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