Annotation of imach/src/imach.c, revision 1.144
1.144 ! brouard 1: /* $Id: imach.c,v 1.143 2014/01/26 09:45:38 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.144 ! brouard 4: Revision 1.143 2014/01/26 09:45:38 brouard
! 5: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
! 6:
! 7: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
! 8: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
! 9:
1.143 brouard 10: Revision 1.142 2014/01/26 03:57:36 brouard
11: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
12:
13: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
14:
1.142 brouard 15: Revision 1.141 2014/01/26 02:42:01 brouard
16: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
17:
1.141 brouard 18: Revision 1.140 2011/09/02 10:37:54 brouard
19: Summary: times.h is ok with mingw32 now.
20:
1.140 brouard 21: Revision 1.139 2010/06/14 07:50:17 brouard
22: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
23: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
24:
1.139 brouard 25: Revision 1.138 2010/04/30 18:19:40 brouard
26: *** empty log message ***
27:
1.138 brouard 28: Revision 1.137 2010/04/29 18:11:38 brouard
29: (Module): Checking covariates for more complex models
30: than V1+V2. A lot of change to be done. Unstable.
31:
1.137 brouard 32: Revision 1.136 2010/04/26 20:30:53 brouard
33: (Module): merging some libgsl code. Fixing computation
34: of likelione (using inter/intrapolation if mle = 0) in order to
35: get same likelihood as if mle=1.
36: Some cleaning of code and comments added.
37:
1.136 brouard 38: Revision 1.135 2009/10/29 15:33:14 brouard
39: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
40:
1.135 brouard 41: Revision 1.134 2009/10/29 13:18:53 brouard
42: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
43:
1.134 brouard 44: Revision 1.133 2009/07/06 10:21:25 brouard
45: just nforces
46:
1.133 brouard 47: Revision 1.132 2009/07/06 08:22:05 brouard
48: Many tings
49:
1.132 brouard 50: Revision 1.131 2009/06/20 16:22:47 brouard
51: Some dimensions resccaled
52:
1.131 brouard 53: Revision 1.130 2009/05/26 06:44:34 brouard
54: (Module): Max Covariate is now set to 20 instead of 8. A
55: lot of cleaning with variables initialized to 0. Trying to make
56: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
57:
1.130 brouard 58: Revision 1.129 2007/08/31 13:49:27 lievre
59: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
60:
1.129 lievre 61: Revision 1.128 2006/06/30 13:02:05 brouard
62: (Module): Clarifications on computing e.j
63:
1.128 brouard 64: Revision 1.127 2006/04/28 18:11:50 brouard
65: (Module): Yes the sum of survivors was wrong since
66: imach-114 because nhstepm was no more computed in the age
67: loop. Now we define nhstepma in the age loop.
68: (Module): In order to speed up (in case of numerous covariates) we
69: compute health expectancies (without variances) in a first step
70: and then all the health expectancies with variances or standard
71: deviation (needs data from the Hessian matrices) which slows the
72: computation.
73: In the future we should be able to stop the program is only health
74: expectancies and graph are needed without standard deviations.
75:
1.127 brouard 76: Revision 1.126 2006/04/28 17:23:28 brouard
77: (Module): Yes the sum of survivors was wrong since
78: imach-114 because nhstepm was no more computed in the age
79: loop. Now we define nhstepma in the age loop.
80: Version 0.98h
81:
1.126 brouard 82: Revision 1.125 2006/04/04 15:20:31 lievre
83: Errors in calculation of health expectancies. Age was not initialized.
84: Forecasting file added.
85:
86: Revision 1.124 2006/03/22 17:13:53 lievre
87: Parameters are printed with %lf instead of %f (more numbers after the comma).
88: The log-likelihood is printed in the log file
89:
90: Revision 1.123 2006/03/20 10:52:43 brouard
91: * imach.c (Module): <title> changed, corresponds to .htm file
92: name. <head> headers where missing.
93:
94: * imach.c (Module): Weights can have a decimal point as for
95: English (a comma might work with a correct LC_NUMERIC environment,
96: otherwise the weight is truncated).
97: Modification of warning when the covariates values are not 0 or
98: 1.
99: Version 0.98g
100:
101: Revision 1.122 2006/03/20 09:45:41 brouard
102: (Module): Weights can have a decimal point as for
103: English (a comma might work with a correct LC_NUMERIC environment,
104: otherwise the weight is truncated).
105: Modification of warning when the covariates values are not 0 or
106: 1.
107: Version 0.98g
108:
109: Revision 1.121 2006/03/16 17:45:01 lievre
110: * imach.c (Module): Comments concerning covariates added
111:
112: * imach.c (Module): refinements in the computation of lli if
113: status=-2 in order to have more reliable computation if stepm is
114: not 1 month. Version 0.98f
115:
116: Revision 1.120 2006/03/16 15:10:38 lievre
117: (Module): refinements in the computation of lli if
118: status=-2 in order to have more reliable computation if stepm is
119: not 1 month. Version 0.98f
120:
121: Revision 1.119 2006/03/15 17:42:26 brouard
122: (Module): Bug if status = -2, the loglikelihood was
123: computed as likelihood omitting the logarithm. Version O.98e
124:
125: Revision 1.118 2006/03/14 18:20:07 brouard
126: (Module): varevsij Comments added explaining the second
127: table of variances if popbased=1 .
128: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
129: (Module): Function pstamp added
130: (Module): Version 0.98d
131:
132: Revision 1.117 2006/03/14 17:16:22 brouard
133: (Module): varevsij Comments added explaining the second
134: table of variances if popbased=1 .
135: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
136: (Module): Function pstamp added
137: (Module): Version 0.98d
138:
139: Revision 1.116 2006/03/06 10:29:27 brouard
140: (Module): Variance-covariance wrong links and
141: varian-covariance of ej. is needed (Saito).
142:
143: Revision 1.115 2006/02/27 12:17:45 brouard
144: (Module): One freematrix added in mlikeli! 0.98c
145:
146: Revision 1.114 2006/02/26 12:57:58 brouard
147: (Module): Some improvements in processing parameter
148: filename with strsep.
149:
150: Revision 1.113 2006/02/24 14:20:24 brouard
151: (Module): Memory leaks checks with valgrind and:
152: datafile was not closed, some imatrix were not freed and on matrix
153: allocation too.
154:
155: Revision 1.112 2006/01/30 09:55:26 brouard
156: (Module): Back to gnuplot.exe instead of wgnuplot.exe
157:
158: Revision 1.111 2006/01/25 20:38:18 brouard
159: (Module): Lots of cleaning and bugs added (Gompertz)
160: (Module): Comments can be added in data file. Missing date values
161: can be a simple dot '.'.
162:
163: Revision 1.110 2006/01/25 00:51:50 brouard
164: (Module): Lots of cleaning and bugs added (Gompertz)
165:
166: Revision 1.109 2006/01/24 19:37:15 brouard
167: (Module): Comments (lines starting with a #) are allowed in data.
168:
169: Revision 1.108 2006/01/19 18:05:42 lievre
170: Gnuplot problem appeared...
171: To be fixed
172:
173: Revision 1.107 2006/01/19 16:20:37 brouard
174: Test existence of gnuplot in imach path
175:
176: Revision 1.106 2006/01/19 13:24:36 brouard
177: Some cleaning and links added in html output
178:
179: Revision 1.105 2006/01/05 20:23:19 lievre
180: *** empty log message ***
181:
182: Revision 1.104 2005/09/30 16:11:43 lievre
183: (Module): sump fixed, loop imx fixed, and simplifications.
184: (Module): If the status is missing at the last wave but we know
185: that the person is alive, then we can code his/her status as -2
186: (instead of missing=-1 in earlier versions) and his/her
187: contributions to the likelihood is 1 - Prob of dying from last
188: health status (= 1-p13= p11+p12 in the easiest case of somebody in
189: the healthy state at last known wave). Version is 0.98
190:
191: Revision 1.103 2005/09/30 15:54:49 lievre
192: (Module): sump fixed, loop imx fixed, and simplifications.
193:
194: Revision 1.102 2004/09/15 17:31:30 brouard
195: Add the possibility to read data file including tab characters.
196:
197: Revision 1.101 2004/09/15 10:38:38 brouard
198: Fix on curr_time
199:
200: Revision 1.100 2004/07/12 18:29:06 brouard
201: Add version for Mac OS X. Just define UNIX in Makefile
202:
203: Revision 1.99 2004/06/05 08:57:40 brouard
204: *** empty log message ***
205:
206: Revision 1.98 2004/05/16 15:05:56 brouard
207: New version 0.97 . First attempt to estimate force of mortality
208: directly from the data i.e. without the need of knowing the health
209: state at each age, but using a Gompertz model: log u =a + b*age .
210: This is the basic analysis of mortality and should be done before any
211: other analysis, in order to test if the mortality estimated from the
212: cross-longitudinal survey is different from the mortality estimated
213: from other sources like vital statistic data.
214:
215: The same imach parameter file can be used but the option for mle should be -3.
216:
1.133 brouard 217: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 218: former routines in order to include the new code within the former code.
219:
220: The output is very simple: only an estimate of the intercept and of
221: the slope with 95% confident intervals.
222:
223: Current limitations:
224: A) Even if you enter covariates, i.e. with the
225: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
226: B) There is no computation of Life Expectancy nor Life Table.
227:
228: Revision 1.97 2004/02/20 13:25:42 lievre
229: Version 0.96d. Population forecasting command line is (temporarily)
230: suppressed.
231:
232: Revision 1.96 2003/07/15 15:38:55 brouard
233: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
234: rewritten within the same printf. Workaround: many printfs.
235:
236: Revision 1.95 2003/07/08 07:54:34 brouard
237: * imach.c (Repository):
238: (Repository): Using imachwizard code to output a more meaningful covariance
239: matrix (cov(a12,c31) instead of numbers.
240:
241: Revision 1.94 2003/06/27 13:00:02 brouard
242: Just cleaning
243:
244: Revision 1.93 2003/06/25 16:33:55 brouard
245: (Module): On windows (cygwin) function asctime_r doesn't
246: exist so I changed back to asctime which exists.
247: (Module): Version 0.96b
248:
249: Revision 1.92 2003/06/25 16:30:45 brouard
250: (Module): On windows (cygwin) function asctime_r doesn't
251: exist so I changed back to asctime which exists.
252:
253: Revision 1.91 2003/06/25 15:30:29 brouard
254: * imach.c (Repository): Duplicated warning errors corrected.
255: (Repository): Elapsed time after each iteration is now output. It
256: helps to forecast when convergence will be reached. Elapsed time
257: is stamped in powell. We created a new html file for the graphs
258: concerning matrix of covariance. It has extension -cov.htm.
259:
260: Revision 1.90 2003/06/24 12:34:15 brouard
261: (Module): Some bugs corrected for windows. Also, when
262: mle=-1 a template is output in file "or"mypar.txt with the design
263: of the covariance matrix to be input.
264:
265: Revision 1.89 2003/06/24 12:30:52 brouard
266: (Module): Some bugs corrected for windows. Also, when
267: mle=-1 a template is output in file "or"mypar.txt with the design
268: of the covariance matrix to be input.
269:
270: Revision 1.88 2003/06/23 17:54:56 brouard
271: * 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.
272:
273: Revision 1.87 2003/06/18 12:26:01 brouard
274: Version 0.96
275:
276: Revision 1.86 2003/06/17 20:04:08 brouard
277: (Module): Change position of html and gnuplot routines and added
278: routine fileappend.
279:
280: Revision 1.85 2003/06/17 13:12:43 brouard
281: * imach.c (Repository): Check when date of death was earlier that
282: current date of interview. It may happen when the death was just
283: prior to the death. In this case, dh was negative and likelihood
284: was wrong (infinity). We still send an "Error" but patch by
285: assuming that the date of death was just one stepm after the
286: interview.
287: (Repository): Because some people have very long ID (first column)
288: we changed int to long in num[] and we added a new lvector for
289: memory allocation. But we also truncated to 8 characters (left
290: truncation)
291: (Repository): No more line truncation errors.
292:
293: Revision 1.84 2003/06/13 21:44:43 brouard
294: * imach.c (Repository): Replace "freqsummary" at a correct
295: place. It differs from routine "prevalence" which may be called
296: many times. Probs is memory consuming and must be used with
297: parcimony.
298: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
299:
300: Revision 1.83 2003/06/10 13:39:11 lievre
301: *** empty log message ***
302:
303: Revision 1.82 2003/06/05 15:57:20 brouard
304: Add log in imach.c and fullversion number is now printed.
305:
306: */
307: /*
308: Interpolated Markov Chain
309:
310: Short summary of the programme:
311:
312: This program computes Healthy Life Expectancies from
313: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
314: first survey ("cross") where individuals from different ages are
315: interviewed on their health status or degree of disability (in the
316: case of a health survey which is our main interest) -2- at least a
317: second wave of interviews ("longitudinal") which measure each change
318: (if any) in individual health status. Health expectancies are
319: computed from the time spent in each health state according to a
320: model. More health states you consider, more time is necessary to reach the
321: Maximum Likelihood of the parameters involved in the model. The
322: simplest model is the multinomial logistic model where pij is the
323: probability to be observed in state j at the second wave
324: conditional to be observed in state i at the first wave. Therefore
325: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
326: 'age' is age and 'sex' is a covariate. If you want to have a more
327: complex model than "constant and age", you should modify the program
328: where the markup *Covariates have to be included here again* invites
329: you to do it. More covariates you add, slower the
330: convergence.
331:
332: The advantage of this computer programme, compared to a simple
333: multinomial logistic model, is clear when the delay between waves is not
334: identical for each individual. Also, if a individual missed an
335: intermediate interview, the information is lost, but taken into
336: account using an interpolation or extrapolation.
337:
338: hPijx is the probability to be observed in state i at age x+h
339: conditional to the observed state i at age x. The delay 'h' can be
340: split into an exact number (nh*stepm) of unobserved intermediate
341: states. This elementary transition (by month, quarter,
342: semester or year) is modelled as a multinomial logistic. The hPx
343: matrix is simply the matrix product of nh*stepm elementary matrices
344: and the contribution of each individual to the likelihood is simply
345: hPijx.
346:
347: Also this programme outputs the covariance matrix of the parameters but also
348: of the life expectancies. It also computes the period (stable) prevalence.
349:
1.133 brouard 350: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
351: Institut national d'études démographiques, Paris.
1.126 brouard 352: This software have been partly granted by Euro-REVES, a concerted action
353: from the European Union.
354: It is copyrighted identically to a GNU software product, ie programme and
355: software can be distributed freely for non commercial use. Latest version
356: can be accessed at http://euroreves.ined.fr/imach .
357:
358: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
359: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
360:
361: **********************************************************************/
362: /*
363: main
364: read parameterfile
365: read datafile
366: concatwav
367: freqsummary
368: if (mle >= 1)
369: mlikeli
370: print results files
371: if mle==1
372: computes hessian
373: read end of parameter file: agemin, agemax, bage, fage, estepm
374: begin-prev-date,...
375: open gnuplot file
376: open html file
377: period (stable) prevalence
378: for age prevalim()
379: h Pij x
380: variance of p varprob
381: forecasting if prevfcast==1 prevforecast call prevalence()
382: health expectancies
383: Variance-covariance of DFLE
384: prevalence()
385: movingaverage()
386: varevsij()
387: if popbased==1 varevsij(,popbased)
388: total life expectancies
389: Variance of period (stable) prevalence
390: end
391: */
392:
393:
394:
395:
396: #include <math.h>
397: #include <stdio.h>
398: #include <stdlib.h>
399: #include <string.h>
400: #include <unistd.h>
401:
402: #include <limits.h>
403: #include <sys/types.h>
404: #include <sys/stat.h>
405: #include <errno.h>
406: extern int errno;
407:
1.141 brouard 408: #ifdef LINUX
1.126 brouard 409: #include <time.h>
410: #include "timeval.h"
1.141 brouard 411: #else
412: #include <sys/time.h>
413: #endif
1.126 brouard 414:
1.136 brouard 415: #ifdef GSL
416: #include <gsl/gsl_errno.h>
417: #include <gsl/gsl_multimin.h>
418: #endif
419:
1.126 brouard 420: /* #include <libintl.h> */
421: /* #define _(String) gettext (String) */
422:
1.141 brouard 423: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 424:
425: #define GNUPLOTPROGRAM "gnuplot"
426: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
427: #define FILENAMELENGTH 132
428:
429: #define GLOCK_ERROR_NOPATH -1 /* empty path */
430: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
431:
1.144 ! brouard 432: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
! 433: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 434:
435: #define NINTERVMAX 8
1.144 ! brouard 436: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
! 437: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
! 438: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.126 brouard 439: #define MAXN 20000
1.144 ! brouard 440: #define YEARM 12. /**< Number of months per year */
1.126 brouard 441: #define AGESUP 130
442: #define AGEBASE 40
1.144 ! brouard 443: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
1.126 brouard 444: #ifdef UNIX
445: #define DIRSEPARATOR '/'
446: #define CHARSEPARATOR "/"
447: #define ODIRSEPARATOR '\\'
448: #else
449: #define DIRSEPARATOR '\\'
450: #define CHARSEPARATOR "\\"
451: #define ODIRSEPARATOR '/'
452: #endif
453:
1.144 ! brouard 454: /* $Id: imach.c,v 1.143 2014/01/26 09:45:38 brouard Exp $ */
1.126 brouard 455: /* $State: Exp $ */
456:
1.143 brouard 457: char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
1.144 ! brouard 458: char fullversion[]="$Revision: 1.143 $ $Date: 2014/01/26 09:45:38 $";
1.126 brouard 459: char strstart[80];
460: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 461: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 462: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.130 brouard 463: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
1.126 brouard 464: int npar=NPARMAX;
465: int nlstate=2; /* Number of live states */
466: int ndeath=1; /* Number of dead states */
1.130 brouard 467: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 468: int popbased=0;
469:
470: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 471: int maxwav=0; /* Maxim number of waves */
472: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
473: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
474: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 475: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 476: int mle=1, weightopt=0;
1.126 brouard 477: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
478: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
479: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
480: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 481: double jmean=1; /* Mean space between 2 waves */
1.126 brouard 482: double **oldm, **newm, **savm; /* Working pointers to matrices */
483: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 484: /*FILE *fic ; */ /* Used in readdata only */
485: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 486: FILE *ficlog, *ficrespow;
1.130 brouard 487: int globpr=0; /* Global variable for printing or not */
1.126 brouard 488: double fretone; /* Only one call to likelihood */
1.130 brouard 489: long ipmx=0; /* Number of contributions */
1.126 brouard 490: double sw; /* Sum of weights */
491: char filerespow[FILENAMELENGTH];
492: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
493: FILE *ficresilk;
494: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
495: FILE *ficresprobmorprev;
496: FILE *fichtm, *fichtmcov; /* Html File */
497: FILE *ficreseij;
498: char filerese[FILENAMELENGTH];
499: FILE *ficresstdeij;
500: char fileresstde[FILENAMELENGTH];
501: FILE *ficrescveij;
502: char filerescve[FILENAMELENGTH];
503: FILE *ficresvij;
504: char fileresv[FILENAMELENGTH];
505: FILE *ficresvpl;
506: char fileresvpl[FILENAMELENGTH];
507: char title[MAXLINE];
508: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
509: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
510: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
511: char command[FILENAMELENGTH];
512: int outcmd=0;
513:
514: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
515:
516: char filelog[FILENAMELENGTH]; /* Log file */
517: char filerest[FILENAMELENGTH];
518: char fileregp[FILENAMELENGTH];
519: char popfile[FILENAMELENGTH];
520:
521: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
522:
523: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
524: struct timezone tzp;
525: extern int gettimeofday();
526: struct tm tmg, tm, tmf, *gmtime(), *localtime();
527: long time_value;
528: extern long time();
529: char strcurr[80], strfor[80];
530:
531: char *endptr;
532: long lval;
533: double dval;
534:
535: #define NR_END 1
536: #define FREE_ARG char*
537: #define FTOL 1.0e-10
538:
539: #define NRANSI
540: #define ITMAX 200
541:
542: #define TOL 2.0e-4
543:
544: #define CGOLD 0.3819660
545: #define ZEPS 1.0e-10
546: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
547:
548: #define GOLD 1.618034
549: #define GLIMIT 100.0
550: #define TINY 1.0e-20
551:
552: static double maxarg1,maxarg2;
553: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
554: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
555:
556: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
557: #define rint(a) floor(a+0.5)
558:
559: static double sqrarg;
560: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
561: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
562: int agegomp= AGEGOMP;
563:
564: int imx;
565: int stepm=1;
566: /* Stepm, step in month: minimum step interpolation*/
567:
568: int estepm;
569: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
570:
571: int m,nb;
572: long *num;
573: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
574: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
575: double **pmmij, ***probs;
576: double *ageexmed,*agecens;
577: double dateintmean=0;
578:
579: double *weight;
580: int **s; /* Status */
1.141 brouard 581: double *agedc;
582: double **covar; /**< covar[i,j], value of jth covariate for individual i,
583: * covar=matrix(0,NCOVMAX,1,n);
584: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
585: double idx;
586: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
587: int **codtab; /**< codtab=imatrix(1,100,1,10); */
588: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 589: double *lsurv, *lpop, *tpop;
590:
1.143 brouard 591: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
592: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 593:
594: /**************** split *************************/
595: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
596: {
597: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
598: the name of the file (name), its extension only (ext) and its first part of the name (finame)
599: */
600: char *ss; /* pointer */
601: int l1, l2; /* length counters */
602:
603: l1 = strlen(path ); /* length of path */
604: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
605: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
606: if ( ss == NULL ) { /* no directory, so determine current directory */
607: strcpy( name, path ); /* we got the fullname name because no directory */
608: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
609: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
610: /* get current working directory */
611: /* extern char* getcwd ( char *buf , int len);*/
612: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
613: return( GLOCK_ERROR_GETCWD );
614: }
615: /* got dirc from getcwd*/
616: printf(" DIRC = %s \n",dirc);
617: } else { /* strip direcotry from path */
618: ss++; /* after this, the filename */
619: l2 = strlen( ss ); /* length of filename */
620: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
621: strcpy( name, ss ); /* save file name */
622: strncpy( dirc, path, l1 - l2 ); /* now the directory */
623: dirc[l1-l2] = 0; /* add zero */
624: printf(" DIRC2 = %s \n",dirc);
625: }
626: /* We add a separator at the end of dirc if not exists */
627: l1 = strlen( dirc ); /* length of directory */
628: if( dirc[l1-1] != DIRSEPARATOR ){
629: dirc[l1] = DIRSEPARATOR;
630: dirc[l1+1] = 0;
631: printf(" DIRC3 = %s \n",dirc);
632: }
633: ss = strrchr( name, '.' ); /* find last / */
634: if (ss >0){
635: ss++;
636: strcpy(ext,ss); /* save extension */
637: l1= strlen( name);
638: l2= strlen(ss)+1;
639: strncpy( finame, name, l1-l2);
640: finame[l1-l2]= 0;
641: }
642:
643: return( 0 ); /* we're done */
644: }
645:
646:
647: /******************************************/
648:
649: void replace_back_to_slash(char *s, char*t)
650: {
651: int i;
652: int lg=0;
653: i=0;
654: lg=strlen(t);
655: for(i=0; i<= lg; i++) {
656: (s[i] = t[i]);
657: if (t[i]== '\\') s[i]='/';
658: }
659: }
660:
1.132 brouard 661: char *trimbb(char *out, char *in)
1.137 brouard 662: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 663: char *s;
664: s=out;
665: while (*in != '\0'){
1.137 brouard 666: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 667: in++;
668: }
669: *out++ = *in++;
670: }
671: *out='\0';
672: return s;
673: }
674:
1.137 brouard 675: char *cutv(char *blocc, char *alocc, char *in, char occ)
676: {
677: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
678: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
679: gives blocc="abcdef2ghi" and alocc="j".
680: If occ is not found blocc is null and alocc is equal to in. Returns alocc
681: */
682: char *s, *t;
683: t=in;s=in;
684: while (*in != '\0'){
685: while( *in == occ){
686: *blocc++ = *in++;
687: s=in;
688: }
689: *blocc++ = *in++;
690: }
691: if (s == t) /* occ not found */
692: *(blocc-(in-s))='\0';
693: else
694: *(blocc-(in-s)-1)='\0';
695: in=s;
696: while ( *in != '\0'){
697: *alocc++ = *in++;
698: }
699:
700: *alocc='\0';
701: return s;
702: }
703:
1.126 brouard 704: int nbocc(char *s, char occ)
705: {
706: int i,j=0;
707: int lg=20;
708: i=0;
709: lg=strlen(s);
710: for(i=0; i<= lg; i++) {
711: if (s[i] == occ ) j++;
712: }
713: return j;
714: }
715:
1.137 brouard 716: /* void cutv(char *u,char *v, char*t, char occ) */
717: /* { */
718: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
719: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
720: /* gives u="abcdef2ghi" and v="j" *\/ */
721: /* int i,lg,j,p=0; */
722: /* i=0; */
723: /* lg=strlen(t); */
724: /* for(j=0; j<=lg-1; j++) { */
725: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
726: /* } */
1.126 brouard 727:
1.137 brouard 728: /* for(j=0; j<p; j++) { */
729: /* (u[j] = t[j]); */
730: /* } */
731: /* u[p]='\0'; */
1.126 brouard 732:
1.137 brouard 733: /* for(j=0; j<= lg; j++) { */
734: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
735: /* } */
736: /* } */
1.126 brouard 737:
738: /********************** nrerror ********************/
739:
740: void nrerror(char error_text[])
741: {
742: fprintf(stderr,"ERREUR ...\n");
743: fprintf(stderr,"%s\n",error_text);
744: exit(EXIT_FAILURE);
745: }
746: /*********************** vector *******************/
747: double *vector(int nl, int nh)
748: {
749: double *v;
750: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
751: if (!v) nrerror("allocation failure in vector");
752: return v-nl+NR_END;
753: }
754:
755: /************************ free vector ******************/
756: void free_vector(double*v, int nl, int nh)
757: {
758: free((FREE_ARG)(v+nl-NR_END));
759: }
760:
761: /************************ivector *******************************/
762: int *ivector(long nl,long nh)
763: {
764: int *v;
765: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
766: if (!v) nrerror("allocation failure in ivector");
767: return v-nl+NR_END;
768: }
769:
770: /******************free ivector **************************/
771: void free_ivector(int *v, long nl, long nh)
772: {
773: free((FREE_ARG)(v+nl-NR_END));
774: }
775:
776: /************************lvector *******************************/
777: long *lvector(long nl,long nh)
778: {
779: long *v;
780: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
781: if (!v) nrerror("allocation failure in ivector");
782: return v-nl+NR_END;
783: }
784:
785: /******************free lvector **************************/
786: void free_lvector(long *v, long nl, long nh)
787: {
788: free((FREE_ARG)(v+nl-NR_END));
789: }
790:
791: /******************* imatrix *******************************/
792: int **imatrix(long nrl, long nrh, long ncl, long nch)
793: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
794: {
795: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
796: int **m;
797:
798: /* allocate pointers to rows */
799: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
800: if (!m) nrerror("allocation failure 1 in matrix()");
801: m += NR_END;
802: m -= nrl;
803:
804:
805: /* allocate rows and set pointers to them */
806: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
807: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
808: m[nrl] += NR_END;
809: m[nrl] -= ncl;
810:
811: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
812:
813: /* return pointer to array of pointers to rows */
814: return m;
815: }
816:
817: /****************** free_imatrix *************************/
818: void free_imatrix(m,nrl,nrh,ncl,nch)
819: int **m;
820: long nch,ncl,nrh,nrl;
821: /* free an int matrix allocated by imatrix() */
822: {
823: free((FREE_ARG) (m[nrl]+ncl-NR_END));
824: free((FREE_ARG) (m+nrl-NR_END));
825: }
826:
827: /******************* matrix *******************************/
828: double **matrix(long nrl, long nrh, long ncl, long nch)
829: {
830: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
831: double **m;
832:
833: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
834: if (!m) nrerror("allocation failure 1 in matrix()");
835: m += NR_END;
836: m -= nrl;
837:
838: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
839: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
840: m[nrl] += NR_END;
841: m[nrl] -= ncl;
842:
843: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
844: return m;
845: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
846: */
847: }
848:
849: /*************************free matrix ************************/
850: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
851: {
852: free((FREE_ARG)(m[nrl]+ncl-NR_END));
853: free((FREE_ARG)(m+nrl-NR_END));
854: }
855:
856: /******************* ma3x *******************************/
857: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
858: {
859: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
860: double ***m;
861:
862: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
863: if (!m) nrerror("allocation failure 1 in matrix()");
864: m += NR_END;
865: m -= nrl;
866:
867: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
868: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
869: m[nrl] += NR_END;
870: m[nrl] -= ncl;
871:
872: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
873:
874: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
875: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
876: m[nrl][ncl] += NR_END;
877: m[nrl][ncl] -= nll;
878: for (j=ncl+1; j<=nch; j++)
879: m[nrl][j]=m[nrl][j-1]+nlay;
880:
881: for (i=nrl+1; i<=nrh; i++) {
882: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
883: for (j=ncl+1; j<=nch; j++)
884: m[i][j]=m[i][j-1]+nlay;
885: }
886: return m;
887: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
888: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
889: */
890: }
891:
892: /*************************free ma3x ************************/
893: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
894: {
895: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
896: free((FREE_ARG)(m[nrl]+ncl-NR_END));
897: free((FREE_ARG)(m+nrl-NR_END));
898: }
899:
900: /*************** function subdirf ***********/
901: char *subdirf(char fileres[])
902: {
903: /* Caution optionfilefiname is hidden */
904: strcpy(tmpout,optionfilefiname);
905: strcat(tmpout,"/"); /* Add to the right */
906: strcat(tmpout,fileres);
907: return tmpout;
908: }
909:
910: /*************** function subdirf2 ***********/
911: char *subdirf2(char fileres[], char *preop)
912: {
913:
914: /* Caution optionfilefiname is hidden */
915: strcpy(tmpout,optionfilefiname);
916: strcat(tmpout,"/");
917: strcat(tmpout,preop);
918: strcat(tmpout,fileres);
919: return tmpout;
920: }
921:
922: /*************** function subdirf3 ***********/
923: char *subdirf3(char fileres[], char *preop, char *preop2)
924: {
925:
926: /* Caution optionfilefiname is hidden */
927: strcpy(tmpout,optionfilefiname);
928: strcat(tmpout,"/");
929: strcat(tmpout,preop);
930: strcat(tmpout,preop2);
931: strcat(tmpout,fileres);
932: return tmpout;
933: }
934:
935: /***************** f1dim *************************/
936: extern int ncom;
937: extern double *pcom,*xicom;
938: extern double (*nrfunc)(double []);
939:
940: double f1dim(double x)
941: {
942: int j;
943: double f;
944: double *xt;
945:
946: xt=vector(1,ncom);
947: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
948: f=(*nrfunc)(xt);
949: free_vector(xt,1,ncom);
950: return f;
951: }
952:
953: /*****************brent *************************/
954: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
955: {
956: int iter;
957: double a,b,d,etemp;
958: double fu,fv,fw,fx;
959: double ftemp;
960: double p,q,r,tol1,tol2,u,v,w,x,xm;
961: double e=0.0;
962:
963: a=(ax < cx ? ax : cx);
964: b=(ax > cx ? ax : cx);
965: x=w=v=bx;
966: fw=fv=fx=(*f)(x);
967: for (iter=1;iter<=ITMAX;iter++) {
968: xm=0.5*(a+b);
969: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
970: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
971: printf(".");fflush(stdout);
972: fprintf(ficlog,".");fflush(ficlog);
973: #ifdef DEBUG
974: 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);
975: 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);
976: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
977: #endif
978: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
979: *xmin=x;
980: return fx;
981: }
982: ftemp=fu;
983: if (fabs(e) > tol1) {
984: r=(x-w)*(fx-fv);
985: q=(x-v)*(fx-fw);
986: p=(x-v)*q-(x-w)*r;
987: q=2.0*(q-r);
988: if (q > 0.0) p = -p;
989: q=fabs(q);
990: etemp=e;
991: e=d;
992: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
993: d=CGOLD*(e=(x >= xm ? a-x : b-x));
994: else {
995: d=p/q;
996: u=x+d;
997: if (u-a < tol2 || b-u < tol2)
998: d=SIGN(tol1,xm-x);
999: }
1000: } else {
1001: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1002: }
1003: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1004: fu=(*f)(u);
1005: if (fu <= fx) {
1006: if (u >= x) a=x; else b=x;
1007: SHFT(v,w,x,u)
1008: SHFT(fv,fw,fx,fu)
1009: } else {
1010: if (u < x) a=u; else b=u;
1011: if (fu <= fw || w == x) {
1012: v=w;
1013: w=u;
1014: fv=fw;
1015: fw=fu;
1016: } else if (fu <= fv || v == x || v == w) {
1017: v=u;
1018: fv=fu;
1019: }
1020: }
1021: }
1022: nrerror("Too many iterations in brent");
1023: *xmin=x;
1024: return fx;
1025: }
1026:
1027: /****************** mnbrak ***********************/
1028:
1029: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1030: double (*func)(double))
1031: {
1032: double ulim,u,r,q, dum;
1033: double fu;
1034:
1035: *fa=(*func)(*ax);
1036: *fb=(*func)(*bx);
1037: if (*fb > *fa) {
1038: SHFT(dum,*ax,*bx,dum)
1039: SHFT(dum,*fb,*fa,dum)
1040: }
1041: *cx=(*bx)+GOLD*(*bx-*ax);
1042: *fc=(*func)(*cx);
1043: while (*fb > *fc) {
1044: r=(*bx-*ax)*(*fb-*fc);
1045: q=(*bx-*cx)*(*fb-*fa);
1046: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1047: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1048: ulim=(*bx)+GLIMIT*(*cx-*bx);
1049: if ((*bx-u)*(u-*cx) > 0.0) {
1050: fu=(*func)(u);
1051: } else if ((*cx-u)*(u-ulim) > 0.0) {
1052: fu=(*func)(u);
1053: if (fu < *fc) {
1054: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1055: SHFT(*fb,*fc,fu,(*func)(u))
1056: }
1057: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1058: u=ulim;
1059: fu=(*func)(u);
1060: } else {
1061: u=(*cx)+GOLD*(*cx-*bx);
1062: fu=(*func)(u);
1063: }
1064: SHFT(*ax,*bx,*cx,u)
1065: SHFT(*fa,*fb,*fc,fu)
1066: }
1067: }
1068:
1069: /*************** linmin ************************/
1070:
1071: int ncom;
1072: double *pcom,*xicom;
1073: double (*nrfunc)(double []);
1074:
1075: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1076: {
1077: double brent(double ax, double bx, double cx,
1078: double (*f)(double), double tol, double *xmin);
1079: double f1dim(double x);
1080: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1081: double *fc, double (*func)(double));
1082: int j;
1083: double xx,xmin,bx,ax;
1084: double fx,fb,fa;
1085:
1086: ncom=n;
1087: pcom=vector(1,n);
1088: xicom=vector(1,n);
1089: nrfunc=func;
1090: for (j=1;j<=n;j++) {
1091: pcom[j]=p[j];
1092: xicom[j]=xi[j];
1093: }
1094: ax=0.0;
1095: xx=1.0;
1096: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1097: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1098: #ifdef DEBUG
1099: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1100: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1101: #endif
1102: for (j=1;j<=n;j++) {
1103: xi[j] *= xmin;
1104: p[j] += xi[j];
1105: }
1106: free_vector(xicom,1,n);
1107: free_vector(pcom,1,n);
1108: }
1109:
1110: char *asc_diff_time(long time_sec, char ascdiff[])
1111: {
1112: long sec_left, days, hours, minutes;
1113: days = (time_sec) / (60*60*24);
1114: sec_left = (time_sec) % (60*60*24);
1115: hours = (sec_left) / (60*60) ;
1116: sec_left = (sec_left) %(60*60);
1117: minutes = (sec_left) /60;
1118: sec_left = (sec_left) % (60);
1.141 brouard 1119: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1.126 brouard 1120: return ascdiff;
1121: }
1122:
1123: /*************** powell ************************/
1124: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1125: double (*func)(double []))
1126: {
1127: void linmin(double p[], double xi[], int n, double *fret,
1128: double (*func)(double []));
1129: int i,ibig,j;
1130: double del,t,*pt,*ptt,*xit;
1131: double fp,fptt;
1132: double *xits;
1133: int niterf, itmp;
1134:
1135: pt=vector(1,n);
1136: ptt=vector(1,n);
1137: xit=vector(1,n);
1138: xits=vector(1,n);
1139: *fret=(*func)(p);
1140: for (j=1;j<=n;j++) pt[j]=p[j];
1141: for (*iter=1;;++(*iter)) {
1142: fp=(*fret);
1143: ibig=0;
1144: del=0.0;
1145: last_time=curr_time;
1146: (void) gettimeofday(&curr_time,&tzp);
1147: 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);
1148: 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);
1149: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1150: for (i=1;i<=n;i++) {
1151: printf(" %d %.12f",i, p[i]);
1152: fprintf(ficlog," %d %.12lf",i, p[i]);
1153: fprintf(ficrespow," %.12lf", p[i]);
1154: }
1155: printf("\n");
1156: fprintf(ficlog,"\n");
1157: fprintf(ficrespow,"\n");fflush(ficrespow);
1158: if(*iter <=3){
1159: tm = *localtime(&curr_time.tv_sec);
1160: strcpy(strcurr,asctime(&tm));
1161: /* asctime_r(&tm,strcurr); */
1162: forecast_time=curr_time;
1163: itmp = strlen(strcurr);
1164: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1165: strcurr[itmp-1]='\0';
1166: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1167: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1168: for(niterf=10;niterf<=30;niterf+=10){
1169: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1170: tmf = *localtime(&forecast_time.tv_sec);
1171: /* asctime_r(&tmf,strfor); */
1172: strcpy(strfor,asctime(&tmf));
1173: itmp = strlen(strfor);
1174: if(strfor[itmp-1]=='\n')
1175: strfor[itmp-1]='\0';
1176: 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);
1177: 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);
1178: }
1179: }
1180: for (i=1;i<=n;i++) {
1181: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1182: fptt=(*fret);
1183: #ifdef DEBUG
1184: printf("fret=%lf \n",*fret);
1185: fprintf(ficlog,"fret=%lf \n",*fret);
1186: #endif
1187: printf("%d",i);fflush(stdout);
1188: fprintf(ficlog,"%d",i);fflush(ficlog);
1189: linmin(p,xit,n,fret,func);
1190: if (fabs(fptt-(*fret)) > del) {
1191: del=fabs(fptt-(*fret));
1192: ibig=i;
1193: }
1194: #ifdef DEBUG
1195: printf("%d %.12e",i,(*fret));
1196: fprintf(ficlog,"%d %.12e",i,(*fret));
1197: for (j=1;j<=n;j++) {
1198: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1199: printf(" x(%d)=%.12e",j,xit[j]);
1200: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1201: }
1202: for(j=1;j<=n;j++) {
1203: printf(" p=%.12e",p[j]);
1204: fprintf(ficlog," p=%.12e",p[j]);
1205: }
1206: printf("\n");
1207: fprintf(ficlog,"\n");
1208: #endif
1209: }
1210: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1211: #ifdef DEBUG
1212: int k[2],l;
1213: k[0]=1;
1214: k[1]=-1;
1215: printf("Max: %.12e",(*func)(p));
1216: fprintf(ficlog,"Max: %.12e",(*func)(p));
1217: for (j=1;j<=n;j++) {
1218: printf(" %.12e",p[j]);
1219: fprintf(ficlog," %.12e",p[j]);
1220: }
1221: printf("\n");
1222: fprintf(ficlog,"\n");
1223: for(l=0;l<=1;l++) {
1224: for (j=1;j<=n;j++) {
1225: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1226: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1227: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1228: }
1229: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1230: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1231: }
1232: #endif
1233:
1234:
1235: free_vector(xit,1,n);
1236: free_vector(xits,1,n);
1237: free_vector(ptt,1,n);
1238: free_vector(pt,1,n);
1239: return;
1240: }
1241: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1242: for (j=1;j<=n;j++) {
1243: ptt[j]=2.0*p[j]-pt[j];
1244: xit[j]=p[j]-pt[j];
1245: pt[j]=p[j];
1246: }
1247: fptt=(*func)(ptt);
1248: if (fptt < fp) {
1249: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1250: if (t < 0.0) {
1251: linmin(p,xit,n,fret,func);
1252: for (j=1;j<=n;j++) {
1253: xi[j][ibig]=xi[j][n];
1254: xi[j][n]=xit[j];
1255: }
1256: #ifdef DEBUG
1257: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1258: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1259: for(j=1;j<=n;j++){
1260: printf(" %.12e",xit[j]);
1261: fprintf(ficlog," %.12e",xit[j]);
1262: }
1263: printf("\n");
1264: fprintf(ficlog,"\n");
1265: #endif
1266: }
1267: }
1268: }
1269: }
1270:
1271: /**** Prevalence limit (stable or period prevalence) ****************/
1272:
1273: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1274: {
1275: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1276: matrix by transitions matrix until convergence is reached */
1277:
1278: int i, ii,j,k;
1279: double min, max, maxmin, maxmax,sumnew=0.;
1280: double **matprod2();
1.131 brouard 1281: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1282: double **newm;
1283: double agefin, delaymax=50 ; /* Max number of years to converge */
1284:
1285: for (ii=1;ii<=nlstate+ndeath;ii++)
1286: for (j=1;j<=nlstate+ndeath;j++){
1287: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1288: }
1289:
1290: cov[1]=1.;
1291:
1292: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1293: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1294: newm=savm;
1295: /* Covariates have to be included here again */
1.138 brouard 1296: cov[2]=agefin;
1297:
1298: for (k=1; k<=cptcovn;k++) {
1299: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1300: /* 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]]);*/
1301: }
1302: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1303: for (k=1; k<=cptcovprod;k++)
1304: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1305:
1306: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1307: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1308: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.142 brouard 1309: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1310:
1.126 brouard 1311: savm=oldm;
1312: oldm=newm;
1313: maxmax=0.;
1314: for(j=1;j<=nlstate;j++){
1315: min=1.;
1316: max=0.;
1317: for(i=1; i<=nlstate; i++) {
1318: sumnew=0;
1319: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1320: prlim[i][j]= newm[i][j]/(1-sumnew);
1321: max=FMAX(max,prlim[i][j]);
1322: min=FMIN(min,prlim[i][j]);
1323: }
1324: maxmin=max-min;
1325: maxmax=FMAX(maxmax,maxmin);
1326: }
1327: if(maxmax < ftolpl){
1328: return prlim;
1329: }
1330: }
1331: }
1332:
1333: /*************** transition probabilities ***************/
1334:
1335: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1336: {
1.138 brouard 1337: /* According to parameters values stored in x and the covariate's values stored in cov,
1338: computes the probability to be observed in state j being in state i by appying the
1339: model to the ncovmodel covariates (including constant and age).
1340: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1341: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1342: ncth covariate in the global vector x is given by the formula:
1343: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1344: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1345: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1346: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1347: Outputs ps[i][j] the probability to be observed in j being in j according to
1348: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1349: */
1350: double s1, lnpijopii;
1.126 brouard 1351: /*double t34;*/
1352: int i,j,j1, nc, ii, jj;
1353:
1354: for(i=1; i<= nlstate; i++){
1355: for(j=1; j<i;j++){
1.138 brouard 1356: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1357: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1358: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1359: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1360: }
1.138 brouard 1361: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1362: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1363: }
1364: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1365: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1366: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1367: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1368: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1369: }
1.138 brouard 1370: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1371: }
1372: }
1373:
1374: for(i=1; i<= nlstate; i++){
1375: s1=0;
1.131 brouard 1376: for(j=1; j<i; j++){
1.138 brouard 1377: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1378: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1379: }
1380: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1381: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1382: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1383: }
1.138 brouard 1384: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1385: ps[i][i]=1./(s1+1.);
1.138 brouard 1386: /* Computing other pijs */
1.126 brouard 1387: for(j=1; j<i; j++)
1388: ps[i][j]= exp(ps[i][j])*ps[i][i];
1389: for(j=i+1; j<=nlstate+ndeath; j++)
1390: ps[i][j]= exp(ps[i][j])*ps[i][i];
1391: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1392: } /* end i */
1393:
1394: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1395: for(jj=1; jj<= nlstate+ndeath; jj++){
1396: ps[ii][jj]=0;
1397: ps[ii][ii]=1;
1398: }
1399: }
1400:
1401:
1402: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1403: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1404: /* printf("ddd %lf ",ps[ii][jj]); */
1405: /* } */
1406: /* printf("\n "); */
1407: /* } */
1408: /* printf("\n ");printf("%lf ",cov[2]); */
1409: /*
1410: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1411: goto end;*/
1412: return ps;
1413: }
1414:
1415: /**************** Product of 2 matrices ******************/
1416:
1417: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1418: {
1419: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1420: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1421: /* in, b, out are matrice of pointers which should have been initialized
1422: before: only the contents of out is modified. The function returns
1423: a pointer to pointers identical to out */
1424: long i, j, k;
1425: for(i=nrl; i<= nrh; i++)
1426: for(k=ncolol; k<=ncoloh; k++)
1427: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1428: out[i][k] +=in[i][j]*b[j][k];
1429:
1430: return out;
1431: }
1432:
1433:
1434: /************* Higher Matrix Product ***************/
1435:
1436: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1437: {
1438: /* Computes the transition matrix starting at age 'age' over
1439: 'nhstepm*hstepm*stepm' months (i.e. until
1440: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1441: nhstepm*hstepm matrices.
1442: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1443: (typically every 2 years instead of every month which is too big
1444: for the memory).
1445: Model is determined by parameters x and covariates have to be
1446: included manually here.
1447:
1448: */
1449:
1450: int i, j, d, h, k;
1.131 brouard 1451: double **out, cov[NCOVMAX+1];
1.126 brouard 1452: double **newm;
1453:
1454: /* Hstepm could be zero and should return the unit matrix */
1455: for (i=1;i<=nlstate+ndeath;i++)
1456: for (j=1;j<=nlstate+ndeath;j++){
1457: oldm[i][j]=(i==j ? 1.0 : 0.0);
1458: po[i][j][0]=(i==j ? 1.0 : 0.0);
1459: }
1460: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1461: for(h=1; h <=nhstepm; h++){
1462: for(d=1; d <=hstepm; d++){
1463: newm=savm;
1464: /* Covariates have to be included here again */
1465: cov[1]=1.;
1466: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1467: for (k=1; k<=cptcovn;k++)
1468: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1469: for (k=1; k<=cptcovage;k++)
1470: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1471: for (k=1; k<=cptcovprod;k++)
1472: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1473:
1474:
1475: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1476: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1477: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1478: pmij(pmmij,cov,ncovmodel,x,nlstate));
1479: savm=oldm;
1480: oldm=newm;
1481: }
1482: for(i=1; i<=nlstate+ndeath; i++)
1483: for(j=1;j<=nlstate+ndeath;j++) {
1484: po[i][j][h]=newm[i][j];
1.128 brouard 1485: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1486: }
1.128 brouard 1487: /*printf("h=%d ",h);*/
1.126 brouard 1488: } /* end h */
1.128 brouard 1489: /* printf("\n H=%d \n",h); */
1.126 brouard 1490: return po;
1491: }
1492:
1493:
1494: /*************** log-likelihood *************/
1495: double func( double *x)
1496: {
1497: int i, ii, j, k, mi, d, kk;
1.131 brouard 1498: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1499: double **out;
1500: double sw; /* Sum of weights */
1501: double lli; /* Individual log likelihood */
1502: int s1, s2;
1503: double bbh, survp;
1504: long ipmx;
1505: /*extern weight */
1506: /* We are differentiating ll according to initial status */
1507: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1508: /*for(i=1;i<imx;i++)
1509: printf(" %d\n",s[4][i]);
1510: */
1511: cov[1]=1.;
1512:
1513: for(k=1; k<=nlstate; k++) ll[k]=0.;
1514:
1515: if(mle==1){
1516: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1517: /* Computes the values of the ncovmodel covariates of the model
1518: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1519: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1520: to be observed in j being in i according to the model.
1521: */
1.126 brouard 1522: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1.137 brouard 1523: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1524: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1525: has been calculated etc */
1.126 brouard 1526: for(mi=1; mi<= wav[i]-1; mi++){
1527: for (ii=1;ii<=nlstate+ndeath;ii++)
1528: for (j=1;j<=nlstate+ndeath;j++){
1529: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1530: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1531: }
1532: for(d=0; d<dh[mi][i]; d++){
1533: newm=savm;
1534: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1535: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1536: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1537: }
1538: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1539: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1540: savm=oldm;
1541: oldm=newm;
1542: } /* end mult */
1543:
1544: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1545: /* But now since version 0.9 we anticipate for bias at large stepm.
1546: * If stepm is larger than one month (smallest stepm) and if the exact delay
1547: * (in months) between two waves is not a multiple of stepm, we rounded to
1548: * the nearest (and in case of equal distance, to the lowest) interval but now
1549: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1550: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1551: * probability in order to take into account the bias as a fraction of the way
1552: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1553: * -stepm/2 to stepm/2 .
1554: * For stepm=1 the results are the same as for previous versions of Imach.
1555: * For stepm > 1 the results are less biased than in previous versions.
1556: */
1557: s1=s[mw[mi][i]][i];
1558: s2=s[mw[mi+1][i]][i];
1559: bbh=(double)bh[mi][i]/(double)stepm;
1560: /* bias bh is positive if real duration
1561: * is higher than the multiple of stepm and negative otherwise.
1562: */
1563: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1564: if( s2 > nlstate){
1565: /* i.e. if s2 is a death state and if the date of death is known
1566: then the contribution to the likelihood is the probability to
1567: die between last step unit time and current step unit time,
1568: which is also equal to probability to die before dh
1569: minus probability to die before dh-stepm .
1570: In version up to 0.92 likelihood was computed
1571: as if date of death was unknown. Death was treated as any other
1572: health state: the date of the interview describes the actual state
1573: and not the date of a change in health state. The former idea was
1574: to consider that at each interview the state was recorded
1575: (healthy, disable or death) and IMaCh was corrected; but when we
1576: introduced the exact date of death then we should have modified
1577: the contribution of an exact death to the likelihood. This new
1578: contribution is smaller and very dependent of the step unit
1579: stepm. It is no more the probability to die between last interview
1580: and month of death but the probability to survive from last
1581: interview up to one month before death multiplied by the
1582: probability to die within a month. Thanks to Chris
1583: Jackson for correcting this bug. Former versions increased
1584: mortality artificially. The bad side is that we add another loop
1585: which slows down the processing. The difference can be up to 10%
1586: lower mortality.
1587: */
1588: lli=log(out[s1][s2] - savm[s1][s2]);
1589:
1590:
1591: } else if (s2==-2) {
1592: for (j=1,survp=0. ; j<=nlstate; j++)
1593: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1594: /*survp += out[s1][j]; */
1595: lli= log(survp);
1596: }
1597:
1598: else if (s2==-4) {
1599: for (j=3,survp=0. ; j<=nlstate; j++)
1600: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1601: lli= log(survp);
1602: }
1603:
1604: else if (s2==-5) {
1605: for (j=1,survp=0. ; j<=2; j++)
1606: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1607: lli= log(survp);
1608: }
1609:
1610: else{
1611: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1612: /* 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 */
1613: }
1614: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1615: /*if(lli ==000.0)*/
1616: /*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); */
1617: ipmx +=1;
1618: sw += weight[i];
1619: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1620: } /* end of wave */
1621: } /* end of individual */
1622: } else if(mle==2){
1623: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1624: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1625: for(mi=1; mi<= wav[i]-1; mi++){
1626: for (ii=1;ii<=nlstate+ndeath;ii++)
1627: for (j=1;j<=nlstate+ndeath;j++){
1628: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1629: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1630: }
1631: for(d=0; d<=dh[mi][i]; d++){
1632: newm=savm;
1633: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1634: for (kk=1; kk<=cptcovage;kk++) {
1635: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1636: }
1637: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1638: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1639: savm=oldm;
1640: oldm=newm;
1641: } /* end mult */
1642:
1643: s1=s[mw[mi][i]][i];
1644: s2=s[mw[mi+1][i]][i];
1645: bbh=(double)bh[mi][i]/(double)stepm;
1646: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1647: ipmx +=1;
1648: sw += weight[i];
1649: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1650: } /* end of wave */
1651: } /* end of individual */
1652: } else if(mle==3){ /* exponential inter-extrapolation */
1653: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1654: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1655: for(mi=1; mi<= wav[i]-1; mi++){
1656: for (ii=1;ii<=nlstate+ndeath;ii++)
1657: for (j=1;j<=nlstate+ndeath;j++){
1658: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1659: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1660: }
1661: for(d=0; d<dh[mi][i]; d++){
1662: newm=savm;
1663: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1664: for (kk=1; kk<=cptcovage;kk++) {
1665: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1666: }
1667: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1668: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1669: savm=oldm;
1670: oldm=newm;
1671: } /* end mult */
1672:
1673: s1=s[mw[mi][i]][i];
1674: s2=s[mw[mi+1][i]][i];
1675: bbh=(double)bh[mi][i]/(double)stepm;
1676: 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 */
1677: ipmx +=1;
1678: sw += weight[i];
1679: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1680: } /* end of wave */
1681: } /* end of individual */
1682: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1683: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1684: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1685: for(mi=1; mi<= wav[i]-1; mi++){
1686: for (ii=1;ii<=nlstate+ndeath;ii++)
1687: for (j=1;j<=nlstate+ndeath;j++){
1688: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1689: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1690: }
1691: for(d=0; d<dh[mi][i]; d++){
1692: newm=savm;
1693: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1694: for (kk=1; kk<=cptcovage;kk++) {
1695: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1696: }
1697:
1698: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1699: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1700: savm=oldm;
1701: oldm=newm;
1702: } /* end mult */
1703:
1704: s1=s[mw[mi][i]][i];
1705: s2=s[mw[mi+1][i]][i];
1706: if( s2 > nlstate){
1707: lli=log(out[s1][s2] - savm[s1][s2]);
1708: }else{
1709: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1710: }
1711: ipmx +=1;
1712: sw += weight[i];
1713: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1714: /* 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]); */
1715: } /* end of wave */
1716: } /* end of individual */
1717: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1718: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1719: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1720: for(mi=1; mi<= wav[i]-1; mi++){
1721: for (ii=1;ii<=nlstate+ndeath;ii++)
1722: for (j=1;j<=nlstate+ndeath;j++){
1723: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1724: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1725: }
1726: for(d=0; d<dh[mi][i]; d++){
1727: newm=savm;
1728: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1729: for (kk=1; kk<=cptcovage;kk++) {
1730: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1731: }
1732:
1733: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1734: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1735: savm=oldm;
1736: oldm=newm;
1737: } /* end mult */
1738:
1739: s1=s[mw[mi][i]][i];
1740: s2=s[mw[mi+1][i]][i];
1741: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1742: ipmx +=1;
1743: sw += weight[i];
1744: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1745: /*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]);*/
1746: } /* end of wave */
1747: } /* end of individual */
1748: } /* End of if */
1749: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1750: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1751: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1752: return -l;
1753: }
1754:
1755: /*************** log-likelihood *************/
1756: double funcone( double *x)
1757: {
1758: /* Same as likeli but slower because of a lot of printf and if */
1759: int i, ii, j, k, mi, d, kk;
1.131 brouard 1760: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1761: double **out;
1762: double lli; /* Individual log likelihood */
1763: double llt;
1764: int s1, s2;
1765: double bbh, survp;
1766: /*extern weight */
1767: /* We are differentiating ll according to initial status */
1768: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1769: /*for(i=1;i<imx;i++)
1770: printf(" %d\n",s[4][i]);
1771: */
1772: cov[1]=1.;
1773:
1774: for(k=1; k<=nlstate; k++) ll[k]=0.;
1775:
1776: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1777: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1778: for(mi=1; mi<= wav[i]-1; mi++){
1779: for (ii=1;ii<=nlstate+ndeath;ii++)
1780: for (j=1;j<=nlstate+ndeath;j++){
1781: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1782: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1783: }
1784: for(d=0; d<dh[mi][i]; d++){
1785: newm=savm;
1786: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1787: for (kk=1; kk<=cptcovage;kk++) {
1788: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1789: }
1790: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1791: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1792: savm=oldm;
1793: oldm=newm;
1794: } /* end mult */
1795:
1796: s1=s[mw[mi][i]][i];
1797: s2=s[mw[mi+1][i]][i];
1798: bbh=(double)bh[mi][i]/(double)stepm;
1799: /* bias is positive if real duration
1800: * is higher than the multiple of stepm and negative otherwise.
1801: */
1802: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1803: lli=log(out[s1][s2] - savm[s1][s2]);
1804: } else if (s2==-2) {
1805: for (j=1,survp=0. ; j<=nlstate; j++)
1806: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1807: lli= log(survp);
1808: }else if (mle==1){
1809: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1810: } else if(mle==2){
1811: 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 */
1812: } else if(mle==3){ /* exponential inter-extrapolation */
1813: 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 */
1814: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1815: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 1816: } else{ /* mle=0 back to 1 */
1817: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1818: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 1819: } /* End of if */
1820: ipmx +=1;
1821: sw += weight[i];
1822: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 1823: /*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 1824: if(globpr){
1.141 brouard 1825: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 1826: %11.6f %11.6f %11.6f ", \
1827: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1828: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1829: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1830: llt +=ll[k]*gipmx/gsw;
1831: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1832: }
1833: fprintf(ficresilk," %10.6f\n", -llt);
1834: }
1835: } /* end of wave */
1836: } /* end of individual */
1837: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1838: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1839: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1840: if(globpr==0){ /* First time we count the contributions and weights */
1841: gipmx=ipmx;
1842: gsw=sw;
1843: }
1844: return -l;
1845: }
1846:
1847:
1848: /*************** function likelione ***********/
1849: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1850: {
1851: /* This routine should help understanding what is done with
1852: the selection of individuals/waves and
1853: to check the exact contribution to the likelihood.
1854: Plotting could be done.
1855: */
1856: int k;
1857:
1858: if(*globpri !=0){ /* Just counts and sums, no printings */
1859: strcpy(fileresilk,"ilk");
1860: strcat(fileresilk,fileres);
1861: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1862: printf("Problem with resultfile: %s\n", fileresilk);
1863: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1864: }
1865: 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");
1866: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1867: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1868: for(k=1; k<=nlstate; k++)
1869: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1870: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1871: }
1872:
1873: *fretone=(*funcone)(p);
1874: if(*globpri !=0){
1875: fclose(ficresilk);
1876: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1877: fflush(fichtm);
1878: }
1879: return;
1880: }
1881:
1882:
1883: /*********** Maximum Likelihood Estimation ***************/
1884:
1885: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1886: {
1887: int i,j, iter;
1888: double **xi;
1889: double fret;
1890: double fretone; /* Only one call to likelihood */
1891: /* char filerespow[FILENAMELENGTH];*/
1892: xi=matrix(1,npar,1,npar);
1893: for (i=1;i<=npar;i++)
1894: for (j=1;j<=npar;j++)
1895: xi[i][j]=(i==j ? 1.0 : 0.0);
1896: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1897: strcpy(filerespow,"pow");
1898: strcat(filerespow,fileres);
1899: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1900: printf("Problem with resultfile: %s\n", filerespow);
1901: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1902: }
1903: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1904: for (i=1;i<=nlstate;i++)
1905: for(j=1;j<=nlstate+ndeath;j++)
1906: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1907: fprintf(ficrespow,"\n");
1908:
1909: powell(p,xi,npar,ftol,&iter,&fret,func);
1910:
1911: free_matrix(xi,1,npar,1,npar);
1912: fclose(ficrespow);
1913: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1914: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1915: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1916:
1917: }
1918:
1919: /**** Computes Hessian and covariance matrix ***/
1920: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1921: {
1922: double **a,**y,*x,pd;
1923: double **hess;
1924: int i, j,jk;
1925: int *indx;
1926:
1927: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1928: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1929: void lubksb(double **a, int npar, int *indx, double b[]) ;
1930: void ludcmp(double **a, int npar, int *indx, double *d) ;
1931: double gompertz(double p[]);
1932: hess=matrix(1,npar,1,npar);
1933:
1934: printf("\nCalculation of the hessian matrix. Wait...\n");
1935: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1936: for (i=1;i<=npar;i++){
1937: printf("%d",i);fflush(stdout);
1938: fprintf(ficlog,"%d",i);fflush(ficlog);
1939:
1940: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1941:
1942: /* printf(" %f ",p[i]);
1943: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1944: }
1945:
1946: for (i=1;i<=npar;i++) {
1947: for (j=1;j<=npar;j++) {
1948: if (j>i) {
1949: printf(".%d%d",i,j);fflush(stdout);
1950: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1951: hess[i][j]=hessij(p,delti,i,j,func,npar);
1952:
1953: hess[j][i]=hess[i][j];
1954: /*printf(" %lf ",hess[i][j]);*/
1955: }
1956: }
1957: }
1958: printf("\n");
1959: fprintf(ficlog,"\n");
1960:
1961: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1962: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1963:
1964: a=matrix(1,npar,1,npar);
1965: y=matrix(1,npar,1,npar);
1966: x=vector(1,npar);
1967: indx=ivector(1,npar);
1968: for (i=1;i<=npar;i++)
1969: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1970: ludcmp(a,npar,indx,&pd);
1971:
1972: for (j=1;j<=npar;j++) {
1973: for (i=1;i<=npar;i++) x[i]=0;
1974: x[j]=1;
1975: lubksb(a,npar,indx,x);
1976: for (i=1;i<=npar;i++){
1977: matcov[i][j]=x[i];
1978: }
1979: }
1980:
1981: printf("\n#Hessian matrix#\n");
1982: fprintf(ficlog,"\n#Hessian matrix#\n");
1983: for (i=1;i<=npar;i++) {
1984: for (j=1;j<=npar;j++) {
1985: printf("%.3e ",hess[i][j]);
1986: fprintf(ficlog,"%.3e ",hess[i][j]);
1987: }
1988: printf("\n");
1989: fprintf(ficlog,"\n");
1990: }
1991:
1992: /* Recompute Inverse */
1993: for (i=1;i<=npar;i++)
1994: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1995: ludcmp(a,npar,indx,&pd);
1996:
1997: /* printf("\n#Hessian matrix recomputed#\n");
1998:
1999: for (j=1;j<=npar;j++) {
2000: for (i=1;i<=npar;i++) x[i]=0;
2001: x[j]=1;
2002: lubksb(a,npar,indx,x);
2003: for (i=1;i<=npar;i++){
2004: y[i][j]=x[i];
2005: printf("%.3e ",y[i][j]);
2006: fprintf(ficlog,"%.3e ",y[i][j]);
2007: }
2008: printf("\n");
2009: fprintf(ficlog,"\n");
2010: }
2011: */
2012:
2013: free_matrix(a,1,npar,1,npar);
2014: free_matrix(y,1,npar,1,npar);
2015: free_vector(x,1,npar);
2016: free_ivector(indx,1,npar);
2017: free_matrix(hess,1,npar,1,npar);
2018:
2019:
2020: }
2021:
2022: /*************** hessian matrix ****************/
2023: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2024: {
2025: int i;
2026: int l=1, lmax=20;
2027: double k1,k2;
1.132 brouard 2028: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2029: double res;
2030: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2031: double fx;
2032: int k=0,kmax=10;
2033: double l1;
2034:
2035: fx=func(x);
2036: for (i=1;i<=npar;i++) p2[i]=x[i];
2037: for(l=0 ; l <=lmax; l++){
2038: l1=pow(10,l);
2039: delts=delt;
2040: for(k=1 ; k <kmax; k=k+1){
2041: delt = delta*(l1*k);
2042: p2[theta]=x[theta] +delt;
2043: k1=func(p2)-fx;
2044: p2[theta]=x[theta]-delt;
2045: k2=func(p2)-fx;
2046: /*res= (k1-2.0*fx+k2)/delt/delt; */
2047: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2048:
1.132 brouard 2049: #ifdef DEBUGHESS
1.126 brouard 2050: 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);
2051: 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);
2052: #endif
2053: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2054: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2055: k=kmax;
2056: }
2057: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2058: k=kmax; l=lmax*10.;
2059: }
2060: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2061: delts=delt;
2062: }
2063: }
2064: }
2065: delti[theta]=delts;
2066: return res;
2067:
2068: }
2069:
2070: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2071: {
2072: int i;
2073: int l=1, l1, lmax=20;
2074: double k1,k2,k3,k4,res,fx;
1.132 brouard 2075: double p2[MAXPARM+1];
1.126 brouard 2076: int k;
2077:
2078: fx=func(x);
2079: for (k=1; k<=2; k++) {
2080: for (i=1;i<=npar;i++) p2[i]=x[i];
2081: p2[thetai]=x[thetai]+delti[thetai]/k;
2082: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2083: k1=func(p2)-fx;
2084:
2085: p2[thetai]=x[thetai]+delti[thetai]/k;
2086: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2087: k2=func(p2)-fx;
2088:
2089: p2[thetai]=x[thetai]-delti[thetai]/k;
2090: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2091: k3=func(p2)-fx;
2092:
2093: p2[thetai]=x[thetai]-delti[thetai]/k;
2094: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2095: k4=func(p2)-fx;
2096: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2097: #ifdef DEBUG
2098: 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);
2099: 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);
2100: #endif
2101: }
2102: return res;
2103: }
2104:
2105: /************** Inverse of matrix **************/
2106: void ludcmp(double **a, int n, int *indx, double *d)
2107: {
2108: int i,imax,j,k;
2109: double big,dum,sum,temp;
2110: double *vv;
2111:
2112: vv=vector(1,n);
2113: *d=1.0;
2114: for (i=1;i<=n;i++) {
2115: big=0.0;
2116: for (j=1;j<=n;j++)
2117: if ((temp=fabs(a[i][j])) > big) big=temp;
2118: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2119: vv[i]=1.0/big;
2120: }
2121: for (j=1;j<=n;j++) {
2122: for (i=1;i<j;i++) {
2123: sum=a[i][j];
2124: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2125: a[i][j]=sum;
2126: }
2127: big=0.0;
2128: for (i=j;i<=n;i++) {
2129: sum=a[i][j];
2130: for (k=1;k<j;k++)
2131: sum -= a[i][k]*a[k][j];
2132: a[i][j]=sum;
2133: if ( (dum=vv[i]*fabs(sum)) >= big) {
2134: big=dum;
2135: imax=i;
2136: }
2137: }
2138: if (j != imax) {
2139: for (k=1;k<=n;k++) {
2140: dum=a[imax][k];
2141: a[imax][k]=a[j][k];
2142: a[j][k]=dum;
2143: }
2144: *d = -(*d);
2145: vv[imax]=vv[j];
2146: }
2147: indx[j]=imax;
2148: if (a[j][j] == 0.0) a[j][j]=TINY;
2149: if (j != n) {
2150: dum=1.0/(a[j][j]);
2151: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2152: }
2153: }
2154: free_vector(vv,1,n); /* Doesn't work */
2155: ;
2156: }
2157:
2158: void lubksb(double **a, int n, int *indx, double b[])
2159: {
2160: int i,ii=0,ip,j;
2161: double sum;
2162:
2163: for (i=1;i<=n;i++) {
2164: ip=indx[i];
2165: sum=b[ip];
2166: b[ip]=b[i];
2167: if (ii)
2168: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2169: else if (sum) ii=i;
2170: b[i]=sum;
2171: }
2172: for (i=n;i>=1;i--) {
2173: sum=b[i];
2174: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2175: b[i]=sum/a[i][i];
2176: }
2177: }
2178:
2179: void pstamp(FILE *fichier)
2180: {
2181: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2182: }
2183:
2184: /************ Frequencies ********************/
2185: 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[])
2186: { /* Some frequencies */
2187:
1.130 brouard 2188: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2189: int first;
2190: double ***freq; /* Frequencies */
2191: double *pp, **prop;
2192: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2193: char fileresp[FILENAMELENGTH];
2194:
2195: pp=vector(1,nlstate);
2196: prop=matrix(1,nlstate,iagemin,iagemax+3);
2197: strcpy(fileresp,"p");
2198: strcat(fileresp,fileres);
2199: if((ficresp=fopen(fileresp,"w"))==NULL) {
2200: printf("Problem with prevalence resultfile: %s\n", fileresp);
2201: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2202: exit(0);
2203: }
2204: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2205: j1=0;
2206:
2207: j=cptcoveff;
2208: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2209:
2210: first=1;
2211:
1.144 ! brouard 2212: for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
1.143 brouard 2213: for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
1.126 brouard 2214: j1++;
2215: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2216: scanf("%d", i);*/
2217: for (i=-5; i<=nlstate+ndeath; i++)
2218: for (jk=-5; jk<=nlstate+ndeath; jk++)
2219: for(m=iagemin; m <= iagemax+3; m++)
2220: freq[i][jk][m]=0;
1.143 brouard 2221:
2222: for (i=1; i<=nlstate; i++)
2223: for(m=iagemin; m <= iagemax+3; m++)
2224: prop[i][m]=0;
1.126 brouard 2225:
2226: dateintsum=0;
2227: k2cpt=0;
2228: for (i=1; i<=imx; i++) {
2229: bool=1;
1.144 ! brouard 2230: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
! 2231: for (z1=1; z1<=cptcoveff; z1++)
! 2232: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
! 2233: bool=0;
! 2234: printf("bool=%d i=%d, z1=%d, i1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
! 2235: bool,i,z1, i1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
! 2236: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);
! 2237: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
! 2238: }
1.126 brouard 2239: }
1.144 ! brouard 2240:
1.126 brouard 2241: if (bool==1){
2242: for(m=firstpass; m<=lastpass; m++){
2243: k2=anint[m][i]+(mint[m][i]/12.);
2244: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2245: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2246: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2247: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2248: if (m<lastpass) {
2249: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2250: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2251: }
2252:
2253: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2254: dateintsum=dateintsum+k2;
2255: k2cpt++;
2256: }
2257: /*}*/
2258: }
2259: }
2260: }
2261:
2262: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2263: pstamp(ficresp);
2264: if (cptcovn>0) {
2265: fprintf(ficresp, "\n#********** Variable ");
2266: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2267: fprintf(ficresp, "**********\n#");
1.143 brouard 2268: fprintf(ficlog, "\n#********** Variable ");
2269: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2270: fprintf(ficlog, "**********\n#");
1.126 brouard 2271: }
2272: for(i=1; i<=nlstate;i++)
2273: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2274: fprintf(ficresp, "\n");
2275:
2276: for(i=iagemin; i <= iagemax+3; i++){
2277: if(i==iagemax+3){
2278: fprintf(ficlog,"Total");
2279: }else{
2280: if(first==1){
2281: first=0;
2282: printf("See log file for details...\n");
2283: }
2284: fprintf(ficlog,"Age %d", i);
2285: }
2286: for(jk=1; jk <=nlstate ; jk++){
2287: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2288: pp[jk] += freq[jk][m][i];
2289: }
2290: for(jk=1; jk <=nlstate ; jk++){
2291: for(m=-1, pos=0; m <=0 ; m++)
2292: pos += freq[jk][m][i];
2293: if(pp[jk]>=1.e-10){
2294: if(first==1){
1.132 brouard 2295: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2296: }
2297: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2298: }else{
2299: if(first==1)
2300: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2301: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2302: }
2303: }
2304:
2305: for(jk=1; jk <=nlstate ; jk++){
2306: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2307: pp[jk] += freq[jk][m][i];
2308: }
2309: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2310: pos += pp[jk];
2311: posprop += prop[jk][i];
2312: }
2313: for(jk=1; jk <=nlstate ; jk++){
2314: if(pos>=1.e-5){
2315: if(first==1)
2316: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2317: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2318: }else{
2319: if(first==1)
2320: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2321: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2322: }
2323: if( i <= iagemax){
2324: if(pos>=1.e-5){
2325: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2326: /*probs[i][jk][j1]= pp[jk]/pos;*/
2327: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2328: }
2329: else
2330: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2331: }
2332: }
2333:
2334: for(jk=-1; jk <=nlstate+ndeath; jk++)
2335: for(m=-1; m <=nlstate+ndeath; m++)
2336: if(freq[jk][m][i] !=0 ) {
2337: if(first==1)
2338: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2339: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2340: }
2341: if(i <= iagemax)
2342: fprintf(ficresp,"\n");
2343: if(first==1)
2344: printf("Others in log...\n");
2345: fprintf(ficlog,"\n");
2346: }
2347: }
2348: }
2349: dateintmean=dateintsum/k2cpt;
2350:
2351: fclose(ficresp);
2352: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2353: free_vector(pp,1,nlstate);
2354: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2355: /* End of Freq */
2356: }
2357:
2358: /************ Prevalence ********************/
2359: 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)
2360: {
2361: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2362: in each health status at the date of interview (if between dateprev1 and dateprev2).
2363: We still use firstpass and lastpass as another selection.
2364: */
2365:
1.130 brouard 2366: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2367: double ***freq; /* Frequencies */
2368: double *pp, **prop;
2369: double pos,posprop;
2370: double y2; /* in fractional years */
2371: int iagemin, iagemax;
2372:
2373: iagemin= (int) agemin;
2374: iagemax= (int) agemax;
2375: /*pp=vector(1,nlstate);*/
2376: prop=matrix(1,nlstate,iagemin,iagemax+3);
2377: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2378: j1=0;
2379:
2380: j=cptcoveff;
2381: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2382:
2383: for(k1=1; k1<=j;k1++){
2384: for(i1=1; i1<=ncodemax[k1];i1++){
2385: j1++;
2386:
2387: for (i=1; i<=nlstate; i++)
2388: for(m=iagemin; m <= iagemax+3; m++)
2389: prop[i][m]=0.0;
2390:
2391: for (i=1; i<=imx; i++) { /* Each individual */
2392: bool=1;
2393: if (cptcovn>0) {
2394: for (z1=1; z1<=cptcoveff; z1++)
2395: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2396: bool=0;
2397: }
2398: if (bool==1) {
2399: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2400: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2401: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2402: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2403: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2404: 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);
2405: if (s[m][i]>0 && s[m][i]<=nlstate) {
2406: /*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]]);*/
2407: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2408: prop[s[m][i]][iagemax+3] += weight[i];
2409: }
2410: }
2411: } /* end selection of waves */
2412: }
2413: }
2414: for(i=iagemin; i <= iagemax+3; i++){
2415:
2416: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2417: posprop += prop[jk][i];
2418: }
2419:
2420: for(jk=1; jk <=nlstate ; jk++){
2421: if( i <= iagemax){
2422: if(posprop>=1.e-5){
2423: probs[i][jk][j1]= prop[jk][i]/posprop;
1.128 brouard 2424: } else
2425: 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 2426: }
2427: }/* end jk */
2428: }/* end i */
2429: } /* end i1 */
2430: } /* end k1 */
2431:
2432: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2433: /*free_vector(pp,1,nlstate);*/
2434: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2435: } /* End of prevalence */
2436:
2437: /************* Waves Concatenation ***************/
2438:
2439: 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)
2440: {
2441: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2442: Death is a valid wave (if date is known).
2443: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2444: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2445: and mw[mi+1][i]. dh depends on stepm.
2446: */
2447:
2448: int i, mi, m;
2449: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2450: double sum=0., jmean=0.;*/
2451: int first;
2452: int j, k=0,jk, ju, jl;
2453: double sum=0.;
2454: first=0;
2455: jmin=1e+5;
2456: jmax=-1;
2457: jmean=0.;
2458: for(i=1; i<=imx; i++){
2459: mi=0;
2460: m=firstpass;
2461: while(s[m][i] <= nlstate){
2462: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2463: mw[++mi][i]=m;
2464: if(m >=lastpass)
2465: break;
2466: else
2467: m++;
2468: }/* end while */
2469: if (s[m][i] > nlstate){
2470: mi++; /* Death is another wave */
2471: /* if(mi==0) never been interviewed correctly before death */
2472: /* Only death is a correct wave */
2473: mw[mi][i]=m;
2474: }
2475:
2476: wav[i]=mi;
2477: if(mi==0){
2478: nbwarn++;
2479: if(first==0){
2480: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2481: first=1;
2482: }
2483: if(first==1){
2484: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2485: }
2486: } /* end mi==0 */
2487: } /* End individuals */
2488:
2489: for(i=1; i<=imx; i++){
2490: for(mi=1; mi<wav[i];mi++){
2491: if (stepm <=0)
2492: dh[mi][i]=1;
2493: else{
2494: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2495: if (agedc[i] < 2*AGESUP) {
2496: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2497: if(j==0) j=1; /* Survives at least one month after exam */
2498: else if(j<0){
2499: nberr++;
2500: 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]);
2501: j=1; /* Temporary Dangerous patch */
2502: 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);
2503: 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]);
2504: 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);
2505: }
2506: k=k+1;
2507: if (j >= jmax){
2508: jmax=j;
2509: ijmax=i;
2510: }
2511: if (j <= jmin){
2512: jmin=j;
2513: ijmin=i;
2514: }
2515: sum=sum+j;
2516: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2517: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2518: }
2519: }
2520: else{
2521: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2522: /* 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]); */
2523:
2524: k=k+1;
2525: if (j >= jmax) {
2526: jmax=j;
2527: ijmax=i;
2528: }
2529: else if (j <= jmin){
2530: jmin=j;
2531: ijmin=i;
2532: }
2533: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2534: /*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]);*/
2535: if(j<0){
2536: nberr++;
2537: 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]);
2538: 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]);
2539: }
2540: sum=sum+j;
2541: }
2542: jk= j/stepm;
2543: jl= j -jk*stepm;
2544: ju= j -(jk+1)*stepm;
2545: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2546: if(jl==0){
2547: dh[mi][i]=jk;
2548: bh[mi][i]=0;
2549: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2550: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2551: dh[mi][i]=jk+1;
2552: bh[mi][i]=ju;
2553: }
2554: }else{
2555: if(jl <= -ju){
2556: dh[mi][i]=jk;
2557: bh[mi][i]=jl; /* bias is positive if real duration
2558: * is higher than the multiple of stepm and negative otherwise.
2559: */
2560: }
2561: else{
2562: dh[mi][i]=jk+1;
2563: bh[mi][i]=ju;
2564: }
2565: if(dh[mi][i]==0){
2566: dh[mi][i]=1; /* At least one step */
2567: bh[mi][i]=ju; /* At least one step */
2568: /* 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);*/
2569: }
2570: } /* end if mle */
2571: }
2572: } /* end wave */
2573: }
2574: jmean=sum/k;
2575: 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 2576: 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 2577: }
2578:
2579: /*********** Tricode ****************************/
2580: void tricode(int *Tvar, int **nbcode, int imx)
2581: {
1.144 ! brouard 2582: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
! 2583: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
! 2584: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
! 2585: /* nbcode[Tvar[j][1]=
! 2586: */
1.130 brouard 2587:
1.131 brouard 2588: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2589: int modmaxcovj=0; /* Modality max of covariates j */
1.126 brouard 2590: cptcoveff=0;
2591:
1.144 ! brouard 2592: for (k=0; k < maxncov; k++) Ndum[k]=0;
! 2593: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2594:
1.136 brouard 2595: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
2596: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
2597: modality of this covariate Vj*/
2598: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
2599: modality of the nth covariate of individual i. */
2600: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.126 brouard 2601: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2602: if (ij > modmaxcovj) modmaxcovj=ij;
2603: /* getting the maximum value of the modality of the covariate
2604: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2605: female is 1, then modmaxcovj=1.*/
1.126 brouard 2606: }
1.137 brouard 2607: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2608: for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
1.136 brouard 2609: if( Ndum[i] != 0 )
2610: ncodemax[j]++;
2611: /* Number of modalities of the j th covariate. In fact
2612: ncodemax[j]=2 (dichotom. variables only) but it could be more for
2613: historical reasons */
1.131 brouard 2614: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2615:
1.136 brouard 2616: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.126 brouard 2617: ij=1;
1.136 brouard 2618: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
1.137 brouard 2619: for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
1.131 brouard 2620: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2621: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2622: k is a modality. If we have model=V1+V1*sex
2623: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2624: ij++;
2625: }
2626: if (ij > ncodemax[j]) break;
1.137 brouard 2627: } /* end of loop on */
2628: } /* end of loop on modality */
2629: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2630:
2631: for (k=0; k< maxncov; k++) Ndum[k]=0;
2632:
2633: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
1.126 brouard 2634: /* 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 2635: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.126 brouard 2636: Ndum[ij]++;
2637: }
2638:
2639: ij=1;
1.137 brouard 2640: 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 2641: if((Ndum[i]!=0) && (i<=ncovcol)){
2642: Tvaraff[ij]=i; /*For printing */
2643: ij++;
2644: }
2645: }
1.131 brouard 2646: ij--;
1.144 ! brouard 2647: cptcoveff=ij; /*Number of total covariates*/
1.126 brouard 2648: }
2649:
2650: /*********** Health Expectancies ****************/
2651:
1.127 brouard 2652: 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 2653:
2654: {
2655: /* Health expectancies, no variances */
2656: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2657: int nhstepma, nstepma; /* Decreasing with age */
2658: double age, agelim, hf;
2659: double ***p3mat;
2660: double eip;
2661:
2662: pstamp(ficreseij);
2663: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2664: fprintf(ficreseij,"# Age");
2665: for(i=1; i<=nlstate;i++){
2666: for(j=1; j<=nlstate;j++){
2667: fprintf(ficreseij," e%1d%1d ",i,j);
2668: }
2669: fprintf(ficreseij," e%1d. ",i);
2670: }
2671: fprintf(ficreseij,"\n");
2672:
2673:
2674: if(estepm < stepm){
2675: printf ("Problem %d lower than %d\n",estepm, stepm);
2676: }
2677: else hstepm=estepm;
2678: /* We compute the life expectancy from trapezoids spaced every estepm months
2679: * This is mainly to measure the difference between two models: for example
2680: * if stepm=24 months pijx are given only every 2 years and by summing them
2681: * we are calculating an estimate of the Life Expectancy assuming a linear
2682: * progression in between and thus overestimating or underestimating according
2683: * to the curvature of the survival function. If, for the same date, we
2684: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2685: * to compare the new estimate of Life expectancy with the same linear
2686: * hypothesis. A more precise result, taking into account a more precise
2687: * curvature will be obtained if estepm is as small as stepm. */
2688:
2689: /* For example we decided to compute the life expectancy with the smallest unit */
2690: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2691: nhstepm is the number of hstepm from age to agelim
2692: nstepm is the number of stepm from age to agelin.
2693: Look at hpijx to understand the reason of that which relies in memory size
2694: and note for a fixed period like estepm months */
2695: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2696: survival function given by stepm (the optimization length). Unfortunately it
2697: means that if the survival funtion is printed only each two years of age and if
2698: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2699: results. So we changed our mind and took the option of the best precision.
2700: */
2701: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2702:
2703: agelim=AGESUP;
2704: /* If stepm=6 months */
2705: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2706: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2707:
2708: /* nhstepm age range expressed in number of stepm */
2709: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2710: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2711: /* if (stepm >= YEARM) hstepm=1;*/
2712: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2713: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2714:
2715: for (age=bage; age<=fage; age ++){
2716: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2717: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2718: /* if (stepm >= YEARM) hstepm=1;*/
2719: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2720:
2721: /* If stepm=6 months */
2722: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2723: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2724:
2725: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2726:
2727: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2728:
2729: printf("%d|",(int)age);fflush(stdout);
2730: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2731:
2732: /* Computing expectancies */
2733: for(i=1; i<=nlstate;i++)
2734: for(j=1; j<=nlstate;j++)
2735: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2736: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2737:
2738: /* 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]);*/
2739:
2740: }
2741:
2742: fprintf(ficreseij,"%3.0f",age );
2743: for(i=1; i<=nlstate;i++){
2744: eip=0;
2745: for(j=1; j<=nlstate;j++){
2746: eip +=eij[i][j][(int)age];
2747: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2748: }
2749: fprintf(ficreseij,"%9.4f", eip );
2750: }
2751: fprintf(ficreseij,"\n");
2752:
2753: }
2754: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2755: printf("\n");
2756: fprintf(ficlog,"\n");
2757:
2758: }
2759:
1.127 brouard 2760: 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 2761:
2762: {
2763: /* Covariances of health expectancies eij and of total life expectancies according
2764: to initial status i, ei. .
2765: */
2766: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2767: int nhstepma, nstepma; /* Decreasing with age */
2768: double age, agelim, hf;
2769: double ***p3matp, ***p3matm, ***varhe;
2770: double **dnewm,**doldm;
2771: double *xp, *xm;
2772: double **gp, **gm;
2773: double ***gradg, ***trgradg;
2774: int theta;
2775:
2776: double eip, vip;
2777:
2778: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2779: xp=vector(1,npar);
2780: xm=vector(1,npar);
2781: dnewm=matrix(1,nlstate*nlstate,1,npar);
2782: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2783:
2784: pstamp(ficresstdeij);
2785: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2786: fprintf(ficresstdeij,"# Age");
2787: for(i=1; i<=nlstate;i++){
2788: for(j=1; j<=nlstate;j++)
2789: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2790: fprintf(ficresstdeij," e%1d. ",i);
2791: }
2792: fprintf(ficresstdeij,"\n");
2793:
2794: pstamp(ficrescveij);
2795: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2796: fprintf(ficrescveij,"# Age");
2797: for(i=1; i<=nlstate;i++)
2798: for(j=1; j<=nlstate;j++){
2799: cptj= (j-1)*nlstate+i;
2800: for(i2=1; i2<=nlstate;i2++)
2801: for(j2=1; j2<=nlstate;j2++){
2802: cptj2= (j2-1)*nlstate+i2;
2803: if(cptj2 <= cptj)
2804: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2805: }
2806: }
2807: fprintf(ficrescveij,"\n");
2808:
2809: if(estepm < stepm){
2810: printf ("Problem %d lower than %d\n",estepm, stepm);
2811: }
2812: else hstepm=estepm;
2813: /* We compute the life expectancy from trapezoids spaced every estepm months
2814: * This is mainly to measure the difference between two models: for example
2815: * if stepm=24 months pijx are given only every 2 years and by summing them
2816: * we are calculating an estimate of the Life Expectancy assuming a linear
2817: * progression in between and thus overestimating or underestimating according
2818: * to the curvature of the survival function. If, for the same date, we
2819: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2820: * to compare the new estimate of Life expectancy with the same linear
2821: * hypothesis. A more precise result, taking into account a more precise
2822: * curvature will be obtained if estepm is as small as stepm. */
2823:
2824: /* For example we decided to compute the life expectancy with the smallest unit */
2825: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2826: nhstepm is the number of hstepm from age to agelim
2827: nstepm is the number of stepm from age to agelin.
2828: Look at hpijx to understand the reason of that which relies in memory size
2829: and note for a fixed period like estepm months */
2830: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2831: survival function given by stepm (the optimization length). Unfortunately it
2832: means that if the survival funtion is printed only each two years of age and if
2833: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2834: results. So we changed our mind and took the option of the best precision.
2835: */
2836: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2837:
2838: /* If stepm=6 months */
2839: /* nhstepm age range expressed in number of stepm */
2840: agelim=AGESUP;
2841: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2842: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2843: /* if (stepm >= YEARM) hstepm=1;*/
2844: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2845:
2846: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2847: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2848: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2849: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2850: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2851: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2852:
2853: for (age=bage; age<=fage; age ++){
2854: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2855: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2856: /* if (stepm >= YEARM) hstepm=1;*/
2857: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2858:
2859: /* If stepm=6 months */
2860: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2861: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2862:
2863: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2864:
2865: /* Computing Variances of health expectancies */
2866: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2867: decrease memory allocation */
2868: for(theta=1; theta <=npar; theta++){
2869: for(i=1; i<=npar; i++){
2870: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2871: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2872: }
2873: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2874: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2875:
2876: for(j=1; j<= nlstate; j++){
2877: for(i=1; i<=nlstate; i++){
2878: for(h=0; h<=nhstepm-1; h++){
2879: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2880: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2881: }
2882: }
2883: }
2884:
2885: for(ij=1; ij<= nlstate*nlstate; ij++)
2886: for(h=0; h<=nhstepm-1; h++){
2887: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2888: }
2889: }/* End theta */
2890:
2891:
2892: for(h=0; h<=nhstepm-1; h++)
2893: for(j=1; j<=nlstate*nlstate;j++)
2894: for(theta=1; theta <=npar; theta++)
2895: trgradg[h][j][theta]=gradg[h][theta][j];
2896:
2897:
2898: for(ij=1;ij<=nlstate*nlstate;ij++)
2899: for(ji=1;ji<=nlstate*nlstate;ji++)
2900: varhe[ij][ji][(int)age] =0.;
2901:
2902: printf("%d|",(int)age);fflush(stdout);
2903: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2904: for(h=0;h<=nhstepm-1;h++){
2905: for(k=0;k<=nhstepm-1;k++){
2906: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2907: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2908: for(ij=1;ij<=nlstate*nlstate;ij++)
2909: for(ji=1;ji<=nlstate*nlstate;ji++)
2910: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2911: }
2912: }
2913:
2914: /* Computing expectancies */
2915: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2916: for(i=1; i<=nlstate;i++)
2917: for(j=1; j<=nlstate;j++)
2918: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2919: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2920:
2921: /* 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]);*/
2922:
2923: }
2924:
2925: fprintf(ficresstdeij,"%3.0f",age );
2926: for(i=1; i<=nlstate;i++){
2927: eip=0.;
2928: vip=0.;
2929: for(j=1; j<=nlstate;j++){
2930: eip += eij[i][j][(int)age];
2931: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2932: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2933: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2934: }
2935: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2936: }
2937: fprintf(ficresstdeij,"\n");
2938:
2939: fprintf(ficrescveij,"%3.0f",age );
2940: for(i=1; i<=nlstate;i++)
2941: for(j=1; j<=nlstate;j++){
2942: cptj= (j-1)*nlstate+i;
2943: for(i2=1; i2<=nlstate;i2++)
2944: for(j2=1; j2<=nlstate;j2++){
2945: cptj2= (j2-1)*nlstate+i2;
2946: if(cptj2 <= cptj)
2947: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2948: }
2949: }
2950: fprintf(ficrescveij,"\n");
2951:
2952: }
2953: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2954: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2955: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2956: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2957: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2958: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2959: printf("\n");
2960: fprintf(ficlog,"\n");
2961:
2962: free_vector(xm,1,npar);
2963: free_vector(xp,1,npar);
2964: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2965: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2966: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2967: }
2968:
2969: /************ Variance ******************/
2970: 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[])
2971: {
2972: /* Variance of health expectancies */
2973: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2974: /* double **newm;*/
2975: double **dnewm,**doldm;
2976: double **dnewmp,**doldmp;
2977: int i, j, nhstepm, hstepm, h, nstepm ;
2978: int k, cptcode;
2979: double *xp;
2980: double **gp, **gm; /* for var eij */
2981: double ***gradg, ***trgradg; /*for var eij */
2982: double **gradgp, **trgradgp; /* for var p point j */
2983: double *gpp, *gmp; /* for var p point j */
2984: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2985: double ***p3mat;
2986: double age,agelim, hf;
2987: double ***mobaverage;
2988: int theta;
2989: char digit[4];
2990: char digitp[25];
2991:
2992: char fileresprobmorprev[FILENAMELENGTH];
2993:
2994: if(popbased==1){
2995: if(mobilav!=0)
2996: strcpy(digitp,"-populbased-mobilav-");
2997: else strcpy(digitp,"-populbased-nomobil-");
2998: }
2999: else
3000: strcpy(digitp,"-stablbased-");
3001:
3002: if (mobilav!=0) {
3003: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3004: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3005: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3006: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3007: }
3008: }
3009:
3010: strcpy(fileresprobmorprev,"prmorprev");
3011: sprintf(digit,"%-d",ij);
3012: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3013: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3014: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3015: strcat(fileresprobmorprev,fileres);
3016: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3017: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3018: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3019: }
3020: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3021:
3022: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3023: pstamp(ficresprobmorprev);
3024: 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);
3025: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3026: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3027: fprintf(ficresprobmorprev," p.%-d SE",j);
3028: for(i=1; i<=nlstate;i++)
3029: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3030: }
3031: fprintf(ficresprobmorprev,"\n");
3032: fprintf(ficgp,"\n# Routine varevsij");
3033: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3034: 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");
3035: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3036: /* } */
3037: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3038: pstamp(ficresvij);
3039: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3040: if(popbased==1)
1.128 brouard 3041: 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 3042: else
3043: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3044: fprintf(ficresvij,"# Age");
3045: for(i=1; i<=nlstate;i++)
3046: for(j=1; j<=nlstate;j++)
3047: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3048: fprintf(ficresvij,"\n");
3049:
3050: xp=vector(1,npar);
3051: dnewm=matrix(1,nlstate,1,npar);
3052: doldm=matrix(1,nlstate,1,nlstate);
3053: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3054: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3055:
3056: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3057: gpp=vector(nlstate+1,nlstate+ndeath);
3058: gmp=vector(nlstate+1,nlstate+ndeath);
3059: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3060:
3061: if(estepm < stepm){
3062: printf ("Problem %d lower than %d\n",estepm, stepm);
3063: }
3064: else hstepm=estepm;
3065: /* For example we decided to compute the life expectancy with the smallest unit */
3066: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3067: nhstepm is the number of hstepm from age to agelim
3068: nstepm is the number of stepm from age to agelin.
1.128 brouard 3069: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3070: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3071: survival function given by stepm (the optimization length). Unfortunately it
3072: means that if the survival funtion is printed every two years of age and if
3073: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3074: results. So we changed our mind and took the option of the best precision.
3075: */
3076: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3077: agelim = AGESUP;
3078: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3079: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3080: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3081: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3082: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3083: gp=matrix(0,nhstepm,1,nlstate);
3084: gm=matrix(0,nhstepm,1,nlstate);
3085:
3086:
3087: for(theta=1; theta <=npar; theta++){
3088: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3089: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3090: }
3091: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3092: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3093:
3094: if (popbased==1) {
3095: if(mobilav ==0){
3096: for(i=1; i<=nlstate;i++)
3097: prlim[i][i]=probs[(int)age][i][ij];
3098: }else{ /* mobilav */
3099: for(i=1; i<=nlstate;i++)
3100: prlim[i][i]=mobaverage[(int)age][i][ij];
3101: }
3102: }
3103:
3104: for(j=1; j<= nlstate; j++){
3105: for(h=0; h<=nhstepm; h++){
3106: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3107: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3108: }
3109: }
3110: /* This for computing probability of death (h=1 means
3111: computed over hstepm matrices product = hstepm*stepm months)
3112: as a weighted average of prlim.
3113: */
3114: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3115: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3116: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3117: }
3118: /* end probability of death */
3119:
3120: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3121: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3122: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3123: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3124:
3125: if (popbased==1) {
3126: if(mobilav ==0){
3127: for(i=1; i<=nlstate;i++)
3128: prlim[i][i]=probs[(int)age][i][ij];
3129: }else{ /* mobilav */
3130: for(i=1; i<=nlstate;i++)
3131: prlim[i][i]=mobaverage[(int)age][i][ij];
3132: }
3133: }
3134:
1.128 brouard 3135: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3136: for(h=0; h<=nhstepm; h++){
3137: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3138: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3139: }
3140: }
3141: /* This for computing probability of death (h=1 means
3142: computed over hstepm matrices product = hstepm*stepm months)
3143: as a weighted average of prlim.
3144: */
3145: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3146: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3147: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3148: }
3149: /* end probability of death */
3150:
3151: for(j=1; j<= nlstate; j++) /* vareij */
3152: for(h=0; h<=nhstepm; h++){
3153: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3154: }
3155:
3156: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3157: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3158: }
3159:
3160: } /* End theta */
3161:
3162: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3163:
3164: for(h=0; h<=nhstepm; h++) /* veij */
3165: for(j=1; j<=nlstate;j++)
3166: for(theta=1; theta <=npar; theta++)
3167: trgradg[h][j][theta]=gradg[h][theta][j];
3168:
3169: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3170: for(theta=1; theta <=npar; theta++)
3171: trgradgp[j][theta]=gradgp[theta][j];
3172:
3173:
3174: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3175: for(i=1;i<=nlstate;i++)
3176: for(j=1;j<=nlstate;j++)
3177: vareij[i][j][(int)age] =0.;
3178:
3179: for(h=0;h<=nhstepm;h++){
3180: for(k=0;k<=nhstepm;k++){
3181: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3182: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3183: for(i=1;i<=nlstate;i++)
3184: for(j=1;j<=nlstate;j++)
3185: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3186: }
3187: }
3188:
3189: /* pptj */
3190: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3191: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3192: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3193: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3194: varppt[j][i]=doldmp[j][i];
3195: /* end ppptj */
3196: /* x centered again */
3197: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3198: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3199:
3200: if (popbased==1) {
3201: if(mobilav ==0){
3202: for(i=1; i<=nlstate;i++)
3203: prlim[i][i]=probs[(int)age][i][ij];
3204: }else{ /* mobilav */
3205: for(i=1; i<=nlstate;i++)
3206: prlim[i][i]=mobaverage[(int)age][i][ij];
3207: }
3208: }
3209:
3210: /* This for computing probability of death (h=1 means
3211: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3212: as a weighted average of prlim.
3213: */
3214: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3215: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3216: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3217: }
3218: /* end probability of death */
3219:
3220: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3221: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3222: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3223: for(i=1; i<=nlstate;i++){
3224: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3225: }
3226: }
3227: fprintf(ficresprobmorprev,"\n");
3228:
3229: fprintf(ficresvij,"%.0f ",age );
3230: for(i=1; i<=nlstate;i++)
3231: for(j=1; j<=nlstate;j++){
3232: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3233: }
3234: fprintf(ficresvij,"\n");
3235: free_matrix(gp,0,nhstepm,1,nlstate);
3236: free_matrix(gm,0,nhstepm,1,nlstate);
3237: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3238: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3239: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3240: } /* End age */
3241: free_vector(gpp,nlstate+1,nlstate+ndeath);
3242: free_vector(gmp,nlstate+1,nlstate+ndeath);
3243: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3244: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.131 brouard 3245: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
1.126 brouard 3246: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3247: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3248: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3249: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3250: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.142 brouard 3251: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
3252: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
3253: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
1.126 brouard 3254: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3255: 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);
3256: /* 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);
3257: */
3258: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3259: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3260:
3261: free_vector(xp,1,npar);
3262: free_matrix(doldm,1,nlstate,1,nlstate);
3263: free_matrix(dnewm,1,nlstate,1,npar);
3264: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3265: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3266: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3267: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3268: fclose(ficresprobmorprev);
3269: fflush(ficgp);
3270: fflush(fichtm);
3271: } /* end varevsij */
3272:
3273: /************ Variance of prevlim ******************/
3274: 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[])
3275: {
3276: /* Variance of prevalence limit */
3277: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3278: double **newm;
3279: double **dnewm,**doldm;
3280: int i, j, nhstepm, hstepm;
3281: int k, cptcode;
3282: double *xp;
3283: double *gp, *gm;
3284: double **gradg, **trgradg;
3285: double age,agelim;
3286: int theta;
3287:
3288: pstamp(ficresvpl);
3289: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3290: fprintf(ficresvpl,"# Age");
3291: for(i=1; i<=nlstate;i++)
3292: fprintf(ficresvpl," %1d-%1d",i,i);
3293: fprintf(ficresvpl,"\n");
3294:
3295: xp=vector(1,npar);
3296: dnewm=matrix(1,nlstate,1,npar);
3297: doldm=matrix(1,nlstate,1,nlstate);
3298:
3299: hstepm=1*YEARM; /* Every year of age */
3300: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3301: agelim = AGESUP;
3302: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3303: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3304: if (stepm >= YEARM) hstepm=1;
3305: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3306: gradg=matrix(1,npar,1,nlstate);
3307: gp=vector(1,nlstate);
3308: gm=vector(1,nlstate);
3309:
3310: for(theta=1; theta <=npar; theta++){
3311: for(i=1; i<=npar; i++){ /* Computes gradient */
3312: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3313: }
3314: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3315: for(i=1;i<=nlstate;i++)
3316: gp[i] = prlim[i][i];
3317:
3318: for(i=1; i<=npar; i++) /* Computes gradient */
3319: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3320: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3321: for(i=1;i<=nlstate;i++)
3322: gm[i] = prlim[i][i];
3323:
3324: for(i=1;i<=nlstate;i++)
3325: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3326: } /* End theta */
3327:
3328: trgradg =matrix(1,nlstate,1,npar);
3329:
3330: for(j=1; j<=nlstate;j++)
3331: for(theta=1; theta <=npar; theta++)
3332: trgradg[j][theta]=gradg[theta][j];
3333:
3334: for(i=1;i<=nlstate;i++)
3335: varpl[i][(int)age] =0.;
3336: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3337: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3338: for(i=1;i<=nlstate;i++)
3339: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3340:
3341: fprintf(ficresvpl,"%.0f ",age );
3342: for(i=1; i<=nlstate;i++)
3343: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3344: fprintf(ficresvpl,"\n");
3345: free_vector(gp,1,nlstate);
3346: free_vector(gm,1,nlstate);
3347: free_matrix(gradg,1,npar,1,nlstate);
3348: free_matrix(trgradg,1,nlstate,1,npar);
3349: } /* End age */
3350:
3351: free_vector(xp,1,npar);
3352: free_matrix(doldm,1,nlstate,1,npar);
3353: free_matrix(dnewm,1,nlstate,1,nlstate);
3354:
3355: }
3356:
3357: /************ Variance of one-step probabilities ******************/
3358: 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[])
3359: {
3360: int i, j=0, i1, k1, l1, t, tj;
3361: int k2, l2, j1, z1;
3362: int k=0,l, cptcode;
3363: int first=1, first1;
3364: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3365: double **dnewm,**doldm;
3366: double *xp;
3367: double *gp, *gm;
3368: double **gradg, **trgradg;
3369: double **mu;
3370: double age,agelim, cov[NCOVMAX];
3371: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3372: int theta;
3373: char fileresprob[FILENAMELENGTH];
3374: char fileresprobcov[FILENAMELENGTH];
3375: char fileresprobcor[FILENAMELENGTH];
3376:
3377: double ***varpij;
3378:
3379: strcpy(fileresprob,"prob");
3380: strcat(fileresprob,fileres);
3381: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3382: printf("Problem with resultfile: %s\n", fileresprob);
3383: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3384: }
3385: strcpy(fileresprobcov,"probcov");
3386: strcat(fileresprobcov,fileres);
3387: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3388: printf("Problem with resultfile: %s\n", fileresprobcov);
3389: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3390: }
3391: strcpy(fileresprobcor,"probcor");
3392: strcat(fileresprobcor,fileres);
3393: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3394: printf("Problem with resultfile: %s\n", fileresprobcor);
3395: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3396: }
3397: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3398: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3399: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3400: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3401: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3402: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3403: pstamp(ficresprob);
3404: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3405: fprintf(ficresprob,"# Age");
3406: pstamp(ficresprobcov);
3407: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3408: fprintf(ficresprobcov,"# Age");
3409: pstamp(ficresprobcor);
3410: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3411: fprintf(ficresprobcor,"# Age");
3412:
3413:
3414: for(i=1; i<=nlstate;i++)
3415: for(j=1; j<=(nlstate+ndeath);j++){
3416: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3417: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3418: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3419: }
3420: /* fprintf(ficresprob,"\n");
3421: fprintf(ficresprobcov,"\n");
3422: fprintf(ficresprobcor,"\n");
3423: */
1.131 brouard 3424: xp=vector(1,npar);
1.126 brouard 3425: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3426: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3427: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3428: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3429: first=1;
3430: fprintf(ficgp,"\n# Routine varprob");
3431: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3432: fprintf(fichtm,"\n");
3433:
3434: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3435: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3436: file %s<br>\n",optionfilehtmcov);
3437: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3438: and drawn. It helps understanding how is the covariance between two incidences.\
3439: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3440: 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. \
3441: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3442: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3443: standard deviations wide on each axis. <br>\
3444: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3445: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3446: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3447:
3448: cov[1]=1;
3449: tj=cptcoveff;
3450: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3451: j1=0;
3452: for(t=1; t<=tj;t++){
3453: for(i1=1; i1<=ncodemax[t];i1++){
3454: j1++;
3455: if (cptcovn>0) {
3456: fprintf(ficresprob, "\n#********** Variable ");
3457: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3458: fprintf(ficresprob, "**********\n#\n");
3459: fprintf(ficresprobcov, "\n#********** Variable ");
3460: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3461: fprintf(ficresprobcov, "**********\n#\n");
3462:
3463: fprintf(ficgp, "\n#********** Variable ");
3464: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3465: fprintf(ficgp, "**********\n#\n");
3466:
3467:
3468: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3469: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3470: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3471:
3472: fprintf(ficresprobcor, "\n#********** Variable ");
3473: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3474: fprintf(ficresprobcor, "**********\n#");
3475: }
3476:
3477: for (age=bage; age<=fage; age ++){
3478: cov[2]=age;
3479: for (k=1; k<=cptcovn;k++) {
3480: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3481: }
3482: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3483: for (k=1; k<=cptcovprod;k++)
3484: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3485:
3486: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3487: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3488: gp=vector(1,(nlstate)*(nlstate+ndeath));
3489: gm=vector(1,(nlstate)*(nlstate+ndeath));
3490:
3491: for(theta=1; theta <=npar; theta++){
3492: for(i=1; i<=npar; i++)
3493: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3494:
3495: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3496:
3497: k=0;
3498: for(i=1; i<= (nlstate); i++){
3499: for(j=1; j<=(nlstate+ndeath);j++){
3500: k=k+1;
3501: gp[k]=pmmij[i][j];
3502: }
3503: }
3504:
3505: for(i=1; i<=npar; i++)
3506: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3507:
3508: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3509: k=0;
3510: for(i=1; i<=(nlstate); i++){
3511: for(j=1; j<=(nlstate+ndeath);j++){
3512: k=k+1;
3513: gm[k]=pmmij[i][j];
3514: }
3515: }
3516:
3517: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3518: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3519: }
3520:
3521: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3522: for(theta=1; theta <=npar; theta++)
3523: trgradg[j][theta]=gradg[theta][j];
3524:
3525: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3526: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3527: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3528: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3529: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3530: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3531:
3532: pmij(pmmij,cov,ncovmodel,x,nlstate);
3533:
3534: k=0;
3535: for(i=1; i<=(nlstate); i++){
3536: for(j=1; j<=(nlstate+ndeath);j++){
3537: k=k+1;
3538: mu[k][(int) age]=pmmij[i][j];
3539: }
3540: }
3541: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3542: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3543: varpij[i][j][(int)age] = doldm[i][j];
3544:
3545: /*printf("\n%d ",(int)age);
3546: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3547: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3548: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3549: }*/
3550:
3551: fprintf(ficresprob,"\n%d ",(int)age);
3552: fprintf(ficresprobcov,"\n%d ",(int)age);
3553: fprintf(ficresprobcor,"\n%d ",(int)age);
3554:
3555: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3556: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3557: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3558: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3559: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3560: }
3561: i=0;
3562: for (k=1; k<=(nlstate);k++){
3563: for (l=1; l<=(nlstate+ndeath);l++){
3564: i=i++;
3565: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3566: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3567: for (j=1; j<=i;j++){
3568: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3569: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3570: }
3571: }
3572: }/* end of loop for state */
3573: } /* end of loop for age */
3574:
3575: /* Confidence intervalle of pij */
3576: /*
1.131 brouard 3577: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3578: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3579: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3580: 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);
3581: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3582: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3583: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3584: */
3585:
3586: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3587: first1=1;
3588: for (k2=1; k2<=(nlstate);k2++){
3589: for (l2=1; l2<=(nlstate+ndeath);l2++){
3590: if(l2==k2) continue;
3591: j=(k2-1)*(nlstate+ndeath)+l2;
3592: for (k1=1; k1<=(nlstate);k1++){
3593: for (l1=1; l1<=(nlstate+ndeath);l1++){
3594: if(l1==k1) continue;
3595: i=(k1-1)*(nlstate+ndeath)+l1;
3596: if(i<=j) continue;
3597: for (age=bage; age<=fage; age ++){
3598: if ((int)age %5==0){
3599: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3600: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3601: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3602: mu1=mu[i][(int) age]/stepm*YEARM ;
3603: mu2=mu[j][(int) age]/stepm*YEARM;
3604: c12=cv12/sqrt(v1*v2);
3605: /* Computing eigen value of matrix of covariance */
3606: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3607: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3608: if ((lc2 <0) || (lc1 <0) ){
3609: 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);
3610: 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);
3611: lc1=fabs(lc1);
3612: lc2=fabs(lc2);
3613: }
3614:
1.126 brouard 3615: /* Eigen vectors */
3616: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3617: /*v21=sqrt(1.-v11*v11); *//* error */
3618: v21=(lc1-v1)/cv12*v11;
3619: v12=-v21;
3620: v22=v11;
3621: tnalp=v21/v11;
3622: if(first1==1){
3623: first1=0;
3624: 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);
3625: }
3626: 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);
3627: /*printf(fignu*/
3628: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3629: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3630: if(first==1){
3631: first=0;
3632: fprintf(ficgp,"\nset parametric;unset label");
3633: 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);
3634: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3635: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3636: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3637: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3638: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3639: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3640: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3641: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3642: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3643: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3644: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3645: 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",\
3646: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3647: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3648: }else{
3649: first=0;
3650: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3651: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3652: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3653: 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",\
3654: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3655: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3656: }/* if first */
3657: } /* age mod 5 */
3658: } /* end loop age */
3659: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3660: first=1;
3661: } /*l12 */
3662: } /* k12 */
3663: } /*l1 */
3664: }/* k1 */
3665: } /* loop covariates */
3666: }
3667: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3668: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3669: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3670: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3671: free_vector(xp,1,npar);
3672: fclose(ficresprob);
3673: fclose(ficresprobcov);
3674: fclose(ficresprobcor);
3675: fflush(ficgp);
3676: fflush(fichtmcov);
3677: }
3678:
3679:
3680: /******************* Printing html file ***********/
3681: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3682: int lastpass, int stepm, int weightopt, char model[],\
3683: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3684: int popforecast, int estepm ,\
3685: double jprev1, double mprev1,double anprev1, \
3686: double jprev2, double mprev2,double anprev2){
3687: int jj1, k1, i1, cpt;
3688:
3689: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3690: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3691: </ul>");
3692: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3693: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3694: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3695: fprintf(fichtm,"\
3696: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3697: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3698: fprintf(fichtm,"\
3699: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3700: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3701: fprintf(fichtm,"\
1.128 brouard 3702: - (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 3703: <a href=\"%s\">%s</a> <br>\n",
3704: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3705: fprintf(fichtm,"\
3706: - Population projections by age and states: \
3707: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3708:
3709: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3710:
3711: m=cptcoveff;
3712: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3713:
3714: jj1=0;
3715: for(k1=1; k1<=m;k1++){
3716: for(i1=1; i1<=ncodemax[k1];i1++){
3717: jj1++;
3718: if (cptcovn > 0) {
3719: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3720: for (cpt=1; cpt<=cptcoveff;cpt++)
3721: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3722: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3723: }
3724: /* Pij */
3725: 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> \
3726: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3727: /* Quasi-incidences */
3728: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3729: 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> \
3730: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3731: /* Period (stable) prevalence in each health state */
3732: for(cpt=1; cpt<nlstate;cpt++){
3733: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3734: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3735: }
3736: for(cpt=1; cpt<=nlstate;cpt++) {
3737: 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> \
3738: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3739: }
3740: } /* end i1 */
3741: }/* End k1 */
3742: fprintf(fichtm,"</ul>");
3743:
3744:
3745: fprintf(fichtm,"\
3746: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3747: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3748:
3749: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3750: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3751: fprintf(fichtm,"\
3752: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3753: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3754:
3755: fprintf(fichtm,"\
3756: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3757: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3758: fprintf(fichtm,"\
3759: - 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): \
3760: <a href=\"%s\">%s</a> <br>\n</li>",
3761: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3762: fprintf(fichtm,"\
3763: - (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): \
3764: <a href=\"%s\">%s</a> <br>\n</li>",
3765: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3766: fprintf(fichtm,"\
1.128 brouard 3767: - 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 3768: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3769: fprintf(fichtm,"\
1.128 brouard 3770: - 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",
3771: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3772: fprintf(fichtm,"\
3773: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3774: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3775:
3776: /* if(popforecast==1) fprintf(fichtm,"\n */
3777: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3778: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3779: /* <br>",fileres,fileres,fileres,fileres); */
3780: /* else */
3781: /* 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); */
3782: fflush(fichtm);
3783: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3784:
3785: m=cptcoveff;
3786: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3787:
3788: jj1=0;
3789: for(k1=1; k1<=m;k1++){
3790: for(i1=1; i1<=ncodemax[k1];i1++){
3791: jj1++;
3792: if (cptcovn > 0) {
3793: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3794: for (cpt=1; cpt<=cptcoveff;cpt++)
3795: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3796: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3797: }
3798: for(cpt=1; cpt<=nlstate;cpt++) {
3799: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3800: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3801: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3802: }
3803: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3804: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3805: true period expectancies (those weighted with period prevalences are also\
3806: drawn in addition to the population based expectancies computed using\
3807: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3808: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3809: } /* end i1 */
3810: }/* End k1 */
3811: fprintf(fichtm,"</ul>");
3812: fflush(fichtm);
3813: }
3814:
3815: /******************* Gnuplot file **************/
3816: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3817:
3818: char dirfileres[132],optfileres[132];
1.130 brouard 3819: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3820: int ng=0;
1.126 brouard 3821: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3822: /* printf("Problem with file %s",optionfilegnuplot); */
3823: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3824: /* } */
3825:
3826: /*#ifdef windows */
3827: fprintf(ficgp,"cd \"%s\" \n",pathc);
3828: /*#endif */
3829: m=pow(2,cptcoveff);
3830:
3831: strcpy(dirfileres,optionfilefiname);
3832: strcpy(optfileres,"vpl");
3833: /* 1eme*/
3834: for (cpt=1; cpt<= nlstate ; cpt ++) {
3835: for (k1=1; k1<= m ; k1 ++) {
3836: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3837: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3838: fprintf(ficgp,"set xlabel \"Age\" \n\
3839: set ylabel \"Probability\" \n\
3840: set ter png small\n\
3841: set size 0.65,0.65\n\
3842: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3843:
3844: for (i=1; i<= nlstate ; i ++) {
3845: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 3846: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3847: }
1.142 brouard 3848: 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 3849: for (i=1; i<= nlstate ; i ++) {
3850: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3851: else fprintf(ficgp," \%%*lf (\%%*lf)");
3852: }
1.142 brouard 3853: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 3854: for (i=1; i<= nlstate ; i ++) {
3855: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3856: else fprintf(ficgp," \%%*lf (\%%*lf)");
3857: }
1.142 brouard 3858: fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 3859: }
3860: }
3861: /*2 eme*/
3862:
3863: for (k1=1; k1<= m ; k1 ++) {
3864: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3865: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3866:
3867: for (i=1; i<= nlstate+1 ; i ++) {
3868: k=2*i;
3869: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3870: for (j=1; j<= nlstate+1 ; j ++) {
3871: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3872: else fprintf(ficgp," \%%*lf (\%%*lf)");
3873: }
3874: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3875: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3876: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3877: for (j=1; j<= nlstate+1 ; j ++) {
3878: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3879: else fprintf(ficgp," \%%*lf (\%%*lf)");
3880: }
1.142 brouard 3881: fprintf(ficgp,"\" t\"\" w l lt 1,");
1.126 brouard 3882: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3883: for (j=1; j<= nlstate+1 ; j ++) {
3884: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3885: else fprintf(ficgp," \%%*lf (\%%*lf)");
3886: }
1.142 brouard 3887: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
3888: else fprintf(ficgp,"\" t\"\" w l lt 1,");
1.126 brouard 3889: }
3890: }
3891:
3892: /*3eme*/
3893:
3894: for (k1=1; k1<= m ; k1 ++) {
3895: for (cpt=1; cpt<= nlstate ; cpt ++) {
3896: /* k=2+nlstate*(2*cpt-2); */
3897: k=2+(nlstate+1)*(cpt-1);
3898: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3899: fprintf(ficgp,"set ter png small\n\
3900: set size 0.65,0.65\n\
3901: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3902: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3903: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3904: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3905: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3906: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3907: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3908:
3909: */
3910: for (i=1; i< nlstate ; i ++) {
3911: 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);
3912: /* 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);*/
3913:
3914: }
3915: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3916: }
3917: }
3918:
3919: /* CV preval stable (period) */
3920: for (k1=1; k1<= m ; k1 ++) {
3921: for (cpt=1; cpt<=nlstate ; cpt ++) {
3922: k=3;
3923: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3924: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3925: set ter png small\nset size 0.65,0.65\n\
3926: unset log y\n\
3927: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3928:
3929: for (i=1; i< nlstate ; i ++)
3930: fprintf(ficgp,"+$%d",k+i+1);
3931: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3932:
3933: l=3+(nlstate+ndeath)*cpt;
3934: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3935: for (i=1; i< nlstate ; i ++) {
3936: l=3+(nlstate+ndeath)*cpt;
3937: fprintf(ficgp,"+$%d",l+i+1);
3938: }
3939: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3940: }
3941: }
3942:
3943: /* proba elementaires */
3944: for(i=1,jk=1; i <=nlstate; i++){
3945: for(k=1; k <=(nlstate+ndeath); k++){
3946: if (k != i) {
3947: for(j=1; j <=ncovmodel; j++){
3948: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3949: jk++;
3950: fprintf(ficgp,"\n");
3951: }
3952: }
3953: }
3954: }
3955:
3956: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3957: for(jk=1; jk <=m; jk++) {
3958: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3959: if (ng==2)
3960: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3961: else
3962: fprintf(ficgp,"\nset title \"Probability\"\n");
3963: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3964: i=1;
3965: for(k2=1; k2<=nlstate; k2++) {
3966: k3=i;
3967: for(k=1; k<=(nlstate+ndeath); k++) {
3968: if (k != k2){
3969: if(ng==2)
3970: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3971: else
3972: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 3973: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 3974: for(j=3; j <=ncovmodel; j++) {
1.142 brouard 3975: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
1.126 brouard 3976: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3977: ij++;
3978: }
3979: else
3980: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3981: }
3982: fprintf(ficgp,")/(1");
3983:
3984: for(k1=1; k1 <=nlstate; k1++){
3985: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3986: ij=1;
3987: for(j=3; j <=ncovmodel; j++){
3988: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3989: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3990: ij++;
3991: }
3992: else
3993: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3994: }
3995: fprintf(ficgp,")");
3996: }
3997: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3998: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3999: i=i+ncovmodel;
4000: }
4001: } /* end k */
4002: } /* end k2 */
4003: } /* end jk */
4004: } /* end ng */
4005: fflush(ficgp);
4006: } /* end gnuplot */
4007:
4008:
4009: /*************** Moving average **************/
4010: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4011:
4012: int i, cpt, cptcod;
4013: int modcovmax =1;
4014: int mobilavrange, mob;
4015: double age;
4016:
4017: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4018: a covariate has 2 modalities */
4019: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4020:
4021: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4022: if(mobilav==1) mobilavrange=5; /* default */
4023: else mobilavrange=mobilav;
4024: for (age=bage; age<=fage; age++)
4025: for (i=1; i<=nlstate;i++)
4026: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4027: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4028: /* We keep the original values on the extreme ages bage, fage and for
4029: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4030: we use a 5 terms etc. until the borders are no more concerned.
4031: */
4032: for (mob=3;mob <=mobilavrange;mob=mob+2){
4033: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4034: for (i=1; i<=nlstate;i++){
4035: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4036: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4037: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4038: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4039: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4040: }
4041: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4042: }
4043: }
4044: }/* end age */
4045: }/* end mob */
4046: }else return -1;
4047: return 0;
4048: }/* End movingaverage */
4049:
4050:
4051: /************** Forecasting ******************/
4052: 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){
4053: /* proj1, year, month, day of starting projection
4054: agemin, agemax range of age
4055: dateprev1 dateprev2 range of dates during which prevalence is computed
4056: anproj2 year of en of projection (same day and month as proj1).
4057: */
4058: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4059: int *popage;
4060: double agec; /* generic age */
4061: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4062: double *popeffectif,*popcount;
4063: double ***p3mat;
4064: double ***mobaverage;
4065: char fileresf[FILENAMELENGTH];
4066:
4067: agelim=AGESUP;
4068: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4069:
4070: strcpy(fileresf,"f");
4071: strcat(fileresf,fileres);
4072: if((ficresf=fopen(fileresf,"w"))==NULL) {
4073: printf("Problem with forecast resultfile: %s\n", fileresf);
4074: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4075: }
4076: printf("Computing forecasting: result on file '%s' \n", fileresf);
4077: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4078:
4079: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4080:
4081: if (mobilav!=0) {
4082: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4083: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4084: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4085: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4086: }
4087: }
4088:
4089: stepsize=(int) (stepm+YEARM-1)/YEARM;
4090: if (stepm<=12) stepsize=1;
4091: if(estepm < stepm){
4092: printf ("Problem %d lower than %d\n",estepm, stepm);
4093: }
4094: else hstepm=estepm;
4095:
4096: hstepm=hstepm/stepm;
4097: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4098: fractional in yp1 */
4099: anprojmean=yp;
4100: yp2=modf((yp1*12),&yp);
4101: mprojmean=yp;
4102: yp1=modf((yp2*30.5),&yp);
4103: jprojmean=yp;
4104: if(jprojmean==0) jprojmean=1;
4105: if(mprojmean==0) jprojmean=1;
4106:
4107: i1=cptcoveff;
4108: if (cptcovn < 1){i1=1;}
4109:
4110: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4111:
4112: fprintf(ficresf,"#****** Routine prevforecast **\n");
4113:
4114: /* if (h==(int)(YEARM*yearp)){ */
4115: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4116: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4117: k=k+1;
4118: fprintf(ficresf,"\n#******");
4119: for(j=1;j<=cptcoveff;j++) {
4120: 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]]);
4121: }
4122: fprintf(ficresf,"******\n");
4123: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4124: for(j=1; j<=nlstate+ndeath;j++){
4125: for(i=1; i<=nlstate;i++)
4126: fprintf(ficresf," p%d%d",i,j);
4127: fprintf(ficresf," p.%d",j);
4128: }
4129: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4130: fprintf(ficresf,"\n");
4131: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4132:
4133: for (agec=fage; agec>=(ageminpar-1); agec--){
4134: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4135: nhstepm = nhstepm/hstepm;
4136: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4137: oldm=oldms;savm=savms;
4138: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4139:
4140: for (h=0; h<=nhstepm; h++){
4141: if (h*hstepm/YEARM*stepm ==yearp) {
4142: fprintf(ficresf,"\n");
4143: for(j=1;j<=cptcoveff;j++)
4144: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4145: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4146: }
4147: for(j=1; j<=nlstate+ndeath;j++) {
4148: ppij=0.;
4149: for(i=1; i<=nlstate;i++) {
4150: if (mobilav==1)
4151: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4152: else {
4153: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4154: }
4155: if (h*hstepm/YEARM*stepm== yearp) {
4156: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4157: }
4158: } /* end i */
4159: if (h*hstepm/YEARM*stepm==yearp) {
4160: fprintf(ficresf," %.3f", ppij);
4161: }
4162: }/* end j */
4163: } /* end h */
4164: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4165: } /* end agec */
4166: } /* end yearp */
4167: } /* end cptcod */
4168: } /* end cptcov */
4169:
4170: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4171:
4172: fclose(ficresf);
4173: }
4174:
4175: /************** Forecasting *****not tested NB*************/
4176: 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){
4177:
4178: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4179: int *popage;
4180: double calagedatem, agelim, kk1, kk2;
4181: double *popeffectif,*popcount;
4182: double ***p3mat,***tabpop,***tabpopprev;
4183: double ***mobaverage;
4184: char filerespop[FILENAMELENGTH];
4185:
4186: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4187: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4188: agelim=AGESUP;
4189: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4190:
4191: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4192:
4193:
4194: strcpy(filerespop,"pop");
4195: strcat(filerespop,fileres);
4196: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4197: printf("Problem with forecast resultfile: %s\n", filerespop);
4198: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4199: }
4200: printf("Computing forecasting: result on file '%s' \n", filerespop);
4201: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4202:
4203: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4204:
4205: if (mobilav!=0) {
4206: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4207: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4208: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4209: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4210: }
4211: }
4212:
4213: stepsize=(int) (stepm+YEARM-1)/YEARM;
4214: if (stepm<=12) stepsize=1;
4215:
4216: agelim=AGESUP;
4217:
4218: hstepm=1;
4219: hstepm=hstepm/stepm;
4220:
4221: if (popforecast==1) {
4222: if((ficpop=fopen(popfile,"r"))==NULL) {
4223: printf("Problem with population file : %s\n",popfile);exit(0);
4224: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4225: }
4226: popage=ivector(0,AGESUP);
4227: popeffectif=vector(0,AGESUP);
4228: popcount=vector(0,AGESUP);
4229:
4230: i=1;
4231: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4232:
4233: imx=i;
4234: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4235: }
4236:
4237: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4238: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4239: k=k+1;
4240: fprintf(ficrespop,"\n#******");
4241: for(j=1;j<=cptcoveff;j++) {
4242: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4243: }
4244: fprintf(ficrespop,"******\n");
4245: fprintf(ficrespop,"# Age");
4246: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4247: if (popforecast==1) fprintf(ficrespop," [Population]");
4248:
4249: for (cpt=0; cpt<=0;cpt++) {
4250: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4251:
4252: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4253: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4254: nhstepm = nhstepm/hstepm;
4255:
4256: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4257: oldm=oldms;savm=savms;
4258: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4259:
4260: for (h=0; h<=nhstepm; h++){
4261: if (h==(int) (calagedatem+YEARM*cpt)) {
4262: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4263: }
4264: for(j=1; j<=nlstate+ndeath;j++) {
4265: kk1=0.;kk2=0;
4266: for(i=1; i<=nlstate;i++) {
4267: if (mobilav==1)
4268: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4269: else {
4270: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4271: }
4272: }
4273: if (h==(int)(calagedatem+12*cpt)){
4274: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4275: /*fprintf(ficrespop," %.3f", kk1);
4276: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4277: }
4278: }
4279: for(i=1; i<=nlstate;i++){
4280: kk1=0.;
4281: for(j=1; j<=nlstate;j++){
4282: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4283: }
4284: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4285: }
4286:
4287: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4288: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4289: }
4290: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4291: }
4292: }
4293:
4294: /******/
4295:
4296: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4297: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4298: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4299: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4300: nhstepm = nhstepm/hstepm;
4301:
4302: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4303: oldm=oldms;savm=savms;
4304: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4305: for (h=0; h<=nhstepm; h++){
4306: if (h==(int) (calagedatem+YEARM*cpt)) {
4307: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4308: }
4309: for(j=1; j<=nlstate+ndeath;j++) {
4310: kk1=0.;kk2=0;
4311: for(i=1; i<=nlstate;i++) {
4312: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4313: }
4314: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4315: }
4316: }
4317: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4318: }
4319: }
4320: }
4321: }
4322:
4323: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4324:
4325: if (popforecast==1) {
4326: free_ivector(popage,0,AGESUP);
4327: free_vector(popeffectif,0,AGESUP);
4328: free_vector(popcount,0,AGESUP);
4329: }
4330: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4331: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4332: fclose(ficrespop);
4333: } /* End of popforecast */
4334:
4335: int fileappend(FILE *fichier, char *optionfich)
4336: {
4337: if((fichier=fopen(optionfich,"a"))==NULL) {
4338: printf("Problem with file: %s\n", optionfich);
4339: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4340: return (0);
4341: }
4342: fflush(fichier);
4343: return (1);
4344: }
4345:
4346:
4347: /**************** function prwizard **********************/
4348: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4349: {
4350:
4351: /* Wizard to print covariance matrix template */
4352:
4353: char ca[32], cb[32], cc[32];
4354: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4355: int numlinepar;
4356:
4357: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4358: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4359: for(i=1; i <=nlstate; i++){
4360: jj=0;
4361: for(j=1; j <=nlstate+ndeath; j++){
4362: if(j==i) continue;
4363: jj++;
4364: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4365: printf("%1d%1d",i,j);
4366: fprintf(ficparo,"%1d%1d",i,j);
4367: for(k=1; k<=ncovmodel;k++){
4368: /* printf(" %lf",param[i][j][k]); */
4369: /* fprintf(ficparo," %lf",param[i][j][k]); */
4370: printf(" 0.");
4371: fprintf(ficparo," 0.");
4372: }
4373: printf("\n");
4374: fprintf(ficparo,"\n");
4375: }
4376: }
4377: printf("# Scales (for hessian or gradient estimation)\n");
4378: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4379: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4380: for(i=1; i <=nlstate; i++){
4381: jj=0;
4382: for(j=1; j <=nlstate+ndeath; j++){
4383: if(j==i) continue;
4384: jj++;
4385: fprintf(ficparo,"%1d%1d",i,j);
4386: printf("%1d%1d",i,j);
4387: fflush(stdout);
4388: for(k=1; k<=ncovmodel;k++){
4389: /* printf(" %le",delti3[i][j][k]); */
4390: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4391: printf(" 0.");
4392: fprintf(ficparo," 0.");
4393: }
4394: numlinepar++;
4395: printf("\n");
4396: fprintf(ficparo,"\n");
4397: }
4398: }
4399: printf("# Covariance matrix\n");
4400: /* # 121 Var(a12)\n\ */
4401: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4402: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4403: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4404: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4405: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4406: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4407: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4408: fflush(stdout);
4409: fprintf(ficparo,"# Covariance matrix\n");
4410: /* # 121 Var(a12)\n\ */
4411: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4412: /* # ...\n\ */
4413: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4414:
4415: for(itimes=1;itimes<=2;itimes++){
4416: jj=0;
4417: for(i=1; i <=nlstate; i++){
4418: for(j=1; j <=nlstate+ndeath; j++){
4419: if(j==i) continue;
4420: for(k=1; k<=ncovmodel;k++){
4421: jj++;
4422: ca[0]= k+'a'-1;ca[1]='\0';
4423: if(itimes==1){
4424: printf("#%1d%1d%d",i,j,k);
4425: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4426: }else{
4427: printf("%1d%1d%d",i,j,k);
4428: fprintf(ficparo,"%1d%1d%d",i,j,k);
4429: /* printf(" %.5le",matcov[i][j]); */
4430: }
4431: ll=0;
4432: for(li=1;li <=nlstate; li++){
4433: for(lj=1;lj <=nlstate+ndeath; lj++){
4434: if(lj==li) continue;
4435: for(lk=1;lk<=ncovmodel;lk++){
4436: ll++;
4437: if(ll<=jj){
4438: cb[0]= lk +'a'-1;cb[1]='\0';
4439: if(ll<jj){
4440: if(itimes==1){
4441: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4442: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4443: }else{
4444: printf(" 0.");
4445: fprintf(ficparo," 0.");
4446: }
4447: }else{
4448: if(itimes==1){
4449: printf(" Var(%s%1d%1d)",ca,i,j);
4450: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4451: }else{
4452: printf(" 0.");
4453: fprintf(ficparo," 0.");
4454: }
4455: }
4456: }
4457: } /* end lk */
4458: } /* end lj */
4459: } /* end li */
4460: printf("\n");
4461: fprintf(ficparo,"\n");
4462: numlinepar++;
4463: } /* end k*/
4464: } /*end j */
4465: } /* end i */
4466: } /* end itimes */
4467:
4468: } /* end of prwizard */
4469: /******************* Gompertz Likelihood ******************************/
4470: double gompertz(double x[])
4471: {
4472: double A,B,L=0.0,sump=0.,num=0.;
4473: int i,n=0; /* n is the size of the sample */
4474:
4475: for (i=0;i<=imx-1 ; i++) {
4476: sump=sump+weight[i];
4477: /* sump=sump+1;*/
4478: num=num+1;
4479: }
4480:
4481:
4482: /* for (i=0; i<=imx; i++)
4483: 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]);*/
4484:
4485: for (i=1;i<=imx ; i++)
4486: {
4487: if (cens[i] == 1 && wav[i]>1)
4488: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4489:
4490: if (cens[i] == 0 && wav[i]>1)
4491: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4492: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4493:
4494: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4495: if (wav[i] > 1 ) { /* ??? */
4496: L=L+A*weight[i];
4497: /* 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]);*/
4498: }
4499: }
4500:
4501: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4502:
4503: return -2*L*num/sump;
4504: }
4505:
1.136 brouard 4506: #ifdef GSL
4507: /******************* Gompertz_f Likelihood ******************************/
4508: double gompertz_f(const gsl_vector *v, void *params)
4509: {
4510: double A,B,LL=0.0,sump=0.,num=0.;
4511: double *x= (double *) v->data;
4512: int i,n=0; /* n is the size of the sample */
4513:
4514: for (i=0;i<=imx-1 ; i++) {
4515: sump=sump+weight[i];
4516: /* sump=sump+1;*/
4517: num=num+1;
4518: }
4519:
4520:
4521: /* for (i=0; i<=imx; i++)
4522: 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]);*/
4523: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4524: for (i=1;i<=imx ; i++)
4525: {
4526: if (cens[i] == 1 && wav[i]>1)
4527: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4528:
4529: if (cens[i] == 0 && wav[i]>1)
4530: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4531: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4532:
4533: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4534: if (wav[i] > 1 ) { /* ??? */
4535: LL=LL+A*weight[i];
4536: /* 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]);*/
4537: }
4538: }
4539:
4540: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4541: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4542:
4543: return -2*LL*num/sump;
4544: }
4545: #endif
4546:
1.126 brouard 4547: /******************* Printing html file ***********/
4548: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4549: int lastpass, int stepm, int weightopt, char model[],\
4550: int imx, double p[],double **matcov,double agemortsup){
4551: int i,k;
4552:
4553: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4554: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4555: for (i=1;i<=2;i++)
4556: 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]));
4557: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4558: fprintf(fichtm,"</ul>");
4559:
4560: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4561:
4562: 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>");
4563:
4564: for (k=agegomp;k<(agemortsup-2);k++)
4565: 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]);
4566:
4567:
4568: fflush(fichtm);
4569: }
4570:
4571: /******************* Gnuplot file **************/
4572: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4573:
4574: char dirfileres[132],optfileres[132];
4575: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4576: int ng;
4577:
4578:
4579: /*#ifdef windows */
4580: fprintf(ficgp,"cd \"%s\" \n",pathc);
4581: /*#endif */
4582:
4583:
4584: strcpy(dirfileres,optionfilefiname);
4585: strcpy(optfileres,"vpl");
4586: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4587: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4588: fprintf(ficgp, "set ter png small\n set log y\n");
4589: fprintf(ficgp, "set size 0.65,0.65\n");
4590: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4591:
4592: }
4593:
1.136 brouard 4594: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4595: {
1.126 brouard 4596:
1.136 brouard 4597: /*-------- data file ----------*/
4598: FILE *fic;
4599: char dummy[]=" ";
4600: int i, j, n;
4601: int linei, month, year,iout;
4602: char line[MAXLINE], linetmp[MAXLINE];
4603: char stra[80], strb[80];
4604: char *stratrunc;
4605: int lstra;
1.126 brouard 4606:
4607:
1.136 brouard 4608: if((fic=fopen(datafile,"r"))==NULL) {
4609: printf("Problem while opening datafile: %s\n", datafile);return 1;
4610: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4611: }
1.126 brouard 4612:
1.136 brouard 4613: i=1;
4614: linei=0;
4615: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4616: linei=linei+1;
4617: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4618: if(line[j] == '\t')
4619: line[j] = ' ';
4620: }
4621: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4622: ;
4623: };
4624: line[j+1]=0; /* Trims blanks at end of line */
4625: if(line[0]=='#'){
4626: fprintf(ficlog,"Comment line\n%s\n",line);
4627: printf("Comment line\n%s\n",line);
4628: continue;
4629: }
4630: trimbb(linetmp,line); /* Trims multiple blanks in line */
4631: for (j=0; line[j]!='\0';j++){
4632: line[j]=linetmp[j];
4633: }
4634:
1.126 brouard 4635:
1.136 brouard 4636: for (j=maxwav;j>=1;j--){
1.137 brouard 4637: cutv(stra, strb, line, ' ');
1.136 brouard 4638: if(strb[0]=='.') { /* Missing status */
4639: lval=-1;
4640: }else{
4641: errno=0;
4642: lval=strtol(strb,&endptr,10);
4643: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4644: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4645: 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);
4646: 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 4647: return 1;
4648: }
4649: }
4650: s[j][i]=lval;
4651:
4652: strcpy(line,stra);
4653: cutv(stra, strb,line,' ');
4654: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4655: }
4656: else if(iout=sscanf(strb,"%s.") != 0){
4657: month=99;
4658: year=9999;
4659: }else{
1.141 brouard 4660: 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);
4661: 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 4662: return 1;
4663: }
4664: anint[j][i]= (double) year;
4665: mint[j][i]= (double)month;
4666: strcpy(line,stra);
4667: } /* ENd Waves */
4668:
4669: cutv(stra, strb,line,' ');
4670: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4671: }
4672: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4673: month=99;
4674: year=9999;
4675: }else{
1.141 brouard 4676: 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);
4677: 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 4678: return 1;
4679: }
4680: andc[i]=(double) year;
4681: moisdc[i]=(double) month;
4682: strcpy(line,stra);
4683:
4684: cutv(stra, strb,line,' ');
4685: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4686: }
4687: else if(iout=sscanf(strb,"%s.") != 0){
4688: month=99;
4689: year=9999;
4690: }else{
1.141 brouard 4691: 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);
4692: 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 4693: return 1;
4694: }
4695: if (year==9999) {
1.141 brouard 4696: 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);
4697: 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 4698: return 1;
1.126 brouard 4699:
1.136 brouard 4700: }
4701: annais[i]=(double)(year);
4702: moisnais[i]=(double)(month);
4703: strcpy(line,stra);
4704:
4705: cutv(stra, strb,line,' ');
4706: errno=0;
4707: dval=strtod(strb,&endptr);
4708: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4709: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4710: 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 4711: fflush(ficlog);
4712: return 1;
4713: }
4714: weight[i]=dval;
4715: strcpy(line,stra);
4716:
4717: for (j=ncovcol;j>=1;j--){
4718: cutv(stra, strb,line,' ');
4719: if(strb[0]=='.') { /* Missing status */
4720: lval=-1;
4721: }else{
4722: errno=0;
4723: lval=strtol(strb,&endptr,10);
4724: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4725: 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);
4726: 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 4727: return 1;
4728: }
4729: }
4730: if(lval <-1 || lval >1){
1.141 brouard 4731: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4732: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4733: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4734: For example, for multinomial values like 1, 2 and 3,\n \
4735: build V1=0 V2=0 for the reference value (1),\n \
4736: V1=1 V2=0 for (2) \n \
4737: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4738: output of IMaCh is often meaningless.\n \
4739: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 4740: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4741: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4742: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4743: For example, for multinomial values like 1, 2 and 3,\n \
4744: build V1=0 V2=0 for the reference value (1),\n \
4745: V1=1 V2=0 for (2) \n \
4746: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4747: output of IMaCh is often meaningless.\n \
4748: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4749: return 1;
4750: }
4751: covar[j][i]=(double)(lval);
4752: strcpy(line,stra);
4753: }
4754: lstra=strlen(stra);
4755:
4756: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4757: stratrunc = &(stra[lstra-9]);
4758: num[i]=atol(stratrunc);
4759: }
4760: else
4761: num[i]=atol(stra);
4762: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4763: 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;}*/
4764:
4765: i=i+1;
4766: } /* End loop reading data */
1.126 brouard 4767:
1.136 brouard 4768: *imax=i-1; /* Number of individuals */
4769: fclose(fic);
4770:
4771: return (0);
4772: endread:
4773: printf("Exiting readdata: ");
4774: fclose(fic);
4775: return (1);
1.126 brouard 4776:
4777:
4778:
1.136 brouard 4779: }
1.126 brouard 4780:
1.136 brouard 4781: int decodemodel ( char model[], int lastobs)
4782: {
4783: int i, j, k;
4784: int i1, j1, k1, k2;
4785: char modelsav[80];
4786: char stra[80], strb[80], strc[80], strd[80],stre[80];
4787:
4788: if (strlen(model) >1){ /* If there is at least 1 covariate */
4789: j=0, j1=0, k1=1, k2=1;
4790: j=nbocc(model,'+'); /* j=Number of '+' */
4791: j1=nbocc(model,'*'); /* j1=Number of '*' */
4792: cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
4793: but the covariates which are product must be computed and stored. */
4794: cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
4795:
4796: strcpy(modelsav,model);
1.137 brouard 4797: if (strstr(model,"AGE") !=0){
4798: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4799: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 4800: return 1;
4801: }
1.141 brouard 4802: if (strstr(model,"v") !=0){
4803: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4804: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4805: return 1;
4806: }
1.136 brouard 4807:
4808: /* This loop fills the array Tvar from the string 'model'.*/
4809: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 4810: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
4811: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
4812: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
4813: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
4814: /* k=1 Tvar[1]=2 (from V2) */
4815: /* k=5 Tvar[5] */
4816: /* for (k=1; k<=cptcovn;k++) { */
4817: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
4818: /* } */
4819: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4820: for(k=cptcovn; k>=1;k--){
4821: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
4822: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4
1.136 brouard 4823: */
1.137 brouard 4824: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 4825: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4826: /*scanf("%d",i);*/
1.137 brouard 4827: if (strchr(strb,'*')) { /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
1.136 brouard 4828: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
4829: if (strcmp(strc,"age")==0) { /* Vn*age */
4830: cptcovprod--;
4831: cutv(strb,stre,strd,'V'); /* stre="V3" */
1.137 brouard 4832: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 4833: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 4834: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 4835: /*printf("stre=%s ", stre);*/
1.137 brouard 4836: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 4837: cptcovprod--;
4838: cutv(strb,stre,strc,'V');
4839: Tvar[k]=atoi(stre);
4840: cptcovage++;
4841: Tage[cptcovage]=k;
1.137 brouard 4842: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
4843: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.136 brouard 4844: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
1.137 brouard 4845: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
4846: because this model-covariate is a construction we invent a new column
4847: ncovcol + k1
4848: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
4849: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.136 brouard 4850: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 4851: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
4852: Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
4853: Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
4854: Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
4855: Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
4856: for (i=1; i<=lastobs;i++){
4857: /* Computes the new covariate which is a product of
4858: covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
1.136 brouard 4859: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 4860: }
1.136 brouard 4861: k1++;
4862: k2=k2+2;
1.137 brouard 4863: } /* End age is not in the model */
4864: } /* End if model includes a product */
1.136 brouard 4865: else { /* no more sum */
4866: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4867: /* scanf("%d",i);*/
4868: cutv(strd,strc,strb,'V');
1.137 brouard 4869: Tvar[k]=atoi(strc);
1.136 brouard 4870: }
1.137 brouard 4871: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 4872: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4873: scanf("%d",i);*/
4874: } /* end of loop + */
4875: } /* end model */
4876:
4877: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4878: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4879:
4880: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4881: printf("cptcovprod=%d ", cptcovprod);
4882: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4883:
4884: scanf("%d ",i);*/
4885:
4886:
1.137 brouard 4887: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.136 brouard 4888: endread:
4889: printf("Exiting decodemodel: ");
4890: return (1);
4891: }
4892:
4893: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
4894: {
4895: int i, m;
4896:
4897: for (i=1; i<=imx; i++) {
4898: for(m=2; (m<= maxwav); m++) {
4899: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4900: anint[m][i]=9999;
4901: s[m][i]=-1;
4902: }
4903: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4904: *nberr++;
4905: 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);
4906: 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);
4907: s[m][i]=-1;
4908: }
4909: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4910: *nberr++;
4911: 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]);
4912: 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]);
4913: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4914: }
4915: }
4916: }
4917:
4918: for (i=1; i<=imx; i++) {
4919: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4920: for(m=firstpass; (m<= lastpass); m++){
4921: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4922: if (s[m][i] >= nlstate+1) {
4923: if(agedc[i]>0)
4924: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4925: agev[m][i]=agedc[i];
4926: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4927: else {
4928: if ((int)andc[i]!=9999){
4929: nbwarn++;
4930: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4931: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4932: agev[m][i]=-1;
4933: }
4934: }
4935: }
4936: else if(s[m][i] !=9){ /* Standard case, age in fractional
4937: years but with the precision of a month */
4938: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4939: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4940: agev[m][i]=1;
4941: else if(agev[m][i] < *agemin){
4942: *agemin=agev[m][i];
4943: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
4944: }
4945: else if(agev[m][i] >*agemax){
4946: *agemax=agev[m][i];
1.139 brouard 4947: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
1.136 brouard 4948: }
4949: /*agev[m][i]=anint[m][i]-annais[i];*/
4950: /* agev[m][i] = age[i]+2*m;*/
4951: }
4952: else { /* =9 */
4953: agev[m][i]=1;
4954: s[m][i]=-1;
4955: }
4956: }
4957: else /*= 0 Unknown */
4958: agev[m][i]=1;
4959: }
4960:
4961: }
4962: for (i=1; i<=imx; i++) {
4963: for(m=firstpass; (m<=lastpass); m++){
4964: if (s[m][i] > (nlstate+ndeath)) {
4965: *nberr++;
4966: 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);
4967: 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);
4968: return 1;
4969: }
4970: }
4971: }
4972:
4973: /*for (i=1; i<=imx; i++){
4974: for (m=firstpass; (m<lastpass); m++){
4975: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4976: }
4977:
4978: }*/
4979:
4980:
1.139 brouard 4981: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
4982: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 4983:
4984: return (0);
4985: endread:
4986: printf("Exiting calandcheckages: ");
4987: return (1);
4988: }
4989:
4990:
4991: /***********************************************/
4992: /**************** Main Program *****************/
4993: /***********************************************/
4994:
4995: int main(int argc, char *argv[])
4996: {
4997: #ifdef GSL
4998: const gsl_multimin_fminimizer_type *T;
4999: size_t iteri = 0, it;
5000: int rval = GSL_CONTINUE;
5001: int status = GSL_SUCCESS;
5002: double ssval;
5003: #endif
5004: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5005: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5006: int linei, month, year,iout;
5007: int jj, ll, li, lj, lk, imk;
5008: int numlinepar=0; /* Current linenumber of parameter file */
5009: int itimes;
5010: int NDIM=2;
5011: int vpopbased=0;
5012:
5013: char ca[32], cb[32], cc[32];
5014: /* FILE *fichtm; *//* Html File */
5015: /* FILE *ficgp;*/ /*Gnuplot File */
5016: struct stat info;
5017: double agedeb, agefin,hf;
5018: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5019:
5020: double fret;
5021: double **xi,tmp,delta;
5022:
5023: double dum; /* Dummy variable */
5024: double ***p3mat;
5025: double ***mobaverage;
5026: int *indx;
5027: char line[MAXLINE], linepar[MAXLINE];
5028: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5029: char pathr[MAXLINE], pathimach[MAXLINE];
5030: char **bp, *tok, *val; /* pathtot */
5031: int firstobs=1, lastobs=10;
5032: int sdeb, sfin; /* Status at beginning and end */
5033: int c, h , cpt,l;
5034: int ju,jl, mi;
5035: int i1,j1, jk,aa,bb, stepsize, ij;
5036: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5037: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5038: int mobilav=0,popforecast=0;
5039: int hstepm, nhstepm;
5040: int agemortsup;
5041: float sumlpop=0.;
5042: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5043: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5044:
5045: double bage, fage, age, agelim, agebase;
5046: double ftolpl=FTOL;
5047: double **prlim;
5048: double ***param; /* Matrix of parameters */
5049: double *p;
5050: double **matcov; /* Matrix of covariance */
5051: double ***delti3; /* Scale */
5052: double *delti; /* Scale */
5053: double ***eij, ***vareij;
5054: double **varpl; /* Variances of prevalence limits by age */
5055: double *epj, vepp;
5056: double kk1, kk2;
5057: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5058: double **ximort;
5059: char *alph[]={"a","a","b","c","d","e"}, str[4];
5060: int *dcwave;
5061:
5062: char z[1]="c", occ;
5063:
5064: /*char *strt;*/
5065: char strtend[80];
1.126 brouard 5066:
5067: long total_usecs;
5068:
5069: /* setlocale (LC_ALL, ""); */
5070: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5071: /* textdomain (PACKAGE); */
5072: /* setlocale (LC_CTYPE, ""); */
5073: /* setlocale (LC_MESSAGES, ""); */
5074:
5075: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5076: (void) gettimeofday(&start_time,&tzp);
5077: curr_time=start_time;
5078: tm = *localtime(&start_time.tv_sec);
5079: tmg = *gmtime(&start_time.tv_sec);
5080: strcpy(strstart,asctime(&tm));
5081:
5082: /* printf("Localtime (at start)=%s",strstart); */
5083: /* tp.tv_sec = tp.tv_sec +86400; */
5084: /* tm = *localtime(&start_time.tv_sec); */
5085: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5086: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5087: /* tmg.tm_hour=tmg.tm_hour + 1; */
5088: /* tp.tv_sec = mktime(&tmg); */
5089: /* strt=asctime(&tmg); */
5090: /* printf("Time(after) =%s",strstart); */
5091: /* (void) time (&time_value);
5092: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5093: * tm = *localtime(&time_value);
5094: * strstart=asctime(&tm);
5095: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5096: */
5097:
5098: nberr=0; /* Number of errors and warnings */
5099: nbwarn=0;
5100: getcwd(pathcd, size);
5101:
5102: printf("\n%s\n%s",version,fullversion);
5103: if(argc <=1){
5104: printf("\nEnter the parameter file name: ");
5105: fgets(pathr,FILENAMELENGTH,stdin);
5106: i=strlen(pathr);
5107: if(pathr[i-1]=='\n')
5108: pathr[i-1]='\0';
5109: for (tok = pathr; tok != NULL; ){
5110: printf("Pathr |%s|\n",pathr);
5111: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5112: printf("val= |%s| pathr=%s\n",val,pathr);
5113: strcpy (pathtot, val);
5114: if(pathr[0] == '\0') break; /* Dirty */
5115: }
5116: }
5117: else{
5118: strcpy(pathtot,argv[1]);
5119: }
5120: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5121: /*cygwin_split_path(pathtot,path,optionfile);
5122: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5123: /* cutv(path,optionfile,pathtot,'\\');*/
5124:
5125: /* Split argv[0], imach program to get pathimach */
5126: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5127: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5128: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5129: /* strcpy(pathimach,argv[0]); */
5130: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5131: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5132: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5133: chdir(path); /* Can be a relative path */
5134: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5135: printf("Current directory %s!\n",pathcd);
5136: strcpy(command,"mkdir ");
5137: strcat(command,optionfilefiname);
5138: if((outcmd=system(command)) != 0){
5139: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5140: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5141: /* fclose(ficlog); */
5142: /* exit(1); */
5143: }
5144: /* if((imk=mkdir(optionfilefiname))<0){ */
5145: /* perror("mkdir"); */
5146: /* } */
5147:
5148: /*-------- arguments in the command line --------*/
5149:
5150: /* Log file */
5151: strcat(filelog, optionfilefiname);
5152: strcat(filelog,".log"); /* */
5153: if((ficlog=fopen(filelog,"w"))==NULL) {
5154: printf("Problem with logfile %s\n",filelog);
5155: goto end;
5156: }
5157: fprintf(ficlog,"Log filename:%s\n",filelog);
5158: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5159: fprintf(ficlog,"\nEnter the parameter file name: \n");
5160: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5161: path=%s \n\
5162: optionfile=%s\n\
5163: optionfilext=%s\n\
5164: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5165:
5166: printf("Local time (at start):%s",strstart);
5167: fprintf(ficlog,"Local time (at start): %s",strstart);
5168: fflush(ficlog);
5169: /* (void) gettimeofday(&curr_time,&tzp); */
5170: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5171:
5172: /* */
5173: strcpy(fileres,"r");
5174: strcat(fileres, optionfilefiname);
5175: strcat(fileres,".txt"); /* Other files have txt extension */
5176:
5177: /*---------arguments file --------*/
5178:
5179: if((ficpar=fopen(optionfile,"r"))==NULL) {
5180: printf("Problem with optionfile %s\n",optionfile);
5181: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5182: fflush(ficlog);
5183: goto end;
5184: }
5185:
5186:
5187:
5188: strcpy(filereso,"o");
5189: strcat(filereso,fileres);
5190: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5191: printf("Problem with Output resultfile: %s\n", filereso);
5192: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5193: fflush(ficlog);
5194: goto end;
5195: }
5196:
5197: /* Reads comments: lines beginning with '#' */
5198: numlinepar=0;
5199: while((c=getc(ficpar))=='#' && c!= EOF){
5200: ungetc(c,ficpar);
5201: fgets(line, MAXLINE, ficpar);
5202: numlinepar++;
1.141 brouard 5203: fputs(line,stdout);
1.126 brouard 5204: fputs(line,ficparo);
5205: fputs(line,ficlog);
5206: }
5207: ungetc(c,ficpar);
5208:
5209: 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);
5210: numlinepar++;
5211: 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);
5212: 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);
5213: 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);
5214: fflush(ficlog);
5215: while((c=getc(ficpar))=='#' && c!= EOF){
5216: ungetc(c,ficpar);
5217: fgets(line, MAXLINE, ficpar);
5218: numlinepar++;
1.141 brouard 5219: fputs(line, stdout);
5220: //puts(line);
1.126 brouard 5221: fputs(line,ficparo);
5222: fputs(line,ficlog);
5223: }
5224: ungetc(c,ficpar);
5225:
5226:
5227: covar=matrix(0,NCOVMAX,1,n);
1.136 brouard 5228: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5229: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5230: v1+v2*age+v2*v3 makes cptcovn = 3
5231: */
5232: if (strlen(model)>1)
5233: cptcovn=nbocc(model,'+')+1;
5234: /* ncovprod */
5235: 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 5236: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5237: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5238: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5239: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5240: 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);
5241: 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);
5242: fflush(stdout);
5243: fclose (ficlog);
5244: goto end;
5245: }
1.126 brouard 5246: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5247: delti=delti3[1][1];
5248: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5249: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5250: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5251: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5252: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5253: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5254: fclose (ficparo);
5255: fclose (ficlog);
5256: goto end;
5257: exit(0);
5258: }
5259: else if(mle==-3) {
5260: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5261: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5262: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5263: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5264: matcov=matrix(1,npar,1,npar);
5265: }
5266: else{
5267: /* Read guess parameters */
5268: /* Reads comments: lines beginning with '#' */
5269: while((c=getc(ficpar))=='#' && c!= EOF){
5270: ungetc(c,ficpar);
5271: fgets(line, MAXLINE, ficpar);
5272: numlinepar++;
1.141 brouard 5273: fputs(line,stdout);
1.126 brouard 5274: fputs(line,ficparo);
5275: fputs(line,ficlog);
5276: }
5277: ungetc(c,ficpar);
5278:
5279: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5280: for(i=1; i <=nlstate; i++){
5281: j=0;
5282: for(jj=1; jj <=nlstate+ndeath; jj++){
5283: if(jj==i) continue;
5284: j++;
5285: fscanf(ficpar,"%1d%1d",&i1,&j1);
5286: if ((i1 != i) && (j1 != j)){
5287: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5288: It might be a problem of design; if ncovcol and the model are correct\n \
5289: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5290: exit(1);
5291: }
5292: fprintf(ficparo,"%1d%1d",i1,j1);
5293: if(mle==1)
5294: printf("%1d%1d",i,j);
5295: fprintf(ficlog,"%1d%1d",i,j);
5296: for(k=1; k<=ncovmodel;k++){
5297: fscanf(ficpar," %lf",¶m[i][j][k]);
5298: if(mle==1){
5299: printf(" %lf",param[i][j][k]);
5300: fprintf(ficlog," %lf",param[i][j][k]);
5301: }
5302: else
5303: fprintf(ficlog," %lf",param[i][j][k]);
5304: fprintf(ficparo," %lf",param[i][j][k]);
5305: }
5306: fscanf(ficpar,"\n");
5307: numlinepar++;
5308: if(mle==1)
5309: printf("\n");
5310: fprintf(ficlog,"\n");
5311: fprintf(ficparo,"\n");
5312: }
5313: }
5314: fflush(ficlog);
5315:
5316: p=param[1][1];
5317:
5318: /* Reads comments: lines beginning with '#' */
5319: while((c=getc(ficpar))=='#' && c!= EOF){
5320: ungetc(c,ficpar);
5321: fgets(line, MAXLINE, ficpar);
5322: numlinepar++;
1.141 brouard 5323: fputs(line,stdout);
1.126 brouard 5324: fputs(line,ficparo);
5325: fputs(line,ficlog);
5326: }
5327: ungetc(c,ficpar);
5328:
5329: for(i=1; i <=nlstate; i++){
5330: for(j=1; j <=nlstate+ndeath-1; j++){
5331: fscanf(ficpar,"%1d%1d",&i1,&j1);
5332: if ((i1-i)*(j1-j)!=0){
5333: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5334: exit(1);
5335: }
5336: printf("%1d%1d",i,j);
5337: fprintf(ficparo,"%1d%1d",i1,j1);
5338: fprintf(ficlog,"%1d%1d",i1,j1);
5339: for(k=1; k<=ncovmodel;k++){
5340: fscanf(ficpar,"%le",&delti3[i][j][k]);
5341: printf(" %le",delti3[i][j][k]);
5342: fprintf(ficparo," %le",delti3[i][j][k]);
5343: fprintf(ficlog," %le",delti3[i][j][k]);
5344: }
5345: fscanf(ficpar,"\n");
5346: numlinepar++;
5347: printf("\n");
5348: fprintf(ficparo,"\n");
5349: fprintf(ficlog,"\n");
5350: }
5351: }
5352: fflush(ficlog);
5353:
5354: delti=delti3[1][1];
5355:
5356:
5357: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5358:
5359: /* Reads comments: lines beginning with '#' */
5360: while((c=getc(ficpar))=='#' && c!= EOF){
5361: ungetc(c,ficpar);
5362: fgets(line, MAXLINE, ficpar);
5363: numlinepar++;
1.141 brouard 5364: fputs(line,stdout);
1.126 brouard 5365: fputs(line,ficparo);
5366: fputs(line,ficlog);
5367: }
5368: ungetc(c,ficpar);
5369:
5370: matcov=matrix(1,npar,1,npar);
1.131 brouard 5371: for(i=1; i <=npar; i++)
5372: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5373:
1.126 brouard 5374: for(i=1; i <=npar; i++){
5375: fscanf(ficpar,"%s",&str);
5376: if(mle==1)
5377: printf("%s",str);
5378: fprintf(ficlog,"%s",str);
5379: fprintf(ficparo,"%s",str);
5380: for(j=1; j <=i; j++){
5381: fscanf(ficpar," %le",&matcov[i][j]);
5382: if(mle==1){
5383: printf(" %.5le",matcov[i][j]);
5384: }
5385: fprintf(ficlog," %.5le",matcov[i][j]);
5386: fprintf(ficparo," %.5le",matcov[i][j]);
5387: }
5388: fscanf(ficpar,"\n");
5389: numlinepar++;
5390: if(mle==1)
5391: printf("\n");
5392: fprintf(ficlog,"\n");
5393: fprintf(ficparo,"\n");
5394: }
5395: for(i=1; i <=npar; i++)
5396: for(j=i+1;j<=npar;j++)
5397: matcov[i][j]=matcov[j][i];
5398:
5399: if(mle==1)
5400: printf("\n");
5401: fprintf(ficlog,"\n");
5402:
5403: fflush(ficlog);
5404:
5405: /*-------- Rewriting parameter file ----------*/
5406: strcpy(rfileres,"r"); /* "Rparameterfile */
5407: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5408: strcat(rfileres,"."); /* */
5409: strcat(rfileres,optionfilext); /* Other files have txt extension */
5410: if((ficres =fopen(rfileres,"w"))==NULL) {
5411: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5412: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5413: }
5414: fprintf(ficres,"#%s\n",version);
5415: } /* End of mle != -3 */
5416:
5417:
5418: n= lastobs;
5419: num=lvector(1,n);
5420: moisnais=vector(1,n);
5421: annais=vector(1,n);
5422: moisdc=vector(1,n);
5423: andc=vector(1,n);
5424: agedc=vector(1,n);
5425: cod=ivector(1,n);
5426: weight=vector(1,n);
5427: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5428: mint=matrix(1,maxwav,1,n);
5429: anint=matrix(1,maxwav,1,n);
1.131 brouard 5430: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5431: tab=ivector(1,NCOVMAX);
1.144 ! brouard 5432: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5433:
1.136 brouard 5434: /* Reads data from file datafile */
5435: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5436: goto end;
5437:
5438: /* Calculation of the number of parameters from char model */
1.137 brouard 5439: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5440: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5441: k=3 V4 Tvar[k=3]= 4 (from V4)
5442: k=2 V1 Tvar[k=2]= 1 (from V1)
5443: k=1 Tvar[1]=2 (from V2)
5444: */
5445: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5446: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5447: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5448: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5449: */
5450: /* For model-covariate k tells which data-covariate to use but
5451: because this model-covariate is a construction we invent a new column
5452: ncovcol + k1
5453: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5454: Tvar[3=V1*V4]=4+1 etc */
1.141 brouard 5455: Tprod=ivector(1,15); /* Gives the position of a product */
1.137 brouard 5456: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5457: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5458: */
1.136 brouard 5459: Tvaraff=ivector(1,15);
1.141 brouard 5460: 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
5461: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5462: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.137 brouard 5463: Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5464: 4 covariates (3 plus signs)
5465: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5466: */
1.136 brouard 5467:
5468: if(decodemodel(model, lastobs) == 1)
5469: goto end;
5470:
1.137 brouard 5471: if((double)(lastobs-imx)/(double)imx > 1.10){
5472: nbwarn++;
5473: 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);
5474: 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);
5475: }
1.136 brouard 5476: /* if(mle==1){*/
1.137 brouard 5477: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5478: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 5479: }
5480:
5481: /*-calculation of age at interview from date of interview and age at death -*/
5482: agev=matrix(1,maxwav,1,imx);
5483:
5484: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5485: goto end;
5486:
1.126 brouard 5487:
1.136 brouard 5488: agegomp=(int)agemin;
5489: free_vector(moisnais,1,n);
5490: free_vector(annais,1,n);
1.126 brouard 5491: /* free_matrix(mint,1,maxwav,1,n);
5492: free_matrix(anint,1,maxwav,1,n);*/
5493: free_vector(moisdc,1,n);
5494: free_vector(andc,1,n);
5495:
5496:
5497: wav=ivector(1,imx);
5498: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5499: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5500: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5501:
5502: /* Concatenates waves */
5503: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5504:
5505: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5506:
5507: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5508: ncodemax[1]=1;
5509: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5510:
1.144 ! brouard 5511: codtab=imatrix(1,100,1,10); /**< codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1)
! 5512: */
1.126 brouard 5513: h=0;
5514: m=pow(2,cptcoveff);
5515:
1.131 brouard 5516: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 5517: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5518: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5519: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 5520: h++;
1.141 brouard 5521: if (h>m)
1.136 brouard 5522: h=1;
1.144 ! brouard 5523: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 5524: * h 1 2 3 4
5525: *______________________________
5526: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5527: * 2 2 1 1 1
5528: * 3 i=2 1 2 1 1
5529: * 4 2 2 1 1
5530: * 5 i=3 1 i=2 1 2 1
5531: * 6 2 1 2 1
5532: * 7 i=4 1 2 2 1
5533: * 8 2 2 2 1
5534: * 9 i=5 1 i=3 1 i=2 1 1
5535: * 10 2 1 1 1
5536: * 11 i=6 1 2 1 1
5537: * 12 2 2 1 1
5538: * 13 i=7 1 i=4 1 2 1
5539: * 14 2 1 2 1
5540: * 15 i=8 1 2 2 1
5541: * 16 2 2 2 1
5542: */
1.141 brouard 5543: codtab[h][k]=j;
5544: codtab[h][Tvar[k]]=j;
1.130 brouard 5545: 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 5546: }
5547: }
5548: }
5549: }
5550: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5551: codtab[1][2]=1;codtab[2][2]=2; */
5552: /* for(i=1; i <=m ;i++){
5553: for(k=1; k <=cptcovn; k++){
1.131 brouard 5554: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5555: }
5556: printf("\n");
5557: }
5558: scanf("%d",i);*/
5559:
5560: /*------------ gnuplot -------------*/
5561: strcpy(optionfilegnuplot,optionfilefiname);
5562: if(mle==-3)
5563: strcat(optionfilegnuplot,"-mort");
5564: strcat(optionfilegnuplot,".gp");
5565:
5566: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5567: printf("Problem with file %s",optionfilegnuplot);
5568: }
5569: else{
5570: fprintf(ficgp,"\n# %s\n", version);
5571: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 5572: //fprintf(ficgp,"set missing 'NaNq'\n");
5573: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 5574: }
5575: /* fclose(ficgp);*/
5576: /*--------- index.htm --------*/
5577:
5578: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5579: if(mle==-3)
5580: strcat(optionfilehtm,"-mort");
5581: strcat(optionfilehtm,".htm");
5582: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 5583: printf("Problem with %s \n",optionfilehtm);
5584: exit(0);
1.126 brouard 5585: }
5586:
5587: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5588: strcat(optionfilehtmcov,"-cov.htm");
5589: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5590: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5591: }
5592: else{
5593: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5594: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5595: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5596: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5597: }
5598:
5599: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5600: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5601: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5602: \n\
5603: <hr size=\"2\" color=\"#EC5E5E\">\
5604: <ul><li><h4>Parameter files</h4>\n\
5605: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5606: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5607: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5608: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5609: - Date and time at start: %s</ul>\n",\
5610: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5611: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5612: fileres,fileres,\
5613: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5614: fflush(fichtm);
5615:
5616: strcpy(pathr,path);
5617: strcat(pathr,optionfilefiname);
5618: chdir(optionfilefiname); /* Move to directory named optionfile */
5619:
5620: /* Calculates basic frequencies. Computes observed prevalence at single age
5621: and prints on file fileres'p'. */
5622: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5623:
5624: fprintf(fichtm,"\n");
5625: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5626: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5627: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5628: imx,agemin,agemax,jmin,jmax,jmean);
5629: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5630: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5631: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5632: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5633: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5634:
5635:
5636: /* For Powell, parameters are in a vector p[] starting at p[1]
5637: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5638: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5639:
5640: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5641:
5642: if (mle==-3){
1.136 brouard 5643: ximort=matrix(1,NDIM,1,NDIM);
5644: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 5645: cens=ivector(1,n);
5646: ageexmed=vector(1,n);
5647: agecens=vector(1,n);
5648: dcwave=ivector(1,n);
5649:
5650: for (i=1; i<=imx; i++){
5651: dcwave[i]=-1;
5652: for (m=firstpass; m<=lastpass; m++)
5653: if (s[m][i]>nlstate) {
5654: dcwave[i]=m;
5655: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5656: break;
5657: }
5658: }
5659:
5660: for (i=1; i<=imx; i++) {
5661: if (wav[i]>0){
5662: ageexmed[i]=agev[mw[1][i]][i];
5663: j=wav[i];
5664: agecens[i]=1.;
5665:
5666: if (ageexmed[i]> 1 && wav[i] > 0){
5667: agecens[i]=agev[mw[j][i]][i];
5668: cens[i]= 1;
5669: }else if (ageexmed[i]< 1)
5670: cens[i]= -1;
5671: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5672: cens[i]=0 ;
5673: }
5674: else cens[i]=-1;
5675: }
5676:
5677: for (i=1;i<=NDIM;i++) {
5678: for (j=1;j<=NDIM;j++)
5679: ximort[i][j]=(i == j ? 1.0 : 0.0);
5680: }
5681:
5682: p[1]=0.0268; p[NDIM]=0.083;
5683: /*printf("%lf %lf", p[1], p[2]);*/
5684:
5685:
1.136 brouard 5686: #ifdef GSL
5687: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5688: #elsedef
1.126 brouard 5689: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 5690: #endif
1.126 brouard 5691: strcpy(filerespow,"pow-mort");
5692: strcat(filerespow,fileres);
5693: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5694: printf("Problem with resultfile: %s\n", filerespow);
5695: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5696: }
1.136 brouard 5697: #ifdef GSL
5698: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5699: #elsedef
1.126 brouard 5700: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 5701: #endif
1.126 brouard 5702: /* for (i=1;i<=nlstate;i++)
5703: for(j=1;j<=nlstate+ndeath;j++)
5704: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5705: */
5706: fprintf(ficrespow,"\n");
1.136 brouard 5707: #ifdef GSL
5708: /* gsl starts here */
5709: T = gsl_multimin_fminimizer_nmsimplex;
5710: gsl_multimin_fminimizer *sfm = NULL;
5711: gsl_vector *ss, *x;
5712: gsl_multimin_function minex_func;
5713:
5714: /* Initial vertex size vector */
5715: ss = gsl_vector_alloc (NDIM);
5716:
5717: if (ss == NULL){
5718: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5719: }
5720: /* Set all step sizes to 1 */
5721: gsl_vector_set_all (ss, 0.001);
5722:
5723: /* Starting point */
1.126 brouard 5724:
1.136 brouard 5725: x = gsl_vector_alloc (NDIM);
5726:
5727: if (x == NULL){
5728: gsl_vector_free(ss);
5729: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5730: }
5731:
5732: /* Initialize method and iterate */
5733: /* p[1]=0.0268; p[NDIM]=0.083; */
5734: /* gsl_vector_set(x, 0, 0.0268); */
5735: /* gsl_vector_set(x, 1, 0.083); */
5736: gsl_vector_set(x, 0, p[1]);
5737: gsl_vector_set(x, 1, p[2]);
5738:
5739: minex_func.f = &gompertz_f;
5740: minex_func.n = NDIM;
5741: minex_func.params = (void *)&p; /* ??? */
5742:
5743: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5744: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5745:
5746: printf("Iterations beginning .....\n\n");
5747: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5748:
5749: iteri=0;
5750: while (rval == GSL_CONTINUE){
5751: iteri++;
5752: status = gsl_multimin_fminimizer_iterate(sfm);
5753:
5754: if (status) printf("error: %s\n", gsl_strerror (status));
5755: fflush(0);
5756:
5757: if (status)
5758: break;
5759:
5760: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5761: ssval = gsl_multimin_fminimizer_size (sfm);
5762:
5763: if (rval == GSL_SUCCESS)
5764: printf ("converged to a local maximum at\n");
5765:
5766: printf("%5d ", iteri);
5767: for (it = 0; it < NDIM; it++){
5768: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
5769: }
5770: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
5771: }
5772:
5773: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
5774:
5775: gsl_vector_free(x); /* initial values */
5776: gsl_vector_free(ss); /* inital step size */
5777: for (it=0; it<NDIM; it++){
5778: p[it+1]=gsl_vector_get(sfm->x,it);
5779: fprintf(ficrespow," %.12lf", p[it]);
5780: }
5781: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
5782: #endif
5783: #ifdef POWELL
5784: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5785: #endif
1.126 brouard 5786: fclose(ficrespow);
5787:
5788: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5789:
5790: for(i=1; i <=NDIM; i++)
5791: for(j=i+1;j<=NDIM;j++)
5792: matcov[i][j]=matcov[j][i];
5793:
5794: printf("\nCovariance matrix\n ");
5795: for(i=1; i <=NDIM; i++) {
5796: for(j=1;j<=NDIM;j++){
5797: printf("%f ",matcov[i][j]);
5798: }
5799: printf("\n ");
5800: }
5801:
5802: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5803: for (i=1;i<=NDIM;i++)
5804: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5805:
5806: lsurv=vector(1,AGESUP);
5807: lpop=vector(1,AGESUP);
5808: tpop=vector(1,AGESUP);
5809: lsurv[agegomp]=100000;
5810:
5811: for (k=agegomp;k<=AGESUP;k++) {
5812: agemortsup=k;
5813: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5814: }
5815:
5816: for (k=agegomp;k<agemortsup;k++)
5817: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5818:
5819: for (k=agegomp;k<agemortsup;k++){
5820: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5821: sumlpop=sumlpop+lpop[k];
5822: }
5823:
5824: tpop[agegomp]=sumlpop;
5825: for (k=agegomp;k<(agemortsup-3);k++){
5826: /* tpop[k+1]=2;*/
5827: tpop[k+1]=tpop[k]-lpop[k];
5828: }
5829:
5830:
5831: printf("\nAge lx qx dx Lx Tx e(x)\n");
5832: for (k=agegomp;k<(agemortsup-2);k++)
5833: 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]);
5834:
5835:
5836: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5837: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5838:
5839: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5840: stepm, weightopt,\
5841: model,imx,p,matcov,agemortsup);
5842:
5843: free_vector(lsurv,1,AGESUP);
5844: free_vector(lpop,1,AGESUP);
5845: free_vector(tpop,1,AGESUP);
1.136 brouard 5846: #ifdef GSL
5847: free_ivector(cens,1,n);
5848: free_vector(agecens,1,n);
5849: free_ivector(dcwave,1,n);
5850: free_matrix(ximort,1,NDIM,1,NDIM);
5851: #endif
1.126 brouard 5852: } /* Endof if mle==-3 */
5853:
5854: else{ /* For mle >=1 */
1.132 brouard 5855: globpr=0;/* debug */
5856: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 5857: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5858: for (k=1; k<=npar;k++)
5859: printf(" %d %8.5f",k,p[k]);
5860: printf("\n");
5861: globpr=1; /* to print the contributions */
5862: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5863: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5864: for (k=1; k<=npar;k++)
5865: printf(" %d %8.5f",k,p[k]);
5866: printf("\n");
5867: if(mle>=1){ /* Could be 1 or 2 */
5868: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5869: }
5870:
5871: /*--------- results files --------------*/
5872: 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);
5873:
5874:
5875: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5876: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5877: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5878: for(i=1,jk=1; i <=nlstate; i++){
5879: for(k=1; k <=(nlstate+ndeath); k++){
5880: if (k != i) {
5881: printf("%d%d ",i,k);
5882: fprintf(ficlog,"%d%d ",i,k);
5883: fprintf(ficres,"%1d%1d ",i,k);
5884: for(j=1; j <=ncovmodel; j++){
5885: printf("%lf ",p[jk]);
5886: fprintf(ficlog,"%lf ",p[jk]);
5887: fprintf(ficres,"%lf ",p[jk]);
5888: jk++;
5889: }
5890: printf("\n");
5891: fprintf(ficlog,"\n");
5892: fprintf(ficres,"\n");
5893: }
5894: }
5895: }
5896: if(mle!=0){
5897: /* Computing hessian and covariance matrix */
5898: ftolhess=ftol; /* Usually correct */
5899: hesscov(matcov, p, npar, delti, ftolhess, func);
5900: }
5901: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5902: printf("# Scales (for hessian or gradient estimation)\n");
5903: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5904: for(i=1,jk=1; i <=nlstate; i++){
5905: for(j=1; j <=nlstate+ndeath; j++){
5906: if (j!=i) {
5907: fprintf(ficres,"%1d%1d",i,j);
5908: printf("%1d%1d",i,j);
5909: fprintf(ficlog,"%1d%1d",i,j);
5910: for(k=1; k<=ncovmodel;k++){
5911: printf(" %.5e",delti[jk]);
5912: fprintf(ficlog," %.5e",delti[jk]);
5913: fprintf(ficres," %.5e",delti[jk]);
5914: jk++;
5915: }
5916: printf("\n");
5917: fprintf(ficlog,"\n");
5918: fprintf(ficres,"\n");
5919: }
5920: }
5921: }
5922:
5923: 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");
5924: if(mle>=1)
5925: 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");
5926: 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");
5927: /* # 121 Var(a12)\n\ */
5928: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5929: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5930: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5931: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5932: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5933: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5934: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5935:
5936:
5937: /* Just to have a covariance matrix which will be more understandable
5938: even is we still don't want to manage dictionary of variables
5939: */
5940: for(itimes=1;itimes<=2;itimes++){
5941: jj=0;
5942: for(i=1; i <=nlstate; i++){
5943: for(j=1; j <=nlstate+ndeath; j++){
5944: if(j==i) continue;
5945: for(k=1; k<=ncovmodel;k++){
5946: jj++;
5947: ca[0]= k+'a'-1;ca[1]='\0';
5948: if(itimes==1){
5949: if(mle>=1)
5950: printf("#%1d%1d%d",i,j,k);
5951: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5952: fprintf(ficres,"#%1d%1d%d",i,j,k);
5953: }else{
5954: if(mle>=1)
5955: printf("%1d%1d%d",i,j,k);
5956: fprintf(ficlog,"%1d%1d%d",i,j,k);
5957: fprintf(ficres,"%1d%1d%d",i,j,k);
5958: }
5959: ll=0;
5960: for(li=1;li <=nlstate; li++){
5961: for(lj=1;lj <=nlstate+ndeath; lj++){
5962: if(lj==li) continue;
5963: for(lk=1;lk<=ncovmodel;lk++){
5964: ll++;
5965: if(ll<=jj){
5966: cb[0]= lk +'a'-1;cb[1]='\0';
5967: if(ll<jj){
5968: if(itimes==1){
5969: if(mle>=1)
5970: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5971: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5972: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5973: }else{
5974: if(mle>=1)
5975: printf(" %.5e",matcov[jj][ll]);
5976: fprintf(ficlog," %.5e",matcov[jj][ll]);
5977: fprintf(ficres," %.5e",matcov[jj][ll]);
5978: }
5979: }else{
5980: if(itimes==1){
5981: if(mle>=1)
5982: printf(" Var(%s%1d%1d)",ca,i,j);
5983: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5984: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5985: }else{
5986: if(mle>=1)
5987: printf(" %.5e",matcov[jj][ll]);
5988: fprintf(ficlog," %.5e",matcov[jj][ll]);
5989: fprintf(ficres," %.5e",matcov[jj][ll]);
5990: }
5991: }
5992: }
5993: } /* end lk */
5994: } /* end lj */
5995: } /* end li */
5996: if(mle>=1)
5997: printf("\n");
5998: fprintf(ficlog,"\n");
5999: fprintf(ficres,"\n");
6000: numlinepar++;
6001: } /* end k*/
6002: } /*end j */
6003: } /* end i */
6004: } /* end itimes */
6005:
6006: fflush(ficlog);
6007: fflush(ficres);
6008:
6009: while((c=getc(ficpar))=='#' && c!= EOF){
6010: ungetc(c,ficpar);
6011: fgets(line, MAXLINE, ficpar);
1.141 brouard 6012: fputs(line,stdout);
1.126 brouard 6013: fputs(line,ficparo);
6014: }
6015: ungetc(c,ficpar);
6016:
6017: estepm=0;
6018: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6019: if (estepm==0 || estepm < stepm) estepm=stepm;
6020: if (fage <= 2) {
6021: bage = ageminpar;
6022: fage = agemaxpar;
6023: }
6024:
6025: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6026: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6027: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6028:
6029: while((c=getc(ficpar))=='#' && c!= EOF){
6030: ungetc(c,ficpar);
6031: fgets(line, MAXLINE, ficpar);
1.141 brouard 6032: fputs(line,stdout);
1.126 brouard 6033: fputs(line,ficparo);
6034: }
6035: ungetc(c,ficpar);
6036:
6037: 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);
6038: 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);
6039: 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);
6040: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6041: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6042:
6043: while((c=getc(ficpar))=='#' && c!= EOF){
6044: ungetc(c,ficpar);
6045: fgets(line, MAXLINE, ficpar);
1.141 brouard 6046: fputs(line,stdout);
1.126 brouard 6047: fputs(line,ficparo);
6048: }
6049: ungetc(c,ficpar);
6050:
6051:
6052: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6053: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6054:
6055: fscanf(ficpar,"pop_based=%d\n",&popbased);
6056: fprintf(ficparo,"pop_based=%d\n",popbased);
6057: fprintf(ficres,"pop_based=%d\n",popbased);
6058:
6059: while((c=getc(ficpar))=='#' && c!= EOF){
6060: ungetc(c,ficpar);
6061: fgets(line, MAXLINE, ficpar);
1.141 brouard 6062: fputs(line,stdout);
1.126 brouard 6063: fputs(line,ficparo);
6064: }
6065: ungetc(c,ficpar);
6066:
6067: 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);
6068: 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);
6069: 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);
6070: 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);
6071: 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);
6072: /* day and month of proj2 are not used but only year anproj2.*/
6073:
6074:
6075:
6076: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
6077: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
6078:
6079: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6080: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6081:
6082: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6083: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6084: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6085:
6086: /*------------ free_vector -------------*/
6087: /* chdir(path); */
6088:
6089: free_ivector(wav,1,imx);
6090: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6091: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6092: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6093: free_lvector(num,1,n);
6094: free_vector(agedc,1,n);
6095: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6096: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6097: fclose(ficparo);
6098: fclose(ficres);
6099:
6100:
6101: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6102:
6103: strcpy(filerespl,"pl");
6104: strcat(filerespl,fileres);
6105: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6106: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6107: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
6108: }
6109: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6110: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6111: pstamp(ficrespl);
6112: fprintf(ficrespl,"# Period (stable) prevalence \n");
6113: fprintf(ficrespl,"#Age ");
6114: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6115: fprintf(ficrespl,"\n");
6116:
6117: prlim=matrix(1,nlstate,1,nlstate);
6118:
6119: agebase=ageminpar;
6120: agelim=agemaxpar;
6121: ftolpl=1.e-10;
1.143 brouard 6122: i1=pow(2,cptcoveff);
1.126 brouard 6123: if (cptcovn < 1){i1=1;}
6124:
6125: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.143 brouard 6126: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.126 brouard 6127: k=k+1;
1.131 brouard 6128: /* to clean */
1.143 brouard 6129: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
1.126 brouard 6130: fprintf(ficrespl,"\n#******");
6131: printf("\n#******");
6132: fprintf(ficlog,"\n#******");
6133: for(j=1;j<=cptcoveff;j++) {
6134: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6135: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6136: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6137: }
6138: fprintf(ficrespl,"******\n");
6139: printf("******\n");
6140: fprintf(ficlog,"******\n");
6141:
6142: for (age=agebase; age<=agelim; age++){
6143: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6144: fprintf(ficrespl,"%.0f ",age );
6145: for(j=1;j<=cptcoveff;j++)
6146: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6147: for(i=1; i<=nlstate;i++)
6148: fprintf(ficrespl," %.5f", prlim[i][i]);
6149: fprintf(ficrespl,"\n");
1.143 brouard 6150: } /* Age */
6151: /* was end of cptcod */
6152: } /* cptcov */
1.126 brouard 6153: fclose(ficrespl);
6154:
6155: /*------------- h Pij x at various ages ------------*/
6156:
6157: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6158: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6159: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
6160: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
6161: }
6162: printf("Computing pij: result on file '%s' \n", filerespij);
6163: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6164:
6165: stepsize=(int) (stepm+YEARM-1)/YEARM;
6166: /*if (stepm<=24) stepsize=2;*/
6167:
6168: agelim=AGESUP;
6169: hstepm=stepsize*YEARM; /* Every year of age */
6170: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6171:
6172: /* hstepm=1; aff par mois*/
6173: pstamp(ficrespij);
6174: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6175: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6176: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6177: k=k+1;
6178: fprintf(ficrespij,"\n#****** ");
6179: for(j=1;j<=cptcoveff;j++)
6180: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6181: fprintf(ficrespij,"******\n");
6182:
6183: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6184: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6185: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6186:
6187: /* nhstepm=nhstepm*YEARM; aff par mois*/
6188:
6189: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6190: oldm=oldms;savm=savms;
6191: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6192: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6193: for(i=1; i<=nlstate;i++)
6194: for(j=1; j<=nlstate+ndeath;j++)
6195: fprintf(ficrespij," %1d-%1d",i,j);
6196: fprintf(ficrespij,"\n");
6197: for (h=0; h<=nhstepm; h++){
6198: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
6199: for(i=1; i<=nlstate;i++)
6200: for(j=1; j<=nlstate+ndeath;j++)
6201: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6202: fprintf(ficrespij,"\n");
6203: }
6204: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6205: fprintf(ficrespij,"\n");
6206: }
6207: }
6208: }
6209:
6210: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6211:
6212: fclose(ficrespij);
6213:
6214: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6215: for(i=1;i<=AGESUP;i++)
6216: for(j=1;j<=NCOVMAX;j++)
6217: for(k=1;k<=NCOVMAX;k++)
6218: probs[i][j][k]=0.;
6219:
6220: /*---------- Forecasting ------------------*/
6221: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6222: if(prevfcast==1){
6223: /* if(stepm ==1){*/
6224: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6225: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6226: /* } */
6227: /* else{ */
6228: /* erreur=108; */
6229: /* 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); */
6230: /* 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); */
6231: /* } */
6232: }
6233:
6234:
1.127 brouard 6235: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6236:
6237: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6238: /* 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",\
6239: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6240: */
1.126 brouard 6241:
1.127 brouard 6242: if (mobilav!=0) {
6243: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6244: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6245: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6246: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6247: }
1.126 brouard 6248: }
6249:
6250:
1.127 brouard 6251: /*---------- Health expectancies, no variances ------------*/
6252:
1.126 brouard 6253: strcpy(filerese,"e");
6254: strcat(filerese,fileres);
6255: if((ficreseij=fopen(filerese,"w"))==NULL) {
6256: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6257: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6258: }
6259: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6260: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.127 brouard 6261: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6262: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6263: k=k+1;
6264: fprintf(ficreseij,"\n#****** ");
6265: for(j=1;j<=cptcoveff;j++) {
6266: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6267: }
6268: fprintf(ficreseij,"******\n");
6269:
6270: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6271: oldm=oldms;savm=savms;
6272: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6273:
6274: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6275: }
6276: }
6277: fclose(ficreseij);
6278:
6279:
6280: /*---------- Health expectancies and variances ------------*/
6281:
6282:
6283: strcpy(filerest,"t");
6284: strcat(filerest,fileres);
6285: if((ficrest=fopen(filerest,"w"))==NULL) {
6286: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6287: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6288: }
6289: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6290: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6291:
1.126 brouard 6292:
6293: strcpy(fileresstde,"stde");
6294: strcat(fileresstde,fileres);
6295: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6296: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6297: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6298: }
6299: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6300: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6301:
6302: strcpy(filerescve,"cve");
6303: strcat(filerescve,fileres);
6304: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6305: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6306: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6307: }
6308: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6309: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6310:
6311: strcpy(fileresv,"v");
6312: strcat(fileresv,fileres);
6313: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6314: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6315: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6316: }
6317: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6318: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6319:
6320: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6321: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6322: k=k+1;
6323: fprintf(ficrest,"\n#****** ");
6324: for(j=1;j<=cptcoveff;j++)
6325: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6326: fprintf(ficrest,"******\n");
6327:
6328: fprintf(ficresstdeij,"\n#****** ");
6329: fprintf(ficrescveij,"\n#****** ");
6330: for(j=1;j<=cptcoveff;j++) {
6331: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6332: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6333: }
6334: fprintf(ficresstdeij,"******\n");
6335: fprintf(ficrescveij,"******\n");
6336:
6337: fprintf(ficresvij,"\n#****** ");
6338: for(j=1;j<=cptcoveff;j++)
6339: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6340: fprintf(ficresvij,"******\n");
6341:
6342: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6343: oldm=oldms;savm=savms;
1.127 brouard 6344: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.126 brouard 6345:
6346: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6347: pstamp(ficrest);
1.128 brouard 6348: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6349: oldm=oldms;savm=savms;
6350: 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 ");
6351: if(vpopbased==1)
6352: 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);
6353: else
6354: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6355: fprintf(ficrest,"# Age e.. (std) ");
6356: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6357: fprintf(ficrest,"\n");
1.126 brouard 6358:
1.128 brouard 6359: epj=vector(1,nlstate+1);
6360: for(age=bage; age <=fage ;age++){
6361: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6362: if (vpopbased==1) {
6363: if(mobilav ==0){
6364: for(i=1; i<=nlstate;i++)
6365: prlim[i][i]=probs[(int)age][i][k];
6366: }else{ /* mobilav */
6367: for(i=1; i<=nlstate;i++)
6368: prlim[i][i]=mobaverage[(int)age][i][k];
6369: }
1.126 brouard 6370: }
6371:
1.128 brouard 6372: fprintf(ficrest," %4.0f",age);
6373: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6374: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6375: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6376: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6377: }
6378: epj[nlstate+1] +=epj[j];
1.126 brouard 6379: }
6380:
1.128 brouard 6381: for(i=1, vepp=0.;i <=nlstate;i++)
6382: for(j=1;j <=nlstate;j++)
6383: vepp += vareij[i][j][(int)age];
6384: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6385: for(j=1;j <=nlstate;j++){
6386: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6387: }
6388: fprintf(ficrest,"\n");
1.126 brouard 6389: }
6390: }
6391: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6392: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6393: free_vector(epj,1,nlstate+1);
6394: }
6395: }
6396: free_vector(weight,1,n);
6397: free_imatrix(Tvard,1,15,1,2);
6398: free_imatrix(s,1,maxwav+1,1,n);
6399: free_matrix(anint,1,maxwav,1,n);
6400: free_matrix(mint,1,maxwav,1,n);
6401: free_ivector(cod,1,n);
6402: free_ivector(tab,1,NCOVMAX);
6403: fclose(ficresstdeij);
6404: fclose(ficrescveij);
6405: fclose(ficresvij);
6406: fclose(ficrest);
6407: fclose(ficpar);
6408:
6409: /*------- Variance of period (stable) prevalence------*/
6410:
6411: strcpy(fileresvpl,"vpl");
6412: strcat(fileresvpl,fileres);
6413: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6414: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6415: exit(0);
6416: }
6417: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6418:
6419: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6420: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6421: k=k+1;
6422: fprintf(ficresvpl,"\n#****** ");
6423: for(j=1;j<=cptcoveff;j++)
6424: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6425: fprintf(ficresvpl,"******\n");
6426:
6427: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6428: oldm=oldms;savm=savms;
6429: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6430: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6431: }
6432: }
6433:
6434: fclose(ficresvpl);
6435:
6436: /*---------- End : free ----------------*/
6437: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6438: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6439: } /* mle==-3 arrives here for freeing */
1.131 brouard 6440: endfree:
1.141 brouard 6441: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6442: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6443: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6444: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6445: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6446: free_matrix(covar,0,NCOVMAX,1,n);
6447: free_matrix(matcov,1,npar,1,npar);
6448: /*free_vector(delti,1,npar);*/
6449: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6450: free_matrix(agev,1,maxwav,1,imx);
6451: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6452:
6453: free_ivector(ncodemax,1,8);
6454: free_ivector(Tvar,1,15);
6455: free_ivector(Tprod,1,15);
6456: free_ivector(Tvaraff,1,15);
6457: free_ivector(Tage,1,15);
6458:
6459: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6460: free_imatrix(codtab,1,100,1,10);
6461: fflush(fichtm);
6462: fflush(ficgp);
6463:
6464:
6465: if((nberr >0) || (nbwarn>0)){
6466: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6467: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6468: }else{
6469: printf("End of Imach\n");
6470: fprintf(ficlog,"End of Imach\n");
6471: }
6472: printf("See log file on %s\n",filelog);
6473: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6474: (void) gettimeofday(&end_time,&tzp);
6475: tm = *localtime(&end_time.tv_sec);
6476: tmg = *gmtime(&end_time.tv_sec);
6477: strcpy(strtend,asctime(&tm));
6478: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6479: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6480: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6481:
1.141 brouard 6482: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6483: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.141 brouard 6484: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6485: /* printf("Total time was %d uSec.\n", total_usecs);*/
6486: /* if(fileappend(fichtm,optionfilehtm)){ */
6487: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6488: fclose(fichtm);
6489: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6490: fclose(fichtmcov);
6491: fclose(ficgp);
6492: fclose(ficlog);
6493: /*------ End -----------*/
6494:
6495:
6496: printf("Before Current directory %s!\n",pathcd);
6497: if(chdir(pathcd) != 0)
6498: printf("Can't move to directory %s!\n",path);
6499: if(getcwd(pathcd,MAXLINE) > 0)
6500: printf("Current directory %s!\n",pathcd);
6501: /*strcat(plotcmd,CHARSEPARATOR);*/
6502: sprintf(plotcmd,"gnuplot");
6503: #ifndef UNIX
6504: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6505: #endif
6506: if(!stat(plotcmd,&info)){
6507: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6508: if(!stat(getenv("GNUPLOTBIN"),&info)){
6509: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6510: }else
6511: strcpy(pplotcmd,plotcmd);
6512: #ifdef UNIX
6513: strcpy(plotcmd,GNUPLOTPROGRAM);
6514: if(!stat(plotcmd,&info)){
6515: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6516: }else
6517: strcpy(pplotcmd,plotcmd);
6518: #endif
6519: }else
6520: strcpy(pplotcmd,plotcmd);
6521:
6522: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6523: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6524:
6525: if((outcmd=system(plotcmd)) != 0){
6526: printf("\n Problem with gnuplot\n");
6527: }
6528: printf(" Wait...");
6529: while (z[0] != 'q') {
6530: /* chdir(path); */
6531: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6532: scanf("%s",z);
6533: /* if (z[0] == 'c') system("./imach"); */
6534: if (z[0] == 'e') {
6535: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6536: system(optionfilehtm);
6537: }
6538: else if (z[0] == 'g') system(plotcmd);
6539: else if (z[0] == 'q') exit(0);
6540: }
6541: end:
6542: while (z[0] != 'q') {
6543: printf("\nType q for exiting: ");
6544: scanf("%s",z);
6545: }
6546: }
6547:
6548:
6549:
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