(nlstate+ndeath);j++){
3515: k=k+1;
3516: gm[k]=pmmij[i][j];
3517: }
3518: }
3519:
3520: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3521: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3522: }
3523:
3524: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3525: for(theta=1; theta <=npar; theta++)
3526: trgradg[j][theta]=gradg[theta][j];
3527:
3528: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3529: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3530: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3531: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3532: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3533: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3534:
3535: pmij(pmmij,cov,ncovmodel,x,nlstate);
3536:
3537: k=0;
3538: for(i=1; i<=(nlstate); i++){
3539: for(j=1; j<=(nlstate+ndeath);j++){
3540: k=k+1;
3541: mu[k][(int) age]=pmmij[i][j];
3542: }
3543: }
3544: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3545: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3546: varpij[i][j][(int)age] = doldm[i][j];
3547:
3548: /*printf("\n%d ",(int)age);
3549: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3550: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3551: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3552: }*/
3553:
3554: fprintf(ficresprob,"\n%d ",(int)age);
3555: fprintf(ficresprobcov,"\n%d ",(int)age);
3556: fprintf(ficresprobcor,"\n%d ",(int)age);
3557:
3558: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3559: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3560: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3561: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3562: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3563: }
3564: i=0;
3565: for (k=1; k<=(nlstate);k++){
3566: for (l=1; l<=(nlstate+ndeath);l++){
3567: i=i++;
3568: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3569: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3570: for (j=1; j<=i;j++){
3571: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3572: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3573: }
3574: }
3575: }/* end of loop for state */
3576: } /* end of loop for age */
3577:
3578: /* Confidence intervalle of pij */
3579: /*
3580: fprintf(ficgp,"\nunset parametric;unset label");
3581: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3582: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3583: 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);
3584: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3585: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3586: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3587: */
3588:
3589: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3590: first1=1;
3591: for (k2=1; k2<=(nlstate);k2++){
3592: for (l2=1; l2<=(nlstate+ndeath);l2++){
3593: if(l2==k2) continue;
3594: j=(k2-1)*(nlstate+ndeath)+l2;
3595: for (k1=1; k1<=(nlstate);k1++){
3596: for (l1=1; l1<=(nlstate+ndeath);l1++){
3597: if(l1==k1) continue;
3598: i=(k1-1)*(nlstate+ndeath)+l1;
3599: if(i<=j) continue;
3600: for (age=bage; age<=fage; age ++){
3601: if ((int)age %5==0){
3602: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3603: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3604: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3605: mu1=mu[i][(int) age]/stepm*YEARM ;
3606: mu2=mu[j][(int) age]/stepm*YEARM;
3607: c12=cv12/sqrt(v1*v2);
3608: /* Computing eigen value of matrix of covariance */
3609: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3610: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3611: if ((lc2 <0) || (lc1 <0) ){
3612: 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);
3613: 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);
3614: lc1=fabs(lc1);
3615: lc2=fabs(lc2);
3616: }
3617:
3618: /* Eigen vectors */
3619: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3620: /*v21=sqrt(1.-v11*v11); *//* error */
3621: v21=(lc1-v1)/cv12*v11;
3622: v12=-v21;
3623: v22=v11;
3624: tnalp=v21/v11;
3625: if(first1==1){
3626: first1=0;
3627: 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);
3628: }
3629: 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);
3630: /*printf(fignu*/
3631: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3632: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3633: if(first==1){
3634: first=0;
3635: fprintf(ficgp,"\nset parametric;unset label");
3636: 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);
3637: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3638: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3639: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3640: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3641: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3642: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3643: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3644: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3645: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3646: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3647: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3648: 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",\
3649: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3650: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3651: }else{
3652: first=0;
3653: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3654: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3655: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3656: 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",\
3657: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3658: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3659: }/* if first */
3660: } /* age mod 5 */
3661: } /* end loop age */
3662: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3663: first=1;
3664: } /*l12 */
3665: } /* k12 */
3666: } /*l1 */
3667: }/* k1 */
3668: } /* loop covariates */
3669: }
3670: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3671: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3672: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3673: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3674: free_vector(xp,1,npar);
3675: fclose(ficresprob);
3676: fclose(ficresprobcov);
3677: fclose(ficresprobcor);
3678: fflush(ficgp);
3679: fflush(fichtmcov);
3680: }
3681:
3682:
3683: /******************* Printing html file ***********/
3684: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3685: int lastpass, int stepm, int weightopt, char model[],\
3686: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3687: int popforecast, int estepm ,\
3688: double jprev1, double mprev1,double anprev1, \
3689: double jprev2, double mprev2,double anprev2){
3690: int jj1, k1, i1, cpt;
3691:
3692: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3693: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3694: </ul>");
3695: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3696: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3697: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3698: fprintf(fichtm,"\
3699: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3700: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3701: fprintf(fichtm,"\
3702: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3703: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3704: fprintf(fichtm,"\
3705: - (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): \
3706: <a href=\"%s\">%s</a> <br>\n",
3707: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3708: fprintf(fichtm,"\
3709: - Population projections by age and states: \
3710: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3711:
3712: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3713:
3714: m=cptcoveff;
3715: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3716:
3717: jj1=0;
3718: for(k1=1; k1<=m;k1++){
3719: for(i1=1; i1<=ncodemax[k1];i1++){
3720: jj1++;
3721: if (cptcovn > 0) {
3722: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3723: for (cpt=1; cpt<=cptcoveff;cpt++)
3724: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3725: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3726: }
3727: /* Pij */
3728: 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> \
3729: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3730: /* Quasi-incidences */
3731: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3732: 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> \
3733: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3734: /* Period (stable) prevalence in each health state */
3735: for(cpt=1; cpt<nlstate;cpt++){
3736: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3737: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3738: }
3739: for(cpt=1; cpt<=nlstate;cpt++) {
3740: 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> \
3741: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3742: }
3743: } /* end i1 */
3744: }/* End k1 */
3745: fprintf(fichtm,"</ul>");
3746:
3747:
3748: fprintf(fichtm,"\
3749: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3750: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3751:
3752: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3753: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3754: fprintf(fichtm,"\
3755: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3756: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3757:
3758: fprintf(fichtm,"\
3759: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3760: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3761: fprintf(fichtm,"\
3762: - 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): \
3763: <a href=\"%s\">%s</a> <br>\n</li>",
3764: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3765: fprintf(fichtm,"\
3766: - (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): \
3767: <a href=\"%s\">%s</a> <br>\n</li>",
3768: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3769: fprintf(fichtm,"\
3770: - 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",
3771: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3772: fprintf(fichtm,"\
3773: - 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",
3774: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3775: fprintf(fichtm,"\
3776: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3777: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3778:
3779: /* if(popforecast==1) fprintf(fichtm,"\n */
3780: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3781: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3782: /* <br>",fileres,fileres,fileres,fileres); */
3783: /* else */
3784: /* 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); */
3785: fflush(fichtm);
3786: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3787:
3788: m=cptcoveff;
3789: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3790:
3791: jj1=0;
3792: for(k1=1; k1<=m;k1++){
3793: for(i1=1; i1<=ncodemax[k1];i1++){
3794: jj1++;
3795: if (cptcovn > 0) {
3796: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3797: for (cpt=1; cpt<=cptcoveff;cpt++)
3798: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3799: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3800: }
3801: for(cpt=1; cpt<=nlstate;cpt++) {
3802: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3803: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3804: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3805: }
3806: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3807: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3808: true period expectancies (those weighted with period prevalences are also\
3809: drawn in addition to the population based expectancies computed using\
3810: observed and cahotic prevalences: %s%d.png<br>\
3811: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3812: } /* end i1 */
3813: }/* End k1 */
3814: fprintf(fichtm,"</ul>");
3815: fflush(fichtm);
3816: }
3817:
3818: /******************* Gnuplot file **************/
3819: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3820:
3821: char dirfileres[132],optfileres[132];
3822: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3823: int ng=0;
3824: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3825: /* printf("Problem with file %s",optionfilegnuplot); */
3826: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3827: /* } */
3828:
3829: /*#ifdef windows */
3830: fprintf(ficgp,"cd \"%s\" \n",pathc);
3831: /*#endif */
3832: m=pow(2,cptcoveff);
3833:
3834: strcpy(dirfileres,optionfilefiname);
3835: strcpy(optfileres,"vpl");
3836: /* 1eme*/
3837: for (cpt=1; cpt<= nlstate ; cpt ++) {
3838: for (k1=1; k1<= m ; k1 ++) {
3839: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3840: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3841: fprintf(ficgp,"set xlabel \"Age\" \n\
3842: set ylabel \"Probability\" \n\
3843: set ter png small\n\
3844: set size 0.65,0.65\n\
3845: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3846:
3847: for (i=1; i<= nlstate ; i ++) {
3848: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3849: else fprintf(ficgp," \%%*lf (\%%*lf)");
3850: }
3851: 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);
3852: for (i=1; i<= nlstate ; i ++) {
3853: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3854: else fprintf(ficgp," \%%*lf (\%%*lf)");
3855: }
3856: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3857: for (i=1; i<= nlstate ; i ++) {
3858: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3859: else fprintf(ficgp," \%%*lf (\%%*lf)");
3860: }
3861: fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3862: }
3863: }
3864: /*2 eme*/
3865:
3866: for (k1=1; k1<= m ; k1 ++) {
3867: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3868: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3869:
3870: for (i=1; i<= nlstate+1 ; i ++) {
3871: k=2*i;
3872: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3873: for (j=1; j<= nlstate+1 ; j ++) {
3874: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3875: else fprintf(ficgp," \%%*lf (\%%*lf)");
3876: }
3877: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3878: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3879: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3880: for (j=1; j<= nlstate+1 ; j ++) {
3881: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3882: else fprintf(ficgp," \%%*lf (\%%*lf)");
3883: }
3884: fprintf(ficgp,"\" t\"\" w l lt 1,");
3885: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3886: for (j=1; j<= nlstate+1 ; j ++) {
3887: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3888: else fprintf(ficgp," \%%*lf (\%%*lf)");
3889: }
3890: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
3891: else fprintf(ficgp,"\" t\"\" w l lt 1,");
3892: }
3893: }
3894:
3895: /*3eme*/
3896:
3897: for (k1=1; k1<= m ; k1 ++) {
3898: for (cpt=1; cpt<= nlstate ; cpt ++) {
3899: /* k=2+nlstate*(2*cpt-2); */
3900: k=2+(nlstate+1)*(cpt-1);
3901: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3902: fprintf(ficgp,"set ter png small\n\
3903: set size 0.65,0.65\n\
3904: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3905: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3906: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3907: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3908: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3909: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3910: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3911:
3912: */
3913: for (i=1; i< nlstate ; i ++) {
3914: 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);
3915: /* 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);*/
3916:
3917: }
3918: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3919: }
3920: }
3921:
3922: /* CV preval stable (period) */
3923: for (k1=1; k1<= m ; k1 ++) {
3924: for (cpt=1; cpt<=nlstate ; cpt ++) {
3925: k=3;
3926: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3927: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3928: set ter png small\nset size 0.65,0.65\n\
3929: unset log y\n\
3930: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3931:
3932: for (i=1; i< nlstate ; i ++)
3933: fprintf(ficgp,"+$%d",k+i+1);
3934: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3935:
3936: l=3+(nlstate+ndeath)*cpt;
3937: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3938: for (i=1; i< nlstate ; i ++) {
3939: l=3+(nlstate+ndeath)*cpt;
3940: fprintf(ficgp,"+$%d",l+i+1);
3941: }
3942: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3943: }
3944: }
3945:
3946: /* proba elementaires */
3947: for(i=1,jk=1; i <=nlstate; i++){
3948: for(k=1; k <=(nlstate+ndeath); k++){
3949: if (k != i) {
3950: for(j=1; j <=ncovmodel; j++){
3951: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3952: jk++;
3953: fprintf(ficgp,"\n");
3954: }
3955: }
3956: }
3957: }
3958:
3959: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3960: for(jk=1; jk <=m; jk++) {
3961: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3962: if (ng==2)
3963: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3964: else
3965: fprintf(ficgp,"\nset title \"Probability\"\n");
3966: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3967: i=1;
3968: for(k2=1; k2<=nlstate; k2++) {
3969: k3=i;
3970: for(k=1; k<=(nlstate+ndeath); k++) {
3971: if (k != k2){
3972: if(ng==2)
3973: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3974: else
3975: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3976: ij=1;/* To be checked else nbcode[0][0] wrong */
3977: for(j=3; j <=ncovmodel; j++) {
3978: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
3979: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3980: ij++;
3981: }
3982: else
3983: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3984: }
3985: fprintf(ficgp,")/(1");
3986:
3987: for(k1=1; k1 <=nlstate; k1++){
3988: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3989: ij=1;
3990: for(j=3; j <=ncovmodel; j++){
3991: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3992: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3993: ij++;
3994: }
3995: else
3996: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3997: }
3998: fprintf(ficgp,")");
3999: }
4000: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4001: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4002: i=i+ncovmodel;
4003: }
4004: } /* end k */
4005: } /* end k2 */
4006: } /* end jk */
4007: } /* end ng */
4008: fflush(ficgp);
4009: } /* end gnuplot */
4010:
4011:
4012: /*************** Moving average **************/
4013: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4014:
4015: int i, cpt, cptcod;
4016: int modcovmax =1;
4017: int mobilavrange, mob;
4018: double age;
4019:
4020: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4021: a covariate has 2 modalities */
4022: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4023:
4024: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4025: if(mobilav==1) mobilavrange=5; /* default */
4026: else mobilavrange=mobilav;
4027: for (age=bage; age<=fage; age++)
4028: for (i=1; i<=nlstate;i++)
4029: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4030: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4031: /* We keep the original values on the extreme ages bage, fage and for
4032: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4033: we use a 5 terms etc. until the borders are no more concerned.
4034: */
4035: for (mob=3;mob <=mobilavrange;mob=mob+2){
4036: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4037: for (i=1; i<=nlstate;i++){
4038: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4039: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4040: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4041: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4042: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4043: }
4044: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4045: }
4046: }
4047: }/* end age */
4048: }/* end mob */
4049: }else return -1;
4050: return 0;
4051: }/* End movingaverage */
4052:
4053:
4054: /************** Forecasting ******************/
4055: 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){
4056: /* proj1, year, month, day of starting projection
4057: agemin, agemax range of age
4058: dateprev1 dateprev2 range of dates during which prevalence is computed
4059: anproj2 year of en of projection (same day and month as proj1).
4060: */
4061: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4062: int *popage;
4063: double agec; /* generic age */
4064: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4065: double *popeffectif,*popcount;
4066: double ***p3mat;
4067: double ***mobaverage;
4068: char fileresf[FILENAMELENGTH];
4069:
4070: agelim=AGESUP;
4071: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4072:
4073: strcpy(fileresf,"f");
4074: strcat(fileresf,fileres);
4075: if((ficresf=fopen(fileresf,"w"))==NULL) {
4076: printf("Problem with forecast resultfile: %s\n", fileresf);
4077: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4078: }
4079: printf("Computing forecasting: result on file '%s' \n", fileresf);
4080: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4081:
4082: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4083:
4084: if (mobilav!=0) {
4085: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4086: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4087: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4088: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4089: }
4090: }
4091:
4092: stepsize=(int) (stepm+YEARM-1)/YEARM;
4093: if (stepm<=12) stepsize=1;
4094: if(estepm < stepm){
4095: printf ("Problem %d lower than %d\n",estepm, stepm);
4096: }
4097: else hstepm=estepm;
4098:
4099: hstepm=hstepm/stepm;
4100: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4101: fractional in yp1 */
4102: anprojmean=yp;
4103: yp2=modf((yp1*12),&yp);
4104: mprojmean=yp;
4105: yp1=modf((yp2*30.5),&yp);
4106: jprojmean=yp;
4107: if(jprojmean==0) jprojmean=1;
4108: if(mprojmean==0) jprojmean=1;
4109:
4110: i1=cptcoveff;
4111: if (cptcovn < 1){i1=1;}
4112:
4113: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4114:
4115: fprintf(ficresf,"#****** Routine prevforecast **\n");
4116:
4117: /* if (h==(int)(YEARM*yearp)){ */
4118: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4119: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4120: k=k+1;
4121: fprintf(ficresf,"\n#******");
4122: for(j=1;j<=cptcoveff;j++) {
4123: 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]]);
4124: }
4125: fprintf(ficresf,"******\n");
4126: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4127: for(j=1; j<=nlstate+ndeath;j++){
4128: for(i=1; i<=nlstate;i++)
4129: fprintf(ficresf," p%d%d",i,j);
4130: fprintf(ficresf," p.%d",j);
4131: }
4132: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4133: fprintf(ficresf,"\n");
4134: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4135:
4136: for (agec=fage; agec>=(ageminpar-1); agec--){
4137: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4138: nhstepm = nhstepm/hstepm;
4139: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4140: oldm=oldms;savm=savms;
4141: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4142:
4143: for (h=0; h<=nhstepm; h++){
4144: if (h*hstepm/YEARM*stepm ==yearp) {
4145: fprintf(ficresf,"\n");
4146: for(j=1;j<=cptcoveff;j++)
4147: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4148: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4149: }
4150: for(j=1; j<=nlstate+ndeath;j++) {
4151: ppij=0.;
4152: for(i=1; i<=nlstate;i++) {
4153: if (mobilav==1)
4154: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4155: else {
4156: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4157: }
4158: if (h*hstepm/YEARM*stepm== yearp) {
4159: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4160: }
4161: } /* end i */
4162: if (h*hstepm/YEARM*stepm==yearp) {
4163: fprintf(ficresf," %.3f", ppij);
4164: }
4165: }/* end j */
4166: } /* end h */
4167: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4168: } /* end agec */
4169: } /* end yearp */
4170: } /* end cptcod */
4171: } /* end cptcov */
4172:
4173: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4174:
4175: fclose(ficresf);
4176: }
4177:
4178: /************** Forecasting *****not tested NB*************/
4179: 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){
4180:
4181: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4182: int *popage;
4183: double calagedatem, agelim, kk1, kk2;
4184: double *popeffectif,*popcount;
4185: double ***p3mat,***tabpop,***tabpopprev;
4186: double ***mobaverage;
4187: char filerespop[FILENAMELENGTH];
4188:
4189: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4190: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4191: agelim=AGESUP;
4192: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4193:
4194: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4195:
4196:
4197: strcpy(filerespop,"pop");
4198: strcat(filerespop,fileres);
4199: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4200: printf("Problem with forecast resultfile: %s\n", filerespop);
4201: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4202: }
4203: printf("Computing forecasting: result on file '%s' \n", filerespop);
4204: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4205:
4206: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4207:
4208: if (mobilav!=0) {
4209: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4210: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4211: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4212: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4213: }
4214: }
4215:
4216: stepsize=(int) (stepm+YEARM-1)/YEARM;
4217: if (stepm<=12) stepsize=1;
4218:
4219: agelim=AGESUP;
4220:
4221: hstepm=1;
4222: hstepm=hstepm/stepm;
4223:
4224: if (popforecast==1) {
4225: if((ficpop=fopen(popfile,"r"))==NULL) {
4226: printf("Problem with population file : %s\n",popfile);exit(0);
4227: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4228: }
4229: popage=ivector(0,AGESUP);
4230: popeffectif=vector(0,AGESUP);
4231: popcount=vector(0,AGESUP);
4232:
4233: i=1;
4234: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4235:
4236: imx=i;
4237: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4238: }
4239:
4240: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4241: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4242: k=k+1;
4243: fprintf(ficrespop,"\n#******");
4244: for(j=1;j<=cptcoveff;j++) {
4245: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4246: }
4247: fprintf(ficrespop,"******\n");
4248: fprintf(ficrespop,"# Age");
4249: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4250: if (popforecast==1) fprintf(ficrespop," [Population]");
4251:
4252: for (cpt=0; cpt<=0;cpt++) {
4253: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4254:
4255: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4256: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4257: nhstepm = nhstepm/hstepm;
4258:
4259: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4260: oldm=oldms;savm=savms;
4261: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4262:
4263: for (h=0; h<=nhstepm; h++){
4264: if (h==(int) (calagedatem+YEARM*cpt)) {
4265: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4266: }
4267: for(j=1; j<=nlstate+ndeath;j++) {
4268: kk1=0.;kk2=0;
4269: for(i=1; i<=nlstate;i++) {
4270: if (mobilav==1)
4271: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4272: else {
4273: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4274: }
4275: }
4276: if (h==(int)(calagedatem+12*cpt)){
4277: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4278: /*fprintf(ficrespop," %.3f", kk1);
4279: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4280: }
4281: }
4282: for(i=1; i<=nlstate;i++){
4283: kk1=0.;
4284: for(j=1; j<=nlstate;j++){
4285: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4286: }
4287: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4288: }
4289:
4290: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4291: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4292: }
4293: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4294: }
4295: }
4296:
4297: /******/
4298:
4299: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4300: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4301: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4302: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4303: nhstepm = nhstepm/hstepm;
4304:
4305: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4306: oldm=oldms;savm=savms;
4307: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4308: for (h=0; h<=nhstepm; h++){
4309: if (h==(int) (calagedatem+YEARM*cpt)) {
4310: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4311: }
4312: for(j=1; j<=nlstate+ndeath;j++) {
4313: kk1=0.;kk2=0;
4314: for(i=1; i<=nlstate;i++) {
4315: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4316: }
4317: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4318: }
4319: }
4320: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4321: }
4322: }
4323: }
4324: }
4325:
4326: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4327:
4328: if (popforecast==1) {
4329: free_ivector(popage,0,AGESUP);
4330: free_vector(popeffectif,0,AGESUP);
4331: free_vector(popcount,0,AGESUP);
4332: }
4333: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4334: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4335: fclose(ficrespop);
4336: } /* End of popforecast */
4337:
4338: int fileappend(FILE *fichier, char *optionfich)
4339: {
4340: if((fichier=fopen(optionfich,"a"))==NULL) {
4341: printf("Problem with file: %s\n", optionfich);
4342: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4343: return (0);
4344: }
4345: fflush(fichier);
4346: return (1);
4347: }
4348:
4349:
4350: /**************** function prwizard **********************/
4351: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4352: {
4353:
4354: /* Wizard to print covariance matrix template */
4355:
4356: char ca[32], cb[32], cc[32];
4357: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4358: int numlinepar;
4359:
4360: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4361: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
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: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4368: printf("%1d%1d",i,j);
4369: fprintf(ficparo,"%1d%1d",i,j);
4370: for(k=1; k<=ncovmodel;k++){
4371: /* printf(" %lf",param[i][j][k]); */
4372: /* fprintf(ficparo," %lf",param[i][j][k]); */
4373: printf(" 0.");
4374: fprintf(ficparo," 0.");
4375: }
4376: printf("\n");
4377: fprintf(ficparo,"\n");
4378: }
4379: }
4380: printf("# Scales (for hessian or gradient estimation)\n");
4381: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4382: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4383: for(i=1; i <=nlstate; i++){
4384: jj=0;
4385: for(j=1; j <=nlstate+ndeath; j++){
4386: if(j==i) continue;
4387: jj++;
4388: fprintf(ficparo,"%1d%1d",i,j);
4389: printf("%1d%1d",i,j);
4390: fflush(stdout);
4391: for(k=1; k<=ncovmodel;k++){
4392: /* printf(" %le",delti3[i][j][k]); */
4393: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4394: printf(" 0.");
4395: fprintf(ficparo," 0.");
4396: }
4397: numlinepar++;
4398: printf("\n");
4399: fprintf(ficparo,"\n");
4400: }
4401: }
4402: printf("# Covariance matrix\n");
4403: /* # 121 Var(a12)\n\ */
4404: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4405: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4406: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4407: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4408: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4409: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4410: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4411: fflush(stdout);
4412: fprintf(ficparo,"# Covariance matrix\n");
4413: /* # 121 Var(a12)\n\ */
4414: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4415: /* # ...\n\ */
4416: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4417:
4418: for(itimes=1;itimes<=2;itimes++){
4419: jj=0;
4420: for(i=1; i <=nlstate; i++){
4421: for(j=1; j <=nlstate+ndeath; j++){
4422: if(j==i) continue;
4423: for(k=1; k<=ncovmodel;k++){
4424: jj++;
4425: ca[0]= k+'a'-1;ca[1]='\0';
4426: if(itimes==1){
4427: printf("#%1d%1d%d",i,j,k);
4428: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4429: }else{
4430: printf("%1d%1d%d",i,j,k);
4431: fprintf(ficparo,"%1d%1d%d",i,j,k);
4432: /* printf(" %.5le",matcov[i][j]); */
4433: }
4434: ll=0;
4435: for(li=1;li <=nlstate; li++){
4436: for(lj=1;lj <=nlstate+ndeath; lj++){
4437: if(lj==li) continue;
4438: for(lk=1;lk<=ncovmodel;lk++){
4439: ll++;
4440: if(ll<=jj){
4441: cb[0]= lk +'a'-1;cb[1]='\0';
4442: if(ll<jj){
4443: if(itimes==1){
4444: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4445: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4446: }else{
4447: printf(" 0.");
4448: fprintf(ficparo," 0.");
4449: }
4450: }else{
4451: if(itimes==1){
4452: printf(" Var(%s%1d%1d)",ca,i,j);
4453: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4454: }else{
4455: printf(" 0.");
4456: fprintf(ficparo," 0.");
4457: }
4458: }
4459: }
4460: } /* end lk */
4461: } /* end lj */
4462: } /* end li */
4463: printf("\n");
4464: fprintf(ficparo,"\n");
4465: numlinepar++;
4466: } /* end k*/
4467: } /*end j */
4468: } /* end i */
4469: } /* end itimes */
4470:
4471: } /* end of prwizard */
4472: /******************* Gompertz Likelihood ******************************/
4473: double gompertz(double x[])
4474: {
4475: double A,B,L=0.0,sump=0.,num=0.;
4476: int i,n=0; /* n is the size of the sample */
4477:
4478: for (i=0;i<=imx-1 ; i++) {
4479: sump=sump+weight[i];
4480: /* sump=sump+1;*/
4481: num=num+1;
4482: }
4483:
4484:
4485: /* for (i=0; i<=imx; i++)
4486: 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]);*/
4487:
4488: for (i=1;i<=imx ; i++)
4489: {
4490: if (cens[i] == 1 && wav[i]>1)
4491: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4492:
4493: if (cens[i] == 0 && wav[i]>1)
4494: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4495: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4496:
4497: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4498: if (wav[i] > 1 ) { /* ??? */
4499: L=L+A*weight[i];
4500: /* 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]);*/
4501: }
4502: }
4503:
4504: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4505:
4506: return -2*L*num/sump;
4507: }
4508:
4509: #ifdef GSL
4510: /******************* Gompertz_f Likelihood ******************************/
4511: double gompertz_f(const gsl_vector *v, void *params)
4512: {
4513: double A,B,LL=0.0,sump=0.,num=0.;
4514: double *x= (double *) v->data;
4515: int i,n=0; /* n is the size of the sample */
4516:
4517: for (i=0;i<=imx-1 ; i++) {
4518: sump=sump+weight[i];
4519: /* sump=sump+1;*/
4520: num=num+1;
4521: }
4522:
4523:
4524: /* for (i=0; i<=imx; i++)
4525: 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]);*/
4526: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4527: for (i=1;i<=imx ; i++)
4528: {
4529: if (cens[i] == 1 && wav[i]>1)
4530: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4531:
4532: if (cens[i] == 0 && wav[i]>1)
4533: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4534: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4535:
4536: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4537: if (wav[i] > 1 ) { /* ??? */
4538: LL=LL+A*weight[i];
4539: /* 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]);*/
4540: }
4541: }
4542:
4543: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4544: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4545:
4546: return -2*LL*num/sump;
4547: }
4548: #endif
4549:
4550: /******************* Printing html file ***********/
4551: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4552: int lastpass, int stepm, int weightopt, char model[],\
4553: int imx, double p[],double **matcov,double agemortsup){
4554: int i,k;
4555:
4556: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4557: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4558: for (i=1;i<=2;i++)
4559: 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]));
4560: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4561: fprintf(fichtm,"</ul>");
4562:
4563: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4564:
4565: 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>");
4566:
4567: for (k=agegomp;k<(agemortsup-2);k++)
4568: 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]);
4569:
4570:
4571: fflush(fichtm);
4572: }
4573:
4574: /******************* Gnuplot file **************/
4575: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4576:
4577: char dirfileres[132],optfileres[132];
4578: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4579: int ng;
4580:
4581:
4582: /*#ifdef windows */
4583: fprintf(ficgp,"cd \"%s\" \n",pathc);
4584: /*#endif */
4585:
4586:
4587: strcpy(dirfileres,optionfilefiname);
4588: strcpy(optfileres,"vpl");
4589: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4590: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4591: fprintf(ficgp, "set ter png small\n set log y\n");
4592: fprintf(ficgp, "set size 0.65,0.65\n");
4593: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4594:
4595: }
4596:
4597: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4598: {
4599:
4600: /*-------- data file ----------*/
4601: FILE *fic;
4602: char dummy[]=" ";
4603: int i, j, n;
4604: int linei, month, year,iout;
4605: char line[MAXLINE], linetmp[MAXLINE];
4606: char stra[80], strb[80];
4607: char *stratrunc;
4608: int lstra;
4609:
4610:
4611: if((fic=fopen(datafile,"r"))==NULL) {
4612: printf("Problem while opening datafile: %s\n", datafile);return 1;
4613: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4614: }
4615:
4616: i=1;
4617: linei=0;
4618: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4619: linei=linei+1;
4620: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4621: if(line[j] == '\t')
4622: line[j] = ' ';
4623: }
4624: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4625: ;
4626: };
4627: line[j+1]=0; /* Trims blanks at end of line */
4628: if(line[0]=='#'){
4629: fprintf(ficlog,"Comment line\n%s\n",line);
4630: printf("Comment line\n%s\n",line);
4631: continue;
4632: }
4633: trimbb(linetmp,line); /* Trims multiple blanks in line */
4634: for (j=0; line[j]!='\0';j++){
4635: line[j]=linetmp[j];
4636: }
4637:
4638:
4639: for (j=maxwav;j>=1;j--){
4640: cutv(stra, strb, line, ' ');
4641: if(strb[0]=='.') { /* Missing status */
4642: lval=-1;
4643: }else{
4644: errno=0;
4645: lval=strtol(strb,&endptr,10);
4646: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4647: if( strb[0]=='\0' || (*endptr != '\0')){
4648: 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);
4649: 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);
4650: return 1;
4651: }
4652: }
4653: s[j][i]=lval;
4654:
4655: strcpy(line,stra);
4656: cutv(stra, strb,line,' ');
4657: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4658: }
4659: else if(iout=sscanf(strb,"%s.") != 0){
4660: month=99;
4661: year=9999;
4662: }else{
4663: 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);
4664: 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);
4665: return 1;
4666: }
4667: anint[j][i]= (double) year;
4668: mint[j][i]= (double)month;
4669: strcpy(line,stra);
4670: } /* ENd Waves */
4671:
4672: cutv(stra, strb,line,' ');
4673: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4674: }
4675: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4676: month=99;
4677: year=9999;
4678: }else{
4679: 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);
4680: 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);
4681: return 1;
4682: }
4683: andc[i]=(double) year;
4684: moisdc[i]=(double) month;
4685: strcpy(line,stra);
4686:
4687: cutv(stra, strb,line,' ');
4688: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4689: }
4690: else if(iout=sscanf(strb,"%s.") != 0){
4691: month=99;
4692: year=9999;
4693: }else{
4694: 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);
4695: 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);
4696: return 1;
4697: }
4698: if (year==9999) {
4699: 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);
4700: 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);
4701: return 1;
4702:
4703: }
4704: annais[i]=(double)(year);
4705: moisnais[i]=(double)(month);
4706: strcpy(line,stra);
4707:
4708: cutv(stra, strb,line,' ');
4709: errno=0;
4710: dval=strtod(strb,&endptr);
4711: if( strb[0]=='\0' || (*endptr != '\0')){
4712: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4713: 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);
4714: fflush(ficlog);
4715: return 1;
4716: }
4717: weight[i]=dval;
4718: strcpy(line,stra);
4719:
4720: for (j=ncovcol;j>=1;j--){
4721: cutv(stra, strb,line,' ');
4722: if(strb[0]=='.') { /* Missing status */
4723: lval=-1;
4724: }else{
4725: errno=0;
4726: lval=strtol(strb,&endptr,10);
4727: if( strb[0]=='\0' || (*endptr != '\0')){
4728: 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);
4729: 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);
4730: return 1;
4731: }
4732: }
4733: if(lval <-1 || lval >1){
4734: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4735: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4736: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4737: For example, for multinomial values like 1, 2 and 3,\n \
4738: build V1=0 V2=0 for the reference value (1),\n \
4739: V1=1 V2=0 for (2) \n \
4740: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4741: output of IMaCh is often meaningless.\n \
4742: Exiting.\n",lval,linei, i,line,j);
4743: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4744: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4745: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4746: For example, for multinomial values like 1, 2 and 3,\n \
4747: build V1=0 V2=0 for the reference value (1),\n \
4748: V1=1 V2=0 for (2) \n \
4749: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4750: output of IMaCh is often meaningless.\n \
4751: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4752: return 1;
4753: }
4754: covar[j][i]=(double)(lval);
4755: strcpy(line,stra);
4756: }
4757: lstra=strlen(stra);
4758:
4759: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4760: stratrunc = &(stra[lstra-9]);
4761: num[i]=atol(stratrunc);
4762: }
4763: else
4764: num[i]=atol(stra);
4765: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4766: 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;}*/
4767:
4768: i=i+1;
4769: } /* End loop reading data */
4770:
4771: *imax=i-1; /* Number of individuals */
4772: fclose(fic);
4773:
4774: return (0);
4775: endread:
4776: printf("Exiting readdata: ");
4777: fclose(fic);
4778: return (1);
4779:
4780:
4781:
4782: }
4783:
4784: int decodemodel ( char model[], int lastobs)
4785: {
4786: int i, j, k;
4787: int i1, j1, k1, k2;
4788: char modelsav[80];
4789: char stra[80], strb[80], strc[80], strd[80],stre[80];
4790:
4791: if (strlen(model) >1){ /* If there is at least 1 covariate */
4792: j=0, j1=0, k1=1, k2=1;
4793: j=nbocc(model,'+'); /* j=Number of '+' */
4794: j1=nbocc(model,'*'); /* j1=Number of '*' */
4795: cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
4796: but the covariates which are product must be computed and stored. */
4797: cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
4798:
4799: strcpy(modelsav,model);
4800: if (strstr(model,"AGE") !=0){
4801: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4802: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
4803: return 1;
4804: }
4805: if (strstr(model,"v") !=0){
4806: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4807: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4808: return 1;
4809: }
4810:
4811: /* This loop fills the array Tvar from the string 'model'.*/
4812: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
4813: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
4814: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
4815: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
4816: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
4817: /* k=1 Tvar[1]=2 (from V2) */
4818: /* k=5 Tvar[5] */
4819: /* for (k=1; k<=cptcovn;k++) { */
4820: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
4821: /* } */
4822: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4823: for(k=cptcovn; k>=1;k--){
4824: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
4825: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
4826: */
4827: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4828: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4829: /*scanf("%d",i);*/
4830: if (strchr(strb,'*')) { /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
4831: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
4832: if (strcmp(strc,"age")==0) { /* Vn*age */
4833: cptcovprod--;
4834: cutv(strb,stre,strd,'V'); /* stre="V3" */
4835: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
4836: cptcovage++; /* Sums the number of covariates which include age as a product */
4837: Tage[cptcovage]=k; /* Tage[1] = 4 */
4838: /*printf("stre=%s ", stre);*/
4839: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
4840: cptcovprod--;
4841: cutv(strb,stre,strc,'V');
4842: Tvar[k]=atoi(stre);
4843: cptcovage++;
4844: Tage[cptcovage]=k;
4845: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
4846: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
4847: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
4848: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
4849: because this model-covariate is a construction we invent a new column
4850: ncovcol + k1
4851: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
4852: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
4853: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4854: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
4855: Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
4856: Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
4857: Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
4858: Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
4859: for (i=1; i<=lastobs;i++){
4860: /* Computes the new covariate which is a product of
4861: covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
4862: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
4863: }
4864: k1++;
4865: k2=k2+2;
4866: } /* End age is not in the model */
4867: } /* End if model includes a product */
4868: else { /* no more sum */
4869: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4870: /* scanf("%d",i);*/
4871: cutv(strd,strc,strb,'V');
4872: Tvar[k]=atoi(strc);
4873: }
4874: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
4875: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4876: scanf("%d",i);*/
4877: } /* end of loop + */
4878: } /* end model */
4879:
4880: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4881: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4882:
4883: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4884: printf("cptcovprod=%d ", cptcovprod);
4885: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4886:
4887: scanf("%d ",i);*/
4888:
4889:
4890: return (0); /* with covar[new additional covariate if product] and Tage if age */
4891: endread:
4892: printf("Exiting decodemodel: ");
4893: return (1);
4894: }
4895:
4896: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
4897: {
4898: int i, m;
4899:
4900: for (i=1; i<=imx; i++) {
4901: for(m=2; (m<= maxwav); m++) {
4902: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4903: anint[m][i]=9999;
4904: s[m][i]=-1;
4905: }
4906: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4907: *nberr++;
4908: 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);
4909: 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);
4910: s[m][i]=-1;
4911: }
4912: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4913: *nberr++;
4914: 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]);
4915: 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]);
4916: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4917: }
4918: }
4919: }
4920:
4921: for (i=1; i<=imx; i++) {
4922: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4923: for(m=firstpass; (m<= lastpass); m++){
4924: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4925: if (s[m][i] >= nlstate+1) {
4926: if(agedc[i]>0)
4927: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4928: agev[m][i]=agedc[i];
4929: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4930: else {
4931: if ((int)andc[i]!=9999){
4932: nbwarn++;
4933: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4934: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4935: agev[m][i]=-1;
4936: }
4937: }
4938: }
4939: else if(s[m][i] !=9){ /* Standard case, age in fractional
4940: years but with the precision of a month */
4941: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4942: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4943: agev[m][i]=1;
4944: else if(agev[m][i] < *agemin){
4945: *agemin=agev[m][i];
4946: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
4947: }
4948: else if(agev[m][i] >*agemax){
4949: *agemax=agev[m][i];
4950: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
4951: }
4952: /*agev[m][i]=anint[m][i]-annais[i];*/
4953: /* agev[m][i] = age[i]+2*m;*/
4954: }
4955: else { /* =9 */
4956: agev[m][i]=1;
4957: s[m][i]=-1;
4958: }
4959: }
4960: else /*= 0 Unknown */
4961: agev[m][i]=1;
4962: }
4963:
4964: }
4965: for (i=1; i<=imx; i++) {
4966: for(m=firstpass; (m<=lastpass); m++){
4967: if (s[m][i] > (nlstate+ndeath)) {
4968: *nberr++;
4969: 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);
4970: 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);
4971: return 1;
4972: }
4973: }
4974: }
4975:
4976: /*for (i=1; i<=imx; i++){
4977: for (m=firstpass; (m<lastpass); m++){
4978: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4979: }
4980:
4981: }*/
4982:
4983:
4984: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
4985: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
4986:
4987: return (0);
4988: endread:
4989: printf("Exiting calandcheckages: ");
4990: return (1);
4991: }
4992:
4993:
4994: /***********************************************/
4995: /**************** Main Program *****************/
4996: /***********************************************/
4997:
4998: int main(int argc, char *argv[])
4999: {
5000: #ifdef GSL
5001: const gsl_multimin_fminimizer_type *T;
5002: size_t iteri = 0, it;
5003: int rval = GSL_CONTINUE;
5004: int status = GSL_SUCCESS;
5005: double ssval;
5006: #endif
5007: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5008: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5009: int linei, month, year,iout;
5010: int jj, ll, li, lj, lk, imk;
5011: int numlinepar=0; /* Current linenumber of parameter file */
5012: int itimes;
5013: int NDIM=2;
5014: int vpopbased=0;
5015:
5016: char ca[32], cb[32], cc[32];
5017: /* FILE *fichtm; *//* Html File */
5018: /* FILE *ficgp;*/ /*Gnuplot File */
5019: struct stat info;
5020: double agedeb, agefin,hf;
5021: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5022:
5023: double fret;
5024: double **xi,tmp,delta;
5025:
5026: double dum; /* Dummy variable */
5027: double ***p3mat;
5028: double ***mobaverage;
5029: int *indx;
5030: char line[MAXLINE], linepar[MAXLINE];
5031: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5032: char pathr[MAXLINE], pathimach[MAXLINE];
5033: char **bp, *tok, *val; /* pathtot */
5034: int firstobs=1, lastobs=10;
5035: int sdeb, sfin; /* Status at beginning and end */
5036: int c, h , cpt,l;
5037: int ju,jl, mi;
5038: int i1,j1, jk,aa,bb, stepsize, ij;
5039: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5040: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5041: int mobilav=0,popforecast=0;
5042: int hstepm, nhstepm;
5043: int agemortsup;
5044: float sumlpop=0.;
5045: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5046: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5047:
5048: double bage, fage, age, agelim, agebase;
5049: double ftolpl=FTOL;
5050: double **prlim;
5051: double ***param; /* Matrix of parameters */
5052: double *p;
5053: double **matcov; /* Matrix of covariance */
5054: double ***delti3; /* Scale */
5055: double *delti; /* Scale */
5056: double ***eij, ***vareij;
5057: double **varpl; /* Variances of prevalence limits by age */
5058: double *epj, vepp;
5059: double kk1, kk2;
5060: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5061: double **ximort;
5062: char *alph[]={"a","a","b","c","d","e"}, str[4];
5063: int *dcwave;
5064:
5065: char z[1]="c", occ;
5066:
5067: /*char *strt;*/
5068: char strtend[80];
5069:
5070: long total_usecs;
5071:
5072: /* setlocale (LC_ALL, ""); */
5073: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5074: /* textdomain (PACKAGE); */
5075: /* setlocale (LC_CTYPE, ""); */
5076: /* setlocale (LC_MESSAGES, ""); */
5077:
5078: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5079: (void) gettimeofday(&start_time,&tzp);
5080: curr_time=start_time;
5081: tm = *localtime(&start_time.tv_sec);
5082: tmg = *gmtime(&start_time.tv_sec);
5083: strcpy(strstart,asctime(&tm));
5084:
5085: /* printf("Localtime (at start)=%s",strstart); */
5086: /* tp.tv_sec = tp.tv_sec +86400; */
5087: /* tm = *localtime(&start_time.tv_sec); */
5088: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5089: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5090: /* tmg.tm_hour=tmg.tm_hour + 1; */
5091: /* tp.tv_sec = mktime(&tmg); */
5092: /* strt=asctime(&tmg); */
5093: /* printf("Time(after) =%s",strstart); */
5094: /* (void) time (&time_value);
5095: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5096: * tm = *localtime(&time_value);
5097: * strstart=asctime(&tm);
5098: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5099: */
5100:
5101: nberr=0; /* Number of errors and warnings */
5102: nbwarn=0;
5103: getcwd(pathcd, size);
5104:
5105: printf("\n%s\n%s",version,fullversion);
5106: if(argc <=1){
5107: printf("\nEnter the parameter file name: ");
5108: fgets(pathr,FILENAMELENGTH,stdin);
5109: i=strlen(pathr);
5110: if(pathr[i-1]=='\n')
5111: pathr[i-1]='\0';
5112: for (tok = pathr; tok != NULL; ){
5113: printf("Pathr |%s|\n",pathr);
5114: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5115: printf("val= |%s| pathr=%s\n",val,pathr);
5116: strcpy (pathtot, val);
5117: if(pathr[0] == '\0') break; /* Dirty */
5118: }
5119: }
5120: else{
5121: strcpy(pathtot,argv[1]);
5122: }
5123: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5124: /*cygwin_split_path(pathtot,path,optionfile);
5125: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5126: /* cutv(path,optionfile,pathtot,'\\');*/
5127:
5128: /* Split argv[0], imach program to get pathimach */
5129: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5130: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5131: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5132: /* strcpy(pathimach,argv[0]); */
5133: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5134: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5135: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5136: chdir(path); /* Can be a relative path */
5137: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5138: printf("Current directory %s!\n",pathcd);
5139: strcpy(command,"mkdir ");
5140: strcat(command,optionfilefiname);
5141: if((outcmd=system(command)) != 0){
5142: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5143: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5144: /* fclose(ficlog); */
5145: /* exit(1); */
5146: }
5147: /* if((imk=mkdir(optionfilefiname))<0){ */
5148: /* perror("mkdir"); */
5149: /* } */
5150:
5151: /*-------- arguments in the command line --------*/
5152:
5153: /* Log file */
5154: strcat(filelog, optionfilefiname);
5155: strcat(filelog,".log"); /* */
5156: if((ficlog=fopen(filelog,"w"))==NULL) {
5157: printf("Problem with logfile %s\n",filelog);
5158: goto end;
5159: }
5160: fprintf(ficlog,"Log filename:%s\n",filelog);
5161: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5162: fprintf(ficlog,"\nEnter the parameter file name: \n");
5163: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5164: path=%s \n\
5165: optionfile=%s\n\
5166: optionfilext=%s\n\
5167: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5168:
5169: printf("Local time (at start):%s",strstart);
5170: fprintf(ficlog,"Local time (at start): %s",strstart);
5171: fflush(ficlog);
5172: /* (void) gettimeofday(&curr_time,&tzp); */
5173: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5174:
5175: /* */
5176: strcpy(fileres,"r");
5177: strcat(fileres, optionfilefiname);
5178: strcat(fileres,".txt"); /* Other files have txt extension */
5179:
5180: /*---------arguments file --------*/
5181:
5182: if((ficpar=fopen(optionfile,"r"))==NULL) {
5183: printf("Problem with optionfile %s\n",optionfile);
5184: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5185: fflush(ficlog);
5186: goto end;
5187: }
5188:
5189:
5190:
5191: strcpy(filereso,"o");
5192: strcat(filereso,fileres);
5193: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5194: printf("Problem with Output resultfile: %s\n", filereso);
5195: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5196: fflush(ficlog);
5197: goto end;
5198: }
5199:
5200: /* Reads comments: lines beginning with '#' */
5201: numlinepar=0;
5202: while((c=getc(ficpar))=='#' && c!= EOF){
5203: ungetc(c,ficpar);
5204: fgets(line, MAXLINE, ficpar);
5205: numlinepar++;
5206: fputs(line,stdout);
5207: fputs(line,ficparo);
5208: fputs(line,ficlog);
5209: }
5210: ungetc(c,ficpar);
5211:
5212: 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);
5213: numlinepar++;
5214: 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);
5215: 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);
5216: 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);
5217: fflush(ficlog);
5218: while((c=getc(ficpar))=='#' && c!= EOF){
5219: ungetc(c,ficpar);
5220: fgets(line, MAXLINE, ficpar);
5221: numlinepar++;
5222: fputs(line, stdout);
5223: //puts(line);
5224: fputs(line,ficparo);
5225: fputs(line,ficlog);
5226: }
5227: ungetc(c,ficpar);
5228:
5229:
5230: covar=matrix(0,NCOVMAX,1,n);
5231: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5232: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5233: v1+v2*age+v2*v3 makes cptcovn = 3
5234: */
5235: if (strlen(model)>1)
5236: cptcovn=nbocc(model,'+')+1;
5237: /* ncovprod */
5238: ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5239: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5240: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5241: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5242: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5243: 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);
5244: 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);
5245: fflush(stdout);
5246: fclose (ficlog);
5247: goto end;
5248: }
5249: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5250: delti=delti3[1][1];
5251: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5252: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5253: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5254: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5255: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5256: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5257: fclose (ficparo);
5258: fclose (ficlog);
5259: goto end;
5260: exit(0);
5261: }
5262: else if(mle==-3) {
5263: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5264: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5265: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5266: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5267: matcov=matrix(1,npar,1,npar);
5268: }
5269: else{
5270: /* Read guess parameters */
5271: /* Reads comments: lines beginning with '#' */
5272: while((c=getc(ficpar))=='#' && c!= EOF){
5273: ungetc(c,ficpar);
5274: fgets(line, MAXLINE, ficpar);
5275: numlinepar++;
5276: fputs(line,stdout);
5277: fputs(line,ficparo);
5278: fputs(line,ficlog);
5279: }
5280: ungetc(c,ficpar);
5281:
5282: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5283: for(i=1; i <=nlstate; i++){
5284: j=0;
5285: for(jj=1; jj <=nlstate+ndeath; jj++){
5286: if(jj==i) continue;
5287: j++;
5288: fscanf(ficpar,"%1d%1d",&i1,&j1);
5289: if ((i1 != i) && (j1 != j)){
5290: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5291: It might be a problem of design; if ncovcol and the model are correct\n \
5292: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5293: exit(1);
5294: }
5295: fprintf(ficparo,"%1d%1d",i1,j1);
5296: if(mle==1)
5297: printf("%1d%1d",i,j);
5298: fprintf(ficlog,"%1d%1d",i,j);
5299: for(k=1; k<=ncovmodel;k++){
5300: fscanf(ficpar," %lf",¶m[i][j][k]);
5301: if(mle==1){
5302: printf(" %lf",param[i][j][k]);
5303: fprintf(ficlog," %lf",param[i][j][k]);
5304: }
5305: else
5306: fprintf(ficlog," %lf",param[i][j][k]);
5307: fprintf(ficparo," %lf",param[i][j][k]);
5308: }
5309: fscanf(ficpar,"\n");
5310: numlinepar++;
5311: if(mle==1)
5312: printf("\n");
5313: fprintf(ficlog,"\n");
5314: fprintf(ficparo,"\n");
5315: }
5316: }
5317: fflush(ficlog);
5318:
5319: p=param[1][1];
5320:
5321: /* Reads comments: lines beginning with '#' */
5322: while((c=getc(ficpar))=='#' && c!= EOF){
5323: ungetc(c,ficpar);
5324: fgets(line, MAXLINE, ficpar);
5325: numlinepar++;
5326: fputs(line,stdout);
5327: fputs(line,ficparo);
5328: fputs(line,ficlog);
5329: }
5330: ungetc(c,ficpar);
5331:
5332: for(i=1; i <=nlstate; i++){
5333: for(j=1; j <=nlstate+ndeath-1; j++){
5334: fscanf(ficpar,"%1d%1d",&i1,&j1);
5335: if ((i1-i)*(j1-j)!=0){
5336: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5337: exit(1);
5338: }
5339: printf("%1d%1d",i,j);
5340: fprintf(ficparo,"%1d%1d",i1,j1);
5341: fprintf(ficlog,"%1d%1d",i1,j1);
5342: for(k=1; k<=ncovmodel;k++){
5343: fscanf(ficpar,"%le",&delti3[i][j][k]);
5344: printf(" %le",delti3[i][j][k]);
5345: fprintf(ficparo," %le",delti3[i][j][k]);
5346: fprintf(ficlog," %le",delti3[i][j][k]);
5347: }
5348: fscanf(ficpar,"\n");
5349: numlinepar++;
5350: printf("\n");
5351: fprintf(ficparo,"\n");
5352: fprintf(ficlog,"\n");
5353: }
5354: }
5355: fflush(ficlog);
5356:
5357: delti=delti3[1][1];
5358:
5359:
5360: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5361:
5362: /* Reads comments: lines beginning with '#' */
5363: while((c=getc(ficpar))=='#' && c!= EOF){
5364: ungetc(c,ficpar);
5365: fgets(line, MAXLINE, ficpar);
5366: numlinepar++;
5367: fputs(line,stdout);
5368: fputs(line,ficparo);
5369: fputs(line,ficlog);
5370: }
5371: ungetc(c,ficpar);
5372:
5373: matcov=matrix(1,npar,1,npar);
5374: for(i=1; i <=npar; i++)
5375: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5376:
5377: for(i=1; i <=npar; i++){
5378: fscanf(ficpar,"%s",&str);
5379: if(mle==1)
5380: printf("%s",str);
5381: fprintf(ficlog,"%s",str);
5382: fprintf(ficparo,"%s",str);
5383: for(j=1; j <=i; j++){
5384: fscanf(ficpar," %le",&matcov[i][j]);
5385: if(mle==1){
5386: printf(" %.5le",matcov[i][j]);
5387: }
5388: fprintf(ficlog," %.5le",matcov[i][j]);
5389: fprintf(ficparo," %.5le",matcov[i][j]);
5390: }
5391: fscanf(ficpar,"\n");
5392: numlinepar++;
5393: if(mle==1)
5394: printf("\n");
5395: fprintf(ficlog,"\n");
5396: fprintf(ficparo,"\n");
5397: }
5398: for(i=1; i <=npar; i++)
5399: for(j=i+1;j<=npar;j++)
5400: matcov[i][j]=matcov[j][i];
5401:
5402: if(mle==1)
5403: printf("\n");
5404: fprintf(ficlog,"\n");
5405:
5406: fflush(ficlog);
5407:
5408: /*-------- Rewriting parameter file ----------*/
5409: strcpy(rfileres,"r"); /* "Rparameterfile */
5410: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5411: strcat(rfileres,"."); /* */
5412: strcat(rfileres,optionfilext); /* Other files have txt extension */
5413: if((ficres =fopen(rfileres,"w"))==NULL) {
5414: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5415: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5416: }
5417: fprintf(ficres,"#%s\n",version);
5418: } /* End of mle != -3 */
5419:
5420:
5421: n= lastobs;
5422: num=lvector(1,n);
5423: moisnais=vector(1,n);
5424: annais=vector(1,n);
5425: moisdc=vector(1,n);
5426: andc=vector(1,n);
5427: agedc=vector(1,n);
5428: cod=ivector(1,n);
5429: weight=vector(1,n);
5430: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5431: mint=matrix(1,maxwav,1,n);
5432: anint=matrix(1,maxwav,1,n);
5433: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5434: tab=ivector(1,NCOVMAX);
5435: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5436:
5437: /* Reads data from file datafile */
5438: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5439: goto end;
5440:
5441: /* Calculation of the number of parameters from char model */
5442: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5443: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5444: k=3 V4 Tvar[k=3]= 4 (from V4)
5445: k=2 V1 Tvar[k=2]= 1 (from V1)
5446: k=1 Tvar[1]=2 (from V2)
5447: */
5448: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5449: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5450: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5451: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5452: */
5453: /* For model-covariate k tells which data-covariate to use but
5454: because this model-covariate is a construction we invent a new column
5455: ncovcol + k1
5456: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5457: Tvar[3=V1*V4]=4+1 etc */
5458: Tprod=ivector(1,15); /* Gives the position of a product */
5459: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5460: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5461: */
5462: Tvaraff=ivector(1,15);
5463: 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
5464: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5465: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5466: Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5467: 4 covariates (3 plus signs)
5468: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5469: */
5470:
5471: if(decodemodel(model, lastobs) == 1)
5472: goto end;
5473:
5474: if((double)(lastobs-imx)/(double)imx > 1.10){
5475: nbwarn++;
5476: 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);
5477: 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);
5478: }
5479: /* if(mle==1){*/
5480: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5481: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5482: }
5483:
5484: /*-calculation of age at interview from date of interview and age at death -*/
5485: agev=matrix(1,maxwav,1,imx);
5486:
5487: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5488: goto end;
5489:
5490:
5491: agegomp=(int)agemin;
5492: free_vector(moisnais,1,n);
5493: free_vector(annais,1,n);
5494: /* free_matrix(mint,1,maxwav,1,n);
5495: free_matrix(anint,1,maxwav,1,n);*/
5496: free_vector(moisdc,1,n);
5497: free_vector(andc,1,n);
5498:
5499:
5500: wav=ivector(1,imx);
5501: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5502: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5503: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5504:
5505: /* Concatenates waves */
5506: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5507:
5508: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5509:
5510: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5511: ncodemax[1]=1;
5512: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5513:
5514: codtab=imatrix(1,100,1,10); /**< codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1)
5515: */
5516: h=0;
5517: m=pow(2,cptcoveff);
5518:
5519: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5520: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5521: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5522: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5523: h++;
5524: if (h>m)
5525: h=1;
5526: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5527: * h 1 2 3 4
5528: *______________________________
5529: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5530: * 2 2 1 1 1
5531: * 3 i=2 1 2 1 1
5532: * 4 2 2 1 1
5533: * 5 i=3 1 i=2 1 2 1
5534: * 6 2 1 2 1
5535: * 7 i=4 1 2 2 1
5536: * 8 2 2 2 1
5537: * 9 i=5 1 i=3 1 i=2 1 1
5538: * 10 2 1 1 1
5539: * 11 i=6 1 2 1 1
5540: * 12 2 2 1 1
5541: * 13 i=7 1 i=4 1 2 1
5542: * 14 2 1 2 1
5543: * 15 i=8 1 2 2 1
5544: * 16 2 2 2 1
5545: */
5546: codtab[h][k]=j;
5547: codtab[h][Tvar[k]]=j;
5548: 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]]);
5549: }
5550: }
5551: }
5552: }
5553: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5554: codtab[1][2]=1;codtab[2][2]=2; */
5555: /* for(i=1; i <=m ;i++){
5556: for(k=1; k <=cptcovn; k++){
5557: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5558: }
5559: printf("\n");
5560: }
5561: scanf("%d",i);*/
5562:
5563: /*------------ gnuplot -------------*/
5564: strcpy(optionfilegnuplot,optionfilefiname);
5565: if(mle==-3)
5566: strcat(optionfilegnuplot,"-mort");
5567: strcat(optionfilegnuplot,".gp");
5568:
5569: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5570: printf("Problem with file %s",optionfilegnuplot);
5571: }
5572: else{
5573: fprintf(ficgp,"\n# %s\n", version);
5574: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5575: //fprintf(ficgp,"set missing 'NaNq'\n");
5576: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5577: }
5578: /* fclose(ficgp);*/
5579: /*--------- index.htm --------*/
5580:
5581: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5582: if(mle==-3)
5583: strcat(optionfilehtm,"-mort");
5584: strcat(optionfilehtm,".htm");
5585: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5586: printf("Problem with %s \n",optionfilehtm);
5587: exit(0);
5588: }
5589:
5590: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5591: strcat(optionfilehtmcov,"-cov.htm");
5592: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5593: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5594: }
5595: else{
5596: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5597: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5598: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5599: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5600: }
5601:
5602: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5603: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5604: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5605: \n\
5606: <hr size=\"2\" color=\"#EC5E5E\">\
5607: <ul><li><h4>Parameter files</h4>\n\
5608: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5609: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5610: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5611: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5612: - Date and time at start: %s</ul>\n",\
5613: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5614: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5615: fileres,fileres,\
5616: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5617: fflush(fichtm);
5618:
5619: strcpy(pathr,path);
5620: strcat(pathr,optionfilefiname);
5621: chdir(optionfilefiname); /* Move to directory named optionfile */
5622:
5623: /* Calculates basic frequencies. Computes observed prevalence at single age
5624: and prints on file fileres'p'. */
5625: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5626:
5627: fprintf(fichtm,"\n");
5628: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5629: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5630: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5631: imx,agemin,agemax,jmin,jmax,jmean);
5632: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5633: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5634: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5635: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5636: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5637:
5638:
5639: /* For Powell, parameters are in a vector p[] starting at p[1]
5640: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5641: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5642:
5643: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5644:
5645: if (mle==-3){
5646: ximort=matrix(1,NDIM,1,NDIM);
5647: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5648: cens=ivector(1,n);
5649: ageexmed=vector(1,n);
5650: agecens=vector(1,n);
5651: dcwave=ivector(1,n);
5652:
5653: for (i=1; i<=imx; i++){
5654: dcwave[i]=-1;
5655: for (m=firstpass; m<=lastpass; m++)
5656: if (s[m][i]>nlstate) {
5657: dcwave[i]=m;
5658: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5659: break;
5660: }
5661: }
5662:
5663: for (i=1; i<=imx; i++) {
5664: if (wav[i]>0){
5665: ageexmed[i]=agev[mw[1][i]][i];
5666: j=wav[i];
5667: agecens[i]=1.;
5668:
5669: if (ageexmed[i]> 1 && wav[i] > 0){
5670: agecens[i]=agev[mw[j][i]][i];
5671: cens[i]= 1;
5672: }else if (ageexmed[i]< 1)
5673: cens[i]= -1;
5674: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5675: cens[i]=0 ;
5676: }
5677: else cens[i]=-1;
5678: }
5679:
5680: for (i=1;i<=NDIM;i++) {
5681: for (j=1;j<=NDIM;j++)
5682: ximort[i][j]=(i == j ? 1.0 : 0.0);
5683: }
5684:
5685: p[1]=0.0268; p[NDIM]=0.083;
5686: /*printf("%lf %lf", p[1], p[2]);*/
5687:
5688:
5689: #ifdef GSL
5690: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5691: #elsedef
5692: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5693: #endif
5694: strcpy(filerespow,"pow-mort");
5695: strcat(filerespow,fileres);
5696: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5697: printf("Problem with resultfile: %s\n", filerespow);
5698: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5699: }
5700: #ifdef GSL
5701: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5702: #elsedef
5703: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5704: #endif
5705: /* for (i=1;i<=nlstate;i++)
5706: for(j=1;j<=nlstate+ndeath;j++)
5707: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5708: */
5709: fprintf(ficrespow,"\n");
5710: #ifdef GSL
5711: /* gsl starts here */
5712: T = gsl_multimin_fminimizer_nmsimplex;
5713: gsl_multimin_fminimizer *sfm = NULL;
5714: gsl_vector *ss, *x;
5715: gsl_multimin_function minex_func;
5716:
5717: /* Initial vertex size vector */
5718: ss = gsl_vector_alloc (NDIM);
5719:
5720: if (ss == NULL){
5721: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5722: }
5723: /* Set all step sizes to 1 */
5724: gsl_vector_set_all (ss, 0.001);
5725:
5726: /* Starting point */
5727:
5728: x = gsl_vector_alloc (NDIM);
5729:
5730: if (x == NULL){
5731: gsl_vector_free(ss);
5732: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5733: }
5734:
5735: /* Initialize method and iterate */
5736: /* p[1]=0.0268; p[NDIM]=0.083; */
5737: /* gsl_vector_set(x, 0, 0.0268); */
5738: /* gsl_vector_set(x, 1, 0.083); */
5739: gsl_vector_set(x, 0, p[1]);
5740: gsl_vector_set(x, 1, p[2]);
5741:
5742: minex_func.f = &gompertz_f;
5743: minex_func.n = NDIM;
5744: minex_func.params = (void *)&p; /* ??? */
5745:
5746: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5747: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5748:
5749: printf("Iterations beginning .....\n\n");
5750: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5751:
5752: iteri=0;
5753: while (rval == GSL_CONTINUE){
5754: iteri++;
5755: status = gsl_multimin_fminimizer_iterate(sfm);
5756:
5757: if (status) printf("error: %s\n", gsl_strerror (status));
5758: fflush(0);
5759:
5760: if (status)
5761: break;
5762:
5763: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5764: ssval = gsl_multimin_fminimizer_size (sfm);
5765:
5766: if (rval == GSL_SUCCESS)
5767: printf ("converged to a local maximum at\n");
5768:
5769: printf("%5d ", iteri);
5770: for (it = 0; it < NDIM; it++){
5771: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
5772: }
5773: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
5774: }
5775:
5776: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
5777:
5778: gsl_vector_free(x); /* initial values */
5779: gsl_vector_free(ss); /* inital step size */
5780: for (it=0; it<NDIM; it++){
5781: p[it+1]=gsl_vector_get(sfm->x,it);
5782: fprintf(ficrespow," %.12lf", p[it]);
5783: }
5784: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
5785: #endif
5786: #ifdef POWELL
5787: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5788: #endif
5789: fclose(ficrespow);
5790:
5791: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5792:
5793: for(i=1; i <=NDIM; i++)
5794: for(j=i+1;j<=NDIM;j++)
5795: matcov[i][j]=matcov[j][i];
5796:
5797: printf("\nCovariance matrix\n ");
5798: for(i=1; i <=NDIM; i++) {
5799: for(j=1;j<=NDIM;j++){
5800: printf("%f ",matcov[i][j]);
5801: }
5802: printf("\n ");
5803: }
5804:
5805: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5806: for (i=1;i<=NDIM;i++)
5807: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5808:
5809: lsurv=vector(1,AGESUP);
5810: lpop=vector(1,AGESUP);
5811: tpop=vector(1,AGESUP);
5812: lsurv[agegomp]=100000;
5813:
5814: for (k=agegomp;k<=AGESUP;k++) {
5815: agemortsup=k;
5816: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5817: }
5818:
5819: for (k=agegomp;k<agemortsup;k++)
5820: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5821:
5822: for (k=agegomp;k<agemortsup;k++){
5823: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5824: sumlpop=sumlpop+lpop[k];
5825: }
5826:
5827: tpop[agegomp]=sumlpop;
5828: for (k=agegomp;k<(agemortsup-3);k++){
5829: /* tpop[k+1]=2;*/
5830: tpop[k+1]=tpop[k]-lpop[k];
5831: }
5832:
5833:
5834: printf("\nAge lx qx dx Lx Tx e(x)\n");
5835: for (k=agegomp;k<(agemortsup-2);k++)
5836: 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]);
5837:
5838:
5839: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5840: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5841:
5842: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5843: stepm, weightopt,\
5844: model,imx,p,matcov,agemortsup);
5845:
5846: free_vector(lsurv,1,AGESUP);
5847: free_vector(lpop,1,AGESUP);
5848: free_vector(tpop,1,AGESUP);
5849: #ifdef GSL
5850: free_ivector(cens,1,n);
5851: free_vector(agecens,1,n);
5852: free_ivector(dcwave,1,n);
5853: free_matrix(ximort,1,NDIM,1,NDIM);
5854: #endif
5855: } /* Endof if mle==-3 */
5856:
5857: else{ /* For mle >=1 */
5858: globpr=0;/* debug */
5859: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5860: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5861: for (k=1; k<=npar;k++)
5862: printf(" %d %8.5f",k,p[k]);
5863: printf("\n");
5864: globpr=1; /* to print the contributions */
5865: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5866: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5867: for (k=1; k<=npar;k++)
5868: printf(" %d %8.5f",k,p[k]);
5869: printf("\n");
5870: if(mle>=1){ /* Could be 1 or 2 */
5871: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5872: }
5873:
5874: /*--------- results files --------------*/
5875: 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);
5876:
5877:
5878: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5879: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5880: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5881: for(i=1,jk=1; i <=nlstate; i++){
5882: for(k=1; k <=(nlstate+ndeath); k++){
5883: if (k != i) {
5884: printf("%d%d ",i,k);
5885: fprintf(ficlog,"%d%d ",i,k);
5886: fprintf(ficres,"%1d%1d ",i,k);
5887: for(j=1; j <=ncovmodel; j++){
5888: printf("%lf ",p[jk]);
5889: fprintf(ficlog,"%lf ",p[jk]);
5890: fprintf(ficres,"%lf ",p[jk]);
5891: jk++;
5892: }
5893: printf("\n");
5894: fprintf(ficlog,"\n");
5895: fprintf(ficres,"\n");
5896: }
5897: }
5898: }
5899: if(mle!=0){
5900: /* Computing hessian and covariance matrix */
5901: ftolhess=ftol; /* Usually correct */
5902: hesscov(matcov, p, npar, delti, ftolhess, func);
5903: }
5904: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5905: printf("# Scales (for hessian or gradient estimation)\n");
5906: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5907: for(i=1,jk=1; i <=nlstate; i++){
5908: for(j=1; j <=nlstate+ndeath; j++){
5909: if (j!=i) {
5910: fprintf(ficres,"%1d%1d",i,j);
5911: printf("%1d%1d",i,j);
5912: fprintf(ficlog,"%1d%1d",i,j);
5913: for(k=1; k<=ncovmodel;k++){
5914: printf(" %.5e",delti[jk]);
5915: fprintf(ficlog," %.5e",delti[jk]);
5916: fprintf(ficres," %.5e",delti[jk]);
5917: jk++;
5918: }
5919: printf("\n");
5920: fprintf(ficlog,"\n");
5921: fprintf(ficres,"\n");
5922: }
5923: }
5924: }
5925:
5926: 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");
5927: if(mle>=1)
5928: 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");
5929: 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");
5930: /* # 121 Var(a12)\n\ */
5931: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5932: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5933: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5934: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5935: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5936: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5937: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5938:
5939:
5940: /* Just to have a covariance matrix which will be more understandable
5941: even is we still don't want to manage dictionary of variables
5942: */
5943: for(itimes=1;itimes<=2;itimes++){
5944: jj=0;
5945: for(i=1; i <=nlstate; i++){
5946: for(j=1; j <=nlstate+ndeath; j++){
5947: if(j==i) continue;
5948: for(k=1; k<=ncovmodel;k++){
5949: jj++;
5950: ca[0]= k+'a'-1;ca[1]='\0';
5951: if(itimes==1){
5952: if(mle>=1)
5953: printf("#%1d%1d%d",i,j,k);
5954: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5955: fprintf(ficres,"#%1d%1d%d",i,j,k);
5956: }else{
5957: if(mle>=1)
5958: printf("%1d%1d%d",i,j,k);
5959: fprintf(ficlog,"%1d%1d%d",i,j,k);
5960: fprintf(ficres,"%1d%1d%d",i,j,k);
5961: }
5962: ll=0;
5963: for(li=1;li <=nlstate; li++){
5964: for(lj=1;lj <=nlstate+ndeath; lj++){
5965: if(lj==li) continue;
5966: for(lk=1;lk<=ncovmodel;lk++){
5967: ll++;
5968: if(ll<=jj){
5969: cb[0]= lk +'a'-1;cb[1]='\0';
5970: if(ll<jj){
5971: if(itimes==1){
5972: if(mle>=1)
5973: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5974: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5975: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5976: }else{
5977: if(mle>=1)
5978: printf(" %.5e",matcov[jj][ll]);
5979: fprintf(ficlog," %.5e",matcov[jj][ll]);
5980: fprintf(ficres," %.5e",matcov[jj][ll]);
5981: }
5982: }else{
5983: if(itimes==1){
5984: if(mle>=1)
5985: printf(" Var(%s%1d%1d)",ca,i,j);
5986: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5987: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5988: }else{
5989: if(mle>=1)
5990: printf(" %.5e",matcov[jj][ll]);
5991: fprintf(ficlog," %.5e",matcov[jj][ll]);
5992: fprintf(ficres," %.5e",matcov[jj][ll]);
5993: }
5994: }
5995: }
5996: } /* end lk */
5997: } /* end lj */
5998: } /* end li */
5999: if(mle>=1)
6000: printf("\n");
6001: fprintf(ficlog,"\n");
6002: fprintf(ficres,"\n");
6003: numlinepar++;
6004: } /* end k*/
6005: } /*end j */
6006: } /* end i */
6007: } /* end itimes */
6008:
6009: fflush(ficlog);
6010: fflush(ficres);
6011:
6012: while((c=getc(ficpar))=='#' && c!= EOF){
6013: ungetc(c,ficpar);
6014: fgets(line, MAXLINE, ficpar);
6015: fputs(line,stdout);
6016: fputs(line,ficparo);
6017: }
6018: ungetc(c,ficpar);
6019:
6020: estepm=0;
6021: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6022: if (estepm==0 || estepm < stepm) estepm=stepm;
6023: if (fage <= 2) {
6024: bage = ageminpar;
6025: fage = agemaxpar;
6026: }
6027:
6028: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6029: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6030: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6031:
6032: while((c=getc(ficpar))=='#' && c!= EOF){
6033: ungetc(c,ficpar);
6034: fgets(line, MAXLINE, ficpar);
6035: fputs(line,stdout);
6036: fputs(line,ficparo);
6037: }
6038: ungetc(c,ficpar);
6039:
6040: 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);
6041: 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);
6042: 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);
6043: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6044: 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);
6045:
6046: while((c=getc(ficpar))=='#' && c!= EOF){
6047: ungetc(c,ficpar);
6048: fgets(line, MAXLINE, ficpar);
6049: fputs(line,stdout);
6050: fputs(line,ficparo);
6051: }
6052: ungetc(c,ficpar);
6053:
6054:
6055: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6056: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6057:
6058: fscanf(ficpar,"pop_based=%d\n",&popbased);
6059: fprintf(ficparo,"pop_based=%d\n",popbased);
6060: fprintf(ficres,"pop_based=%d\n",popbased);
6061:
6062: while((c=getc(ficpar))=='#' && c!= EOF){
6063: ungetc(c,ficpar);
6064: fgets(line, MAXLINE, ficpar);
6065: fputs(line,stdout);
6066: fputs(line,ficparo);
6067: }
6068: ungetc(c,ficpar);
6069:
6070: 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);
6071: 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);
6072: 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);
6073: 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);
6074: 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);
6075: /* day and month of proj2 are not used but only year anproj2.*/
6076:
6077:
6078:
6079: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
6080: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
6081:
6082: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6083: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6084:
6085: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6086: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6087: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6088:
6089: /*------------ free_vector -------------*/
6090: /* chdir(path); */
6091:
6092: free_ivector(wav,1,imx);
6093: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6094: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6095: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6096: free_lvector(num,1,n);
6097: free_vector(agedc,1,n);
6098: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6099: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6100: fclose(ficparo);
6101: fclose(ficres);
6102:
6103:
6104: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6105:
6106: strcpy(filerespl,"pl");
6107: strcat(filerespl,fileres);
6108: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6109: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6110: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6111: }
6112: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6113: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6114: pstamp(ficrespl);
6115: fprintf(ficrespl,"# Period (stable) prevalence \n");
6116: fprintf(ficrespl,"#Age ");
6117: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6118: fprintf(ficrespl,"\n");
6119:
6120: prlim=matrix(1,nlstate,1,nlstate);
6121:
6122: agebase=ageminpar;
6123: agelim=agemaxpar;
6124: ftolpl=1.e-10;
6125: i1=pow(2,cptcoveff);
6126: if (cptcovn < 1){i1=1;}
6127:
6128: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6129: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6130: k=k+1;
6131: /* to clean */
6132: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6133: fprintf(ficrespl,"\n#******");
6134: printf("\n#******");
6135: fprintf(ficlog,"\n#******");
6136: for(j=1;j<=cptcoveff;j++) {
6137: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6138: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6139: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6140: }
6141: fprintf(ficrespl,"******\n");
6142: printf("******\n");
6143: fprintf(ficlog,"******\n");
6144:
6145: for (age=agebase; age<=agelim; age++){
6146: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6147: fprintf(ficrespl,"%.0f ",age );
6148: for(j=1;j<=cptcoveff;j++)
6149: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6150: for(i=1; i<=nlstate;i++)
6151: fprintf(ficrespl," %.5f", prlim[i][i]);
6152: fprintf(ficrespl,"\n");
6153: } /* Age */
6154: /* was end of cptcod */
6155: } /* cptcov */
6156: fclose(ficrespl);
6157:
6158: /*------------- h Pij x at various ages ------------*/
6159:
6160: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6161: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6162: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
6163: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
6164: }
6165: printf("Computing pij: result on file '%s' \n", filerespij);
6166: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6167:
6168: stepsize=(int) (stepm+YEARM-1)/YEARM;
6169: /*if (stepm<=24) stepsize=2;*/
6170:
6171: agelim=AGESUP;
6172: hstepm=stepsize*YEARM; /* Every year of age */
6173: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6174:
6175: /* hstepm=1; aff par mois*/
6176: pstamp(ficrespij);
6177: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6178: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6179: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6180: k=k+1;
6181: fprintf(ficrespij,"\n#****** ");
6182: for(j=1;j<=cptcoveff;j++)
6183: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6184: fprintf(ficrespij,"******\n");
6185:
6186: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6187: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6188: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6189:
6190: /* nhstepm=nhstepm*YEARM; aff par mois*/
6191:
6192: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6193: oldm=oldms;savm=savms;
6194: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6195: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6196: for(i=1; i<=nlstate;i++)
6197: for(j=1; j<=nlstate+ndeath;j++)
6198: fprintf(ficrespij," %1d-%1d",i,j);
6199: fprintf(ficrespij,"\n");
6200: for (h=0; h<=nhstepm; h++){
6201: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
6202: for(i=1; i<=nlstate;i++)
6203: for(j=1; j<=nlstate+ndeath;j++)
6204: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6205: fprintf(ficrespij,"\n");
6206: }
6207: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6208: fprintf(ficrespij,"\n");
6209: }
6210: }
6211: }
6212:
6213: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6214:
6215: fclose(ficrespij);
6216:
6217: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6218: for(i=1;i<=AGESUP;i++)
6219: for(j=1;j<=NCOVMAX;j++)
6220: for(k=1;k<=NCOVMAX;k++)
6221: probs[i][j][k]=0.;
6222:
6223: /*---------- Forecasting ------------------*/
6224: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6225: if(prevfcast==1){
6226: /* if(stepm ==1){*/
6227: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6228: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6229: /* } */
6230: /* else{ */
6231: /* erreur=108; */
6232: /* 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); */
6233: /* 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); */
6234: /* } */
6235: }
6236:
6237:
6238: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6239:
6240: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6241: /* 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",\
6242: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6243: */
6244:
6245: if (mobilav!=0) {
6246: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6247: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6248: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6249: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6250: }
6251: }
6252:
6253:
6254: /*---------- Health expectancies, no variances ------------*/
6255:
6256: strcpy(filerese,"e");
6257: strcat(filerese,fileres);
6258: if((ficreseij=fopen(filerese,"w"))==NULL) {
6259: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6260: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6261: }
6262: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6263: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6264: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6265: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6266: k=k+1;
6267: fprintf(ficreseij,"\n#****** ");
6268: for(j=1;j<=cptcoveff;j++) {
6269: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6270: }
6271: fprintf(ficreseij,"******\n");
6272:
6273: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6274: oldm=oldms;savm=savms;
6275: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6276:
6277: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6278: }
6279: }
6280: fclose(ficreseij);
6281:
6282:
6283: /*---------- Health expectancies and variances ------------*/
6284:
6285:
6286: strcpy(filerest,"t");
6287: strcat(filerest,fileres);
6288: if((ficrest=fopen(filerest,"w"))==NULL) {
6289: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6290: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6291: }
6292: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6293: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6294:
6295:
6296: strcpy(fileresstde,"stde");
6297: strcat(fileresstde,fileres);
6298: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6299: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6300: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6301: }
6302: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6303: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6304:
6305: strcpy(filerescve,"cve");
6306: strcat(filerescve,fileres);
6307: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6308: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6309: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6310: }
6311: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6312: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6313:
6314: strcpy(fileresv,"v");
6315: strcat(fileresv,fileres);
6316: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6317: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6318: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6319: }
6320: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6321: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6322:
6323: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6324: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6325: k=k+1;
6326: fprintf(ficrest,"\n#****** ");
6327: for(j=1;j<=cptcoveff;j++)
6328: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6329: fprintf(ficrest,"******\n");
6330:
6331: fprintf(ficresstdeij,"\n#****** ");
6332: fprintf(ficrescveij,"\n#****** ");
6333: for(j=1;j<=cptcoveff;j++) {
6334: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6335: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6336: }
6337: fprintf(ficresstdeij,"******\n");
6338: fprintf(ficrescveij,"******\n");
6339:
6340: fprintf(ficresvij,"\n#****** ");
6341: for(j=1;j<=cptcoveff;j++)
6342: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6343: fprintf(ficresvij,"******\n");
6344:
6345: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6346: oldm=oldms;savm=savms;
6347: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6348:
6349: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6350: pstamp(ficrest);
6351: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6352: oldm=oldms;savm=savms;
6353: 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 ");
6354: if(vpopbased==1)
6355: 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);
6356: else
6357: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6358: fprintf(ficrest,"# Age e.. (std) ");
6359: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6360: fprintf(ficrest,"\n");
6361:
6362: epj=vector(1,nlstate+1);
6363: for(age=bage; age <=fage ;age++){
6364: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6365: if (vpopbased==1) {
6366: if(mobilav ==0){
6367: for(i=1; i<=nlstate;i++)
6368: prlim[i][i]=probs[(int)age][i][k];
6369: }else{ /* mobilav */
6370: for(i=1; i<=nlstate;i++)
6371: prlim[i][i]=mobaverage[(int)age][i][k];
6372: }
6373: }
6374:
6375: fprintf(ficrest," %4.0f",age);
6376: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6377: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6378: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6379: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6380: }
6381: epj[nlstate+1] +=epj[j];
6382: }
6383:
6384: for(i=1, vepp=0.;i <=nlstate;i++)
6385: for(j=1;j <=nlstate;j++)
6386: vepp += vareij[i][j][(int)age];
6387: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6388: for(j=1;j <=nlstate;j++){
6389: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6390: }
6391: fprintf(ficrest,"\n");
6392: }
6393: }
6394: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6395: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6396: free_vector(epj,1,nlstate+1);
6397: }
6398: }
6399: free_vector(weight,1,n);
6400: free_imatrix(Tvard,1,15,1,2);
6401: free_imatrix(s,1,maxwav+1,1,n);
6402: free_matrix(anint,1,maxwav,1,n);
6403: free_matrix(mint,1,maxwav,1,n);
6404: free_ivector(cod,1,n);
6405: free_ivector(tab,1,NCOVMAX);
6406: fclose(ficresstdeij);
6407: fclose(ficrescveij);
6408: fclose(ficresvij);
6409: fclose(ficrest);
6410: fclose(ficpar);
6411:
6412: /*------- Variance of period (stable) prevalence------*/
6413:
6414: strcpy(fileresvpl,"vpl");
6415: strcat(fileresvpl,fileres);
6416: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6417: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6418: exit(0);
6419: }
6420: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6421:
6422: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6423: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6424: k=k+1;
6425: fprintf(ficresvpl,"\n#****** ");
6426: for(j=1;j<=cptcoveff;j++)
6427: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6428: fprintf(ficresvpl,"******\n");
6429:
6430: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6431: oldm=oldms;savm=savms;
6432: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6433: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6434: }
6435: }
6436:
6437: fclose(ficresvpl);
6438:
6439: /*---------- End : free ----------------*/
6440: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6441: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6442: } /* mle==-3 arrives here for freeing */
6443: endfree:
6444: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6445: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6446: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6447: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6448: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6449: free_matrix(covar,0,NCOVMAX,1,n);
6450: free_matrix(matcov,1,npar,1,npar);
6451: /*free_vector(delti,1,npar);*/
6452: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6453: free_matrix(agev,1,maxwav,1,imx);
6454: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6455:
6456: free_ivector(ncodemax,1,8);
6457: free_ivector(Tvar,1,15);
6458: free_ivector(Tprod,1,15);
6459: free_ivector(Tvaraff,1,15);
6460: free_ivector(Tage,1,15);
6461:
6462: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6463: free_imatrix(codtab,1,100,1,10);
6464: fflush(fichtm);
6465: fflush(ficgp);
6466:
6467:
6468: if((nberr >0) || (nbwarn>0)){
6469: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6470: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6471: }else{
6472: printf("End of Imach\n");
6473: fprintf(ficlog,"End of Imach\n");
6474: }
6475: printf("See log file on %s\n",filelog);
6476: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6477: (void) gettimeofday(&end_time,&tzp);
6478: tm = *localtime(&end_time.tv_sec);
6479: tmg = *gmtime(&end_time.tv_sec);
6480: strcpy(strtend,asctime(&tm));
6481: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6482: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6483: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6484:
6485: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6486: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6487: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
6488: /* printf("Total time was %d uSec.\n", total_usecs);*/
6489: /* if(fileappend(fichtm,optionfilehtm)){ */
6490: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6491: fclose(fichtm);
6492: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6493: fclose(fichtmcov);
6494: fclose(ficgp);
6495: fclose(ficlog);
6496: /*------ End -----------*/
6497:
6498:
6499: printf("Before Current directory %s!\n",pathcd);
6500: if(chdir(pathcd) != 0)
6501: printf("Can't move to directory %s!\n",path);
6502: if(getcwd(pathcd,MAXLINE) > 0)
6503: printf("Current directory %s!\n",pathcd);
6504: /*strcat(plotcmd,CHARSEPARATOR);*/
6505: sprintf(plotcmd,"gnuplot");
6506: #ifndef UNIX
6507: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6508: #endif
6509: if(!stat(plotcmd,&info)){
6510: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6511: if(!stat(getenv("GNUPLOTBIN"),&info)){
6512: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6513: }else
6514: strcpy(pplotcmd,plotcmd);
6515: #ifdef UNIX
6516: strcpy(plotcmd,GNUPLOTPROGRAM);
6517: if(!stat(plotcmd,&info)){
6518: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6519: }else
6520: strcpy(pplotcmd,plotcmd);
6521: #endif
6522: }else
6523: strcpy(pplotcmd,plotcmd);
6524:
6525: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6526: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6527:
6528: if((outcmd=system(plotcmd)) != 0){
6529: printf("\n Problem with gnuplot\n");
6530: }
6531: printf(" Wait...");
6532: while (z[0] != 'q') {
6533: /* chdir(path); */
6534: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6535: scanf("%s",z);
6536: /* if (z[0] == 'c') system("./imach"); */
6537: if (z[0] == 'e') {
6538: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6539: system(optionfilehtm);
6540: }
6541: else if (z[0] == 'g') system(plotcmd);
6542: else if (z[0] == 'q') exit(0);
6543: }
6544: end:
6545: while (z[0] != 'q') {
6546: printf("\nType q for exiting: ");
6547: scanf("%s",z);
6548: }
6549: }
6550:
6551:
6552:
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