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