Annotation of imach/src/imach.c, revision 1.145
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
1.145 ! brouard 377: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
! 378: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
! 379: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
! 380: freexexit2 possible for memory heap.
! 381:
! 382: h Pij x | pij_nom ficrestpij
! 383: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
! 384: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
! 385: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
! 386:
! 387: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
! 388: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
! 389: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
! 390: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
! 391: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
! 392:
1.126 brouard 393: forecasting if prevfcast==1 prevforecast call prevalence()
394: health expectancies
395: Variance-covariance of DFLE
396: prevalence()
397: movingaverage()
398: varevsij()
399: if popbased==1 varevsij(,popbased)
400: total life expectancies
401: Variance of period (stable) prevalence
402: end
403: */
404:
405:
406:
407:
408: #include <math.h>
409: #include <stdio.h>
410: #include <stdlib.h>
411: #include <string.h>
412: #include <unistd.h>
413:
414: #include <limits.h>
415: #include <sys/types.h>
416: #include <sys/stat.h>
417: #include <errno.h>
418: extern int errno;
419:
1.141 brouard 420: #ifdef LINUX
1.126 brouard 421: #include <time.h>
422: #include "timeval.h"
1.141 brouard 423: #else
424: #include <sys/time.h>
425: #endif
1.126 brouard 426:
1.136 brouard 427: #ifdef GSL
428: #include <gsl/gsl_errno.h>
429: #include <gsl/gsl_multimin.h>
430: #endif
431:
1.126 brouard 432: /* #include <libintl.h> */
433: /* #define _(String) gettext (String) */
434:
1.141 brouard 435: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 436:
437: #define GNUPLOTPROGRAM "gnuplot"
438: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
439: #define FILENAMELENGTH 132
440:
441: #define GLOCK_ERROR_NOPATH -1 /* empty path */
442: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
443:
1.144 brouard 444: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
445: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 446:
447: #define NINTERVMAX 8
1.144 brouard 448: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
449: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
450: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 ! brouard 451: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 452: #define MAXN 20000
1.144 brouard 453: #define YEARM 12. /**< Number of months per year */
1.126 brouard 454: #define AGESUP 130
455: #define AGEBASE 40
1.144 brouard 456: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
1.126 brouard 457: #ifdef UNIX
458: #define DIRSEPARATOR '/'
459: #define CHARSEPARATOR "/"
460: #define ODIRSEPARATOR '\\'
461: #else
462: #define DIRSEPARATOR '\\'
463: #define CHARSEPARATOR "\\"
464: #define ODIRSEPARATOR '/'
465: #endif
466:
1.144 brouard 467: /* $Id: imach.c,v 1.143 2014/01/26 09:45:38 brouard Exp $ */
1.126 brouard 468: /* $State: Exp $ */
469:
1.143 brouard 470: 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 471: char fullversion[]="$Revision: 1.143 $ $Date: 2014/01/26 09:45:38 $";
1.126 brouard 472: char strstart[80];
473: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 474: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 475: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 ! brouard 476: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
! 477: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
! 478: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
! 479: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
! 480: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
! 481: int cptcovprodnoage=0; /**< Number of covariate products without age */
! 482: int cptcoveff=0; /* Total number of covariates to vary for printing results */
! 483: int cptcov=0; /* Working variable */
1.126 brouard 484: int npar=NPARMAX;
485: int nlstate=2; /* Number of live states */
486: int ndeath=1; /* Number of dead states */
1.130 brouard 487: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 488: int popbased=0;
489:
490: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 491: int maxwav=0; /* Maxim number of waves */
492: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
493: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
494: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 495: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 496: int mle=1, weightopt=0;
1.126 brouard 497: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
498: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
499: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
500: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 501: double jmean=1; /* Mean space between 2 waves */
1.145 ! brouard 502: double **matprod2(); /* test */
1.126 brouard 503: double **oldm, **newm, **savm; /* Working pointers to matrices */
504: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 505: /*FILE *fic ; */ /* Used in readdata only */
506: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 507: FILE *ficlog, *ficrespow;
1.130 brouard 508: int globpr=0; /* Global variable for printing or not */
1.126 brouard 509: double fretone; /* Only one call to likelihood */
1.130 brouard 510: long ipmx=0; /* Number of contributions */
1.126 brouard 511: double sw; /* Sum of weights */
512: char filerespow[FILENAMELENGTH];
513: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
514: FILE *ficresilk;
515: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
516: FILE *ficresprobmorprev;
517: FILE *fichtm, *fichtmcov; /* Html File */
518: FILE *ficreseij;
519: char filerese[FILENAMELENGTH];
520: FILE *ficresstdeij;
521: char fileresstde[FILENAMELENGTH];
522: FILE *ficrescveij;
523: char filerescve[FILENAMELENGTH];
524: FILE *ficresvij;
525: char fileresv[FILENAMELENGTH];
526: FILE *ficresvpl;
527: char fileresvpl[FILENAMELENGTH];
528: char title[MAXLINE];
529: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
530: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
531: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
532: char command[FILENAMELENGTH];
533: int outcmd=0;
534:
535: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
536:
537: char filelog[FILENAMELENGTH]; /* Log file */
538: char filerest[FILENAMELENGTH];
539: char fileregp[FILENAMELENGTH];
540: char popfile[FILENAMELENGTH];
541:
542: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
543:
544: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
545: struct timezone tzp;
546: extern int gettimeofday();
547: struct tm tmg, tm, tmf, *gmtime(), *localtime();
548: long time_value;
549: extern long time();
550: char strcurr[80], strfor[80];
551:
552: char *endptr;
553: long lval;
554: double dval;
555:
556: #define NR_END 1
557: #define FREE_ARG char*
558: #define FTOL 1.0e-10
559:
560: #define NRANSI
561: #define ITMAX 200
562:
563: #define TOL 2.0e-4
564:
565: #define CGOLD 0.3819660
566: #define ZEPS 1.0e-10
567: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
568:
569: #define GOLD 1.618034
570: #define GLIMIT 100.0
571: #define TINY 1.0e-20
572:
573: static double maxarg1,maxarg2;
574: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
575: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
576:
577: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
578: #define rint(a) floor(a+0.5)
579:
580: static double sqrarg;
581: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
582: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
583: int agegomp= AGEGOMP;
584:
585: int imx;
586: int stepm=1;
587: /* Stepm, step in month: minimum step interpolation*/
588:
589: int estepm;
590: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
591:
592: int m,nb;
593: long *num;
594: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
595: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
596: double **pmmij, ***probs;
597: double *ageexmed,*agecens;
598: double dateintmean=0;
599:
600: double *weight;
601: int **s; /* Status */
1.141 brouard 602: double *agedc;
1.145 ! brouard 603: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 604: * covar=matrix(0,NCOVMAX,1,n);
605: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
606: double idx;
607: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 ! brouard 608: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 609: int **codtab; /**< codtab=imatrix(1,100,1,10); */
610: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 611: double *lsurv, *lpop, *tpop;
612:
1.143 brouard 613: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
614: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 615:
616: /**************** split *************************/
617: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
618: {
619: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
620: the name of the file (name), its extension only (ext) and its first part of the name (finame)
621: */
622: char *ss; /* pointer */
623: int l1, l2; /* length counters */
624:
625: l1 = strlen(path ); /* length of path */
626: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
627: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
628: if ( ss == NULL ) { /* no directory, so determine current directory */
629: strcpy( name, path ); /* we got the fullname name because no directory */
630: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
631: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
632: /* get current working directory */
633: /* extern char* getcwd ( char *buf , int len);*/
634: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
635: return( GLOCK_ERROR_GETCWD );
636: }
637: /* got dirc from getcwd*/
638: printf(" DIRC = %s \n",dirc);
639: } else { /* strip direcotry from path */
640: ss++; /* after this, the filename */
641: l2 = strlen( ss ); /* length of filename */
642: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
643: strcpy( name, ss ); /* save file name */
644: strncpy( dirc, path, l1 - l2 ); /* now the directory */
645: dirc[l1-l2] = 0; /* add zero */
646: printf(" DIRC2 = %s \n",dirc);
647: }
648: /* We add a separator at the end of dirc if not exists */
649: l1 = strlen( dirc ); /* length of directory */
650: if( dirc[l1-1] != DIRSEPARATOR ){
651: dirc[l1] = DIRSEPARATOR;
652: dirc[l1+1] = 0;
653: printf(" DIRC3 = %s \n",dirc);
654: }
655: ss = strrchr( name, '.' ); /* find last / */
656: if (ss >0){
657: ss++;
658: strcpy(ext,ss); /* save extension */
659: l1= strlen( name);
660: l2= strlen(ss)+1;
661: strncpy( finame, name, l1-l2);
662: finame[l1-l2]= 0;
663: }
664:
665: return( 0 ); /* we're done */
666: }
667:
668:
669: /******************************************/
670:
671: void replace_back_to_slash(char *s, char*t)
672: {
673: int i;
674: int lg=0;
675: i=0;
676: lg=strlen(t);
677: for(i=0; i<= lg; i++) {
678: (s[i] = t[i]);
679: if (t[i]== '\\') s[i]='/';
680: }
681: }
682:
1.132 brouard 683: char *trimbb(char *out, char *in)
1.137 brouard 684: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 685: char *s;
686: s=out;
687: while (*in != '\0'){
1.137 brouard 688: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 689: in++;
690: }
691: *out++ = *in++;
692: }
693: *out='\0';
694: return s;
695: }
696:
1.145 ! brouard 697: char *cutl(char *blocc, char *alocc, char *in, char occ)
! 698: {
! 699: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
! 700: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
! 701: gives blocc="abcdef2ghi" and alocc="j".
! 702: If occ is not found blocc is null and alocc is equal to in. Returns blocc
! 703: */
! 704: char *s, *t, *bl;
! 705: t=in;s=in;
! 706: while ((*in != occ) && (*in != '\0')){
! 707: *alocc++ = *in++;
! 708: }
! 709: if( *in == occ){
! 710: *(alocc)='\0';
! 711: s=++in;
! 712: }
! 713:
! 714: if (s == t) {/* occ not found */
! 715: *(alocc-(in-s))='\0';
! 716: in=s;
! 717: }
! 718: while ( *in != '\0'){
! 719: *blocc++ = *in++;
! 720: }
! 721:
! 722: *blocc='\0';
! 723: return t;
! 724: }
1.137 brouard 725: char *cutv(char *blocc, char *alocc, char *in, char occ)
726: {
727: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
728: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
729: gives blocc="abcdef2ghi" and alocc="j".
730: If occ is not found blocc is null and alocc is equal to in. Returns alocc
731: */
732: char *s, *t;
733: t=in;s=in;
734: while (*in != '\0'){
735: while( *in == occ){
736: *blocc++ = *in++;
737: s=in;
738: }
739: *blocc++ = *in++;
740: }
741: if (s == t) /* occ not found */
742: *(blocc-(in-s))='\0';
743: else
744: *(blocc-(in-s)-1)='\0';
745: in=s;
746: while ( *in != '\0'){
747: *alocc++ = *in++;
748: }
749:
750: *alocc='\0';
751: return s;
752: }
753:
1.126 brouard 754: int nbocc(char *s, char occ)
755: {
756: int i,j=0;
757: int lg=20;
758: i=0;
759: lg=strlen(s);
760: for(i=0; i<= lg; i++) {
761: if (s[i] == occ ) j++;
762: }
763: return j;
764: }
765:
1.137 brouard 766: /* void cutv(char *u,char *v, char*t, char occ) */
767: /* { */
768: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
769: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
770: /* gives u="abcdef2ghi" and v="j" *\/ */
771: /* int i,lg,j,p=0; */
772: /* i=0; */
773: /* lg=strlen(t); */
774: /* for(j=0; j<=lg-1; j++) { */
775: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
776: /* } */
1.126 brouard 777:
1.137 brouard 778: /* for(j=0; j<p; j++) { */
779: /* (u[j] = t[j]); */
780: /* } */
781: /* u[p]='\0'; */
1.126 brouard 782:
1.137 brouard 783: /* for(j=0; j<= lg; j++) { */
784: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
785: /* } */
786: /* } */
1.126 brouard 787:
788: /********************** nrerror ********************/
789:
790: void nrerror(char error_text[])
791: {
792: fprintf(stderr,"ERREUR ...\n");
793: fprintf(stderr,"%s\n",error_text);
794: exit(EXIT_FAILURE);
795: }
796: /*********************** vector *******************/
797: double *vector(int nl, int nh)
798: {
799: double *v;
800: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
801: if (!v) nrerror("allocation failure in vector");
802: return v-nl+NR_END;
803: }
804:
805: /************************ free vector ******************/
806: void free_vector(double*v, int nl, int nh)
807: {
808: free((FREE_ARG)(v+nl-NR_END));
809: }
810:
811: /************************ivector *******************************/
812: int *ivector(long nl,long nh)
813: {
814: int *v;
815: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
816: if (!v) nrerror("allocation failure in ivector");
817: return v-nl+NR_END;
818: }
819:
820: /******************free ivector **************************/
821: void free_ivector(int *v, long nl, long nh)
822: {
823: free((FREE_ARG)(v+nl-NR_END));
824: }
825:
826: /************************lvector *******************************/
827: long *lvector(long nl,long nh)
828: {
829: long *v;
830: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
831: if (!v) nrerror("allocation failure in ivector");
832: return v-nl+NR_END;
833: }
834:
835: /******************free lvector **************************/
836: void free_lvector(long *v, long nl, long nh)
837: {
838: free((FREE_ARG)(v+nl-NR_END));
839: }
840:
841: /******************* imatrix *******************************/
842: int **imatrix(long nrl, long nrh, long ncl, long nch)
843: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
844: {
845: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
846: int **m;
847:
848: /* allocate pointers to rows */
849: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
850: if (!m) nrerror("allocation failure 1 in matrix()");
851: m += NR_END;
852: m -= nrl;
853:
854:
855: /* allocate rows and set pointers to them */
856: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
857: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
858: m[nrl] += NR_END;
859: m[nrl] -= ncl;
860:
861: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
862:
863: /* return pointer to array of pointers to rows */
864: return m;
865: }
866:
867: /****************** free_imatrix *************************/
868: void free_imatrix(m,nrl,nrh,ncl,nch)
869: int **m;
870: long nch,ncl,nrh,nrl;
871: /* free an int matrix allocated by imatrix() */
872: {
873: free((FREE_ARG) (m[nrl]+ncl-NR_END));
874: free((FREE_ARG) (m+nrl-NR_END));
875: }
876:
877: /******************* matrix *******************************/
878: double **matrix(long nrl, long nrh, long ncl, long nch)
879: {
880: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
881: double **m;
882:
883: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
884: if (!m) nrerror("allocation failure 1 in matrix()");
885: m += NR_END;
886: m -= nrl;
887:
888: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
889: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
890: m[nrl] += NR_END;
891: m[nrl] -= ncl;
892:
893: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
894: return m;
1.145 ! brouard 895: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
! 896: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
! 897: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 898: */
899: }
900:
901: /*************************free matrix ************************/
902: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
903: {
904: free((FREE_ARG)(m[nrl]+ncl-NR_END));
905: free((FREE_ARG)(m+nrl-NR_END));
906: }
907:
908: /******************* ma3x *******************************/
909: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
910: {
911: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
912: double ***m;
913:
914: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
915: if (!m) nrerror("allocation failure 1 in matrix()");
916: m += NR_END;
917: m -= nrl;
918:
919: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
920: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
921: m[nrl] += NR_END;
922: m[nrl] -= ncl;
923:
924: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
925:
926: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
927: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
928: m[nrl][ncl] += NR_END;
929: m[nrl][ncl] -= nll;
930: for (j=ncl+1; j<=nch; j++)
931: m[nrl][j]=m[nrl][j-1]+nlay;
932:
933: for (i=nrl+1; i<=nrh; i++) {
934: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
935: for (j=ncl+1; j<=nch; j++)
936: m[i][j]=m[i][j-1]+nlay;
937: }
938: return m;
939: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
940: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
941: */
942: }
943:
944: /*************************free ma3x ************************/
945: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
946: {
947: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
948: free((FREE_ARG)(m[nrl]+ncl-NR_END));
949: free((FREE_ARG)(m+nrl-NR_END));
950: }
951:
952: /*************** function subdirf ***********/
953: char *subdirf(char fileres[])
954: {
955: /* Caution optionfilefiname is hidden */
956: strcpy(tmpout,optionfilefiname);
957: strcat(tmpout,"/"); /* Add to the right */
958: strcat(tmpout,fileres);
959: return tmpout;
960: }
961:
962: /*************** function subdirf2 ***********/
963: char *subdirf2(char fileres[], char *preop)
964: {
965:
966: /* Caution optionfilefiname is hidden */
967: strcpy(tmpout,optionfilefiname);
968: strcat(tmpout,"/");
969: strcat(tmpout,preop);
970: strcat(tmpout,fileres);
971: return tmpout;
972: }
973:
974: /*************** function subdirf3 ***********/
975: char *subdirf3(char fileres[], char *preop, char *preop2)
976: {
977:
978: /* Caution optionfilefiname is hidden */
979: strcpy(tmpout,optionfilefiname);
980: strcat(tmpout,"/");
981: strcat(tmpout,preop);
982: strcat(tmpout,preop2);
983: strcat(tmpout,fileres);
984: return tmpout;
985: }
986:
987: /***************** f1dim *************************/
988: extern int ncom;
989: extern double *pcom,*xicom;
990: extern double (*nrfunc)(double []);
991:
992: double f1dim(double x)
993: {
994: int j;
995: double f;
996: double *xt;
997:
998: xt=vector(1,ncom);
999: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1000: f=(*nrfunc)(xt);
1001: free_vector(xt,1,ncom);
1002: return f;
1003: }
1004:
1005: /*****************brent *************************/
1006: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1007: {
1008: int iter;
1009: double a,b,d,etemp;
1010: double fu,fv,fw,fx;
1011: double ftemp;
1012: double p,q,r,tol1,tol2,u,v,w,x,xm;
1013: double e=0.0;
1014:
1015: a=(ax < cx ? ax : cx);
1016: b=(ax > cx ? ax : cx);
1017: x=w=v=bx;
1018: fw=fv=fx=(*f)(x);
1019: for (iter=1;iter<=ITMAX;iter++) {
1020: xm=0.5*(a+b);
1021: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1022: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1023: printf(".");fflush(stdout);
1024: fprintf(ficlog,".");fflush(ficlog);
1025: #ifdef DEBUG
1026: 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);
1027: 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);
1028: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1029: #endif
1030: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1031: *xmin=x;
1032: return fx;
1033: }
1034: ftemp=fu;
1035: if (fabs(e) > tol1) {
1036: r=(x-w)*(fx-fv);
1037: q=(x-v)*(fx-fw);
1038: p=(x-v)*q-(x-w)*r;
1039: q=2.0*(q-r);
1040: if (q > 0.0) p = -p;
1041: q=fabs(q);
1042: etemp=e;
1043: e=d;
1044: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1045: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1046: else {
1047: d=p/q;
1048: u=x+d;
1049: if (u-a < tol2 || b-u < tol2)
1050: d=SIGN(tol1,xm-x);
1051: }
1052: } else {
1053: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1054: }
1055: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1056: fu=(*f)(u);
1057: if (fu <= fx) {
1058: if (u >= x) a=x; else b=x;
1059: SHFT(v,w,x,u)
1060: SHFT(fv,fw,fx,fu)
1061: } else {
1062: if (u < x) a=u; else b=u;
1063: if (fu <= fw || w == x) {
1064: v=w;
1065: w=u;
1066: fv=fw;
1067: fw=fu;
1068: } else if (fu <= fv || v == x || v == w) {
1069: v=u;
1070: fv=fu;
1071: }
1072: }
1073: }
1074: nrerror("Too many iterations in brent");
1075: *xmin=x;
1076: return fx;
1077: }
1078:
1079: /****************** mnbrak ***********************/
1080:
1081: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1082: double (*func)(double))
1083: {
1084: double ulim,u,r,q, dum;
1085: double fu;
1086:
1087: *fa=(*func)(*ax);
1088: *fb=(*func)(*bx);
1089: if (*fb > *fa) {
1090: SHFT(dum,*ax,*bx,dum)
1091: SHFT(dum,*fb,*fa,dum)
1092: }
1093: *cx=(*bx)+GOLD*(*bx-*ax);
1094: *fc=(*func)(*cx);
1095: while (*fb > *fc) {
1096: r=(*bx-*ax)*(*fb-*fc);
1097: q=(*bx-*cx)*(*fb-*fa);
1098: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1099: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1100: ulim=(*bx)+GLIMIT*(*cx-*bx);
1101: if ((*bx-u)*(u-*cx) > 0.0) {
1102: fu=(*func)(u);
1103: } else if ((*cx-u)*(u-ulim) > 0.0) {
1104: fu=(*func)(u);
1105: if (fu < *fc) {
1106: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1107: SHFT(*fb,*fc,fu,(*func)(u))
1108: }
1109: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1110: u=ulim;
1111: fu=(*func)(u);
1112: } else {
1113: u=(*cx)+GOLD*(*cx-*bx);
1114: fu=(*func)(u);
1115: }
1116: SHFT(*ax,*bx,*cx,u)
1117: SHFT(*fa,*fb,*fc,fu)
1118: }
1119: }
1120:
1121: /*************** linmin ************************/
1122:
1123: int ncom;
1124: double *pcom,*xicom;
1125: double (*nrfunc)(double []);
1126:
1127: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1128: {
1129: double brent(double ax, double bx, double cx,
1130: double (*f)(double), double tol, double *xmin);
1131: double f1dim(double x);
1132: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1133: double *fc, double (*func)(double));
1134: int j;
1135: double xx,xmin,bx,ax;
1136: double fx,fb,fa;
1137:
1138: ncom=n;
1139: pcom=vector(1,n);
1140: xicom=vector(1,n);
1141: nrfunc=func;
1142: for (j=1;j<=n;j++) {
1143: pcom[j]=p[j];
1144: xicom[j]=xi[j];
1145: }
1146: ax=0.0;
1147: xx=1.0;
1148: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1149: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1150: #ifdef DEBUG
1151: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1152: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1153: #endif
1154: for (j=1;j<=n;j++) {
1155: xi[j] *= xmin;
1156: p[j] += xi[j];
1157: }
1158: free_vector(xicom,1,n);
1159: free_vector(pcom,1,n);
1160: }
1161:
1162: char *asc_diff_time(long time_sec, char ascdiff[])
1163: {
1164: long sec_left, days, hours, minutes;
1165: days = (time_sec) / (60*60*24);
1166: sec_left = (time_sec) % (60*60*24);
1167: hours = (sec_left) / (60*60) ;
1168: sec_left = (sec_left) %(60*60);
1169: minutes = (sec_left) /60;
1170: sec_left = (sec_left) % (60);
1.141 brouard 1171: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1.126 brouard 1172: return ascdiff;
1173: }
1174:
1175: /*************** powell ************************/
1176: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1177: double (*func)(double []))
1178: {
1179: void linmin(double p[], double xi[], int n, double *fret,
1180: double (*func)(double []));
1181: int i,ibig,j;
1182: double del,t,*pt,*ptt,*xit;
1183: double fp,fptt;
1184: double *xits;
1185: int niterf, itmp;
1186:
1187: pt=vector(1,n);
1188: ptt=vector(1,n);
1189: xit=vector(1,n);
1190: xits=vector(1,n);
1191: *fret=(*func)(p);
1192: for (j=1;j<=n;j++) pt[j]=p[j];
1193: for (*iter=1;;++(*iter)) {
1194: fp=(*fret);
1195: ibig=0;
1196: del=0.0;
1197: last_time=curr_time;
1198: (void) gettimeofday(&curr_time,&tzp);
1199: 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);
1200: 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);
1201: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1202: for (i=1;i<=n;i++) {
1203: printf(" %d %.12f",i, p[i]);
1204: fprintf(ficlog," %d %.12lf",i, p[i]);
1205: fprintf(ficrespow," %.12lf", p[i]);
1206: }
1207: printf("\n");
1208: fprintf(ficlog,"\n");
1209: fprintf(ficrespow,"\n");fflush(ficrespow);
1210: if(*iter <=3){
1211: tm = *localtime(&curr_time.tv_sec);
1212: strcpy(strcurr,asctime(&tm));
1213: /* asctime_r(&tm,strcurr); */
1214: forecast_time=curr_time;
1215: itmp = strlen(strcurr);
1216: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1217: strcurr[itmp-1]='\0';
1218: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1219: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1220: for(niterf=10;niterf<=30;niterf+=10){
1221: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1222: tmf = *localtime(&forecast_time.tv_sec);
1223: /* asctime_r(&tmf,strfor); */
1224: strcpy(strfor,asctime(&tmf));
1225: itmp = strlen(strfor);
1226: if(strfor[itmp-1]=='\n')
1227: strfor[itmp-1]='\0';
1228: 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);
1229: 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);
1230: }
1231: }
1232: for (i=1;i<=n;i++) {
1233: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1234: fptt=(*fret);
1235: #ifdef DEBUG
1236: printf("fret=%lf \n",*fret);
1237: fprintf(ficlog,"fret=%lf \n",*fret);
1238: #endif
1239: printf("%d",i);fflush(stdout);
1240: fprintf(ficlog,"%d",i);fflush(ficlog);
1241: linmin(p,xit,n,fret,func);
1242: if (fabs(fptt-(*fret)) > del) {
1243: del=fabs(fptt-(*fret));
1244: ibig=i;
1245: }
1246: #ifdef DEBUG
1247: printf("%d %.12e",i,(*fret));
1248: fprintf(ficlog,"%d %.12e",i,(*fret));
1249: for (j=1;j<=n;j++) {
1250: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1251: printf(" x(%d)=%.12e",j,xit[j]);
1252: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1253: }
1254: for(j=1;j<=n;j++) {
1255: printf(" p=%.12e",p[j]);
1256: fprintf(ficlog," p=%.12e",p[j]);
1257: }
1258: printf("\n");
1259: fprintf(ficlog,"\n");
1260: #endif
1261: }
1262: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1263: #ifdef DEBUG
1264: int k[2],l;
1265: k[0]=1;
1266: k[1]=-1;
1267: printf("Max: %.12e",(*func)(p));
1268: fprintf(ficlog,"Max: %.12e",(*func)(p));
1269: for (j=1;j<=n;j++) {
1270: printf(" %.12e",p[j]);
1271: fprintf(ficlog," %.12e",p[j]);
1272: }
1273: printf("\n");
1274: fprintf(ficlog,"\n");
1275: for(l=0;l<=1;l++) {
1276: for (j=1;j<=n;j++) {
1277: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1278: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1279: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1280: }
1281: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1282: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1283: }
1284: #endif
1285:
1286:
1287: free_vector(xit,1,n);
1288: free_vector(xits,1,n);
1289: free_vector(ptt,1,n);
1290: free_vector(pt,1,n);
1291: return;
1292: }
1293: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1294: for (j=1;j<=n;j++) {
1295: ptt[j]=2.0*p[j]-pt[j];
1296: xit[j]=p[j]-pt[j];
1297: pt[j]=p[j];
1298: }
1299: fptt=(*func)(ptt);
1300: if (fptt < fp) {
1301: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1302: if (t < 0.0) {
1303: linmin(p,xit,n,fret,func);
1304: for (j=1;j<=n;j++) {
1305: xi[j][ibig]=xi[j][n];
1306: xi[j][n]=xit[j];
1307: }
1308: #ifdef DEBUG
1309: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1310: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1311: for(j=1;j<=n;j++){
1312: printf(" %.12e",xit[j]);
1313: fprintf(ficlog," %.12e",xit[j]);
1314: }
1315: printf("\n");
1316: fprintf(ficlog,"\n");
1317: #endif
1318: }
1319: }
1320: }
1321: }
1322:
1323: /**** Prevalence limit (stable or period prevalence) ****************/
1324:
1325: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1326: {
1327: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1328: matrix by transitions matrix until convergence is reached */
1329:
1330: int i, ii,j,k;
1331: double min, max, maxmin, maxmax,sumnew=0.;
1.145 ! brouard 1332: /* double **matprod2(); */ /* test */
1.131 brouard 1333: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1334: double **newm;
1335: double agefin, delaymax=50 ; /* Max number of years to converge */
1336:
1337: for (ii=1;ii<=nlstate+ndeath;ii++)
1338: for (j=1;j<=nlstate+ndeath;j++){
1339: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1340: }
1341:
1342: cov[1]=1.;
1343:
1344: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1345: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1346: newm=savm;
1347: /* Covariates have to be included here again */
1.138 brouard 1348: cov[2]=agefin;
1349:
1350: for (k=1; k<=cptcovn;k++) {
1351: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 ! brouard 1352: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1353: }
1.145 ! brouard 1354: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 1355: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
! 1356: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138 brouard 1357:
1358: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1359: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1360: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 ! brouard 1361: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
! 1362: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1363: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1364:
1.126 brouard 1365: savm=oldm;
1366: oldm=newm;
1367: maxmax=0.;
1368: for(j=1;j<=nlstate;j++){
1369: min=1.;
1370: max=0.;
1371: for(i=1; i<=nlstate; i++) {
1372: sumnew=0;
1373: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1374: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 ! brouard 1375: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1376: max=FMAX(max,prlim[i][j]);
1377: min=FMIN(min,prlim[i][j]);
1378: }
1379: maxmin=max-min;
1380: maxmax=FMAX(maxmax,maxmin);
1381: }
1382: if(maxmax < ftolpl){
1383: return prlim;
1384: }
1385: }
1386: }
1387:
1388: /*************** transition probabilities ***************/
1389:
1390: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1391: {
1.138 brouard 1392: /* According to parameters values stored in x and the covariate's values stored in cov,
1393: computes the probability to be observed in state j being in state i by appying the
1394: model to the ncovmodel covariates (including constant and age).
1395: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1396: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1397: ncth covariate in the global vector x is given by the formula:
1398: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1399: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1400: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1401: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1402: Outputs ps[i][j] the probability to be observed in j being in j according to
1403: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1404: */
1405: double s1, lnpijopii;
1.126 brouard 1406: /*double t34;*/
1407: int i,j,j1, nc, ii, jj;
1408:
1409: for(i=1; i<= nlstate; i++){
1410: for(j=1; j<i;j++){
1.138 brouard 1411: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1412: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1413: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1414: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1415: }
1.138 brouard 1416: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1417: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1418: }
1419: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1420: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1421: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1422: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1423: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1424: }
1.138 brouard 1425: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1426: }
1427: }
1428:
1429: for(i=1; i<= nlstate; i++){
1430: s1=0;
1.131 brouard 1431: for(j=1; j<i; j++){
1.138 brouard 1432: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1433: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1434: }
1435: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1436: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1437: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1438: }
1.138 brouard 1439: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1440: ps[i][i]=1./(s1+1.);
1.138 brouard 1441: /* Computing other pijs */
1.126 brouard 1442: for(j=1; j<i; j++)
1443: ps[i][j]= exp(ps[i][j])*ps[i][i];
1444: for(j=i+1; j<=nlstate+ndeath; j++)
1445: ps[i][j]= exp(ps[i][j])*ps[i][i];
1446: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1447: } /* end i */
1448:
1449: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1450: for(jj=1; jj<= nlstate+ndeath; jj++){
1451: ps[ii][jj]=0;
1452: ps[ii][ii]=1;
1453: }
1454: }
1455:
1.145 ! brouard 1456:
! 1457: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
! 1458: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
! 1459: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
! 1460: /* } */
! 1461: /* printf("\n "); */
! 1462: /* } */
! 1463: /* printf("\n ");printf("%lf ",cov[2]);*/
! 1464: /*
1.126 brouard 1465: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1466: goto end;*/
1467: return ps;
1468: }
1469:
1470: /**************** Product of 2 matrices ******************/
1471:
1.145 ! brouard 1472: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1473: {
1474: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1475: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1476: /* in, b, out are matrice of pointers which should have been initialized
1477: before: only the contents of out is modified. The function returns
1478: a pointer to pointers identical to out */
1.145 ! brouard 1479: int i, j, k;
1.126 brouard 1480: for(i=nrl; i<= nrh; i++)
1.145 ! brouard 1481: for(k=ncolol; k<=ncoloh; k++){
! 1482: out[i][k]=0.;
! 1483: for(j=ncl; j<=nch; j++)
! 1484: out[i][k] +=in[i][j]*b[j][k];
! 1485: }
1.126 brouard 1486: return out;
1487: }
1488:
1489:
1490: /************* Higher Matrix Product ***************/
1491:
1492: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1493: {
1494: /* Computes the transition matrix starting at age 'age' over
1495: 'nhstepm*hstepm*stepm' months (i.e. until
1496: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1497: nhstepm*hstepm matrices.
1498: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1499: (typically every 2 years instead of every month which is too big
1500: for the memory).
1501: Model is determined by parameters x and covariates have to be
1502: included manually here.
1503:
1504: */
1505:
1506: int i, j, d, h, k;
1.131 brouard 1507: double **out, cov[NCOVMAX+1];
1.126 brouard 1508: double **newm;
1509:
1510: /* Hstepm could be zero and should return the unit matrix */
1511: for (i=1;i<=nlstate+ndeath;i++)
1512: for (j=1;j<=nlstate+ndeath;j++){
1513: oldm[i][j]=(i==j ? 1.0 : 0.0);
1514: po[i][j][0]=(i==j ? 1.0 : 0.0);
1515: }
1516: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1517: for(h=1; h <=nhstepm; h++){
1518: for(d=1; d <=hstepm; d++){
1519: newm=savm;
1520: /* Covariates have to be included here again */
1521: cov[1]=1.;
1522: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1523: for (k=1; k<=cptcovn;k++)
1524: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1525: for (k=1; k<=cptcovage;k++)
1526: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 ! brouard 1527: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1528: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1529:
1530:
1531: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1532: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1533: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1534: pmij(pmmij,cov,ncovmodel,x,nlstate));
1535: savm=oldm;
1536: oldm=newm;
1537: }
1538: for(i=1; i<=nlstate+ndeath; i++)
1539: for(j=1;j<=nlstate+ndeath;j++) {
1540: po[i][j][h]=newm[i][j];
1.128 brouard 1541: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1542: }
1.128 brouard 1543: /*printf("h=%d ",h);*/
1.126 brouard 1544: } /* end h */
1.128 brouard 1545: /* printf("\n H=%d \n",h); */
1.126 brouard 1546: return po;
1547: }
1548:
1549:
1550: /*************** log-likelihood *************/
1551: double func( double *x)
1552: {
1553: int i, ii, j, k, mi, d, kk;
1.131 brouard 1554: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1555: double **out;
1556: double sw; /* Sum of weights */
1557: double lli; /* Individual log likelihood */
1558: int s1, s2;
1559: double bbh, survp;
1560: long ipmx;
1561: /*extern weight */
1562: /* We are differentiating ll according to initial status */
1563: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1564: /*for(i=1;i<imx;i++)
1565: printf(" %d\n",s[4][i]);
1566: */
1567: cov[1]=1.;
1568:
1569: for(k=1; k<=nlstate; k++) ll[k]=0.;
1570:
1571: if(mle==1){
1572: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1573: /* Computes the values of the ncovmodel covariates of the model
1574: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1575: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1576: to be observed in j being in i according to the model.
1577: */
1.145 ! brouard 1578: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
! 1579: cov[2+k]=covar[Tvar[k]][i];
! 1580: }
1.137 brouard 1581: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1582: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1583: has been calculated etc */
1.126 brouard 1584: for(mi=1; mi<= wav[i]-1; mi++){
1585: for (ii=1;ii<=nlstate+ndeath;ii++)
1586: for (j=1;j<=nlstate+ndeath;j++){
1587: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1588: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1589: }
1590: for(d=0; d<dh[mi][i]; d++){
1591: newm=savm;
1592: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1593: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1594: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1595: }
1596: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1597: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1598: savm=oldm;
1599: oldm=newm;
1600: } /* end mult */
1601:
1602: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1603: /* But now since version 0.9 we anticipate for bias at large stepm.
1604: * If stepm is larger than one month (smallest stepm) and if the exact delay
1605: * (in months) between two waves is not a multiple of stepm, we rounded to
1606: * the nearest (and in case of equal distance, to the lowest) interval but now
1607: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1608: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1609: * probability in order to take into account the bias as a fraction of the way
1610: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1611: * -stepm/2 to stepm/2 .
1612: * For stepm=1 the results are the same as for previous versions of Imach.
1613: * For stepm > 1 the results are less biased than in previous versions.
1614: */
1615: s1=s[mw[mi][i]][i];
1616: s2=s[mw[mi+1][i]][i];
1617: bbh=(double)bh[mi][i]/(double)stepm;
1618: /* bias bh is positive if real duration
1619: * is higher than the multiple of stepm and negative otherwise.
1620: */
1621: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1622: if( s2 > nlstate){
1623: /* i.e. if s2 is a death state and if the date of death is known
1624: then the contribution to the likelihood is the probability to
1625: die between last step unit time and current step unit time,
1626: which is also equal to probability to die before dh
1627: minus probability to die before dh-stepm .
1628: In version up to 0.92 likelihood was computed
1629: as if date of death was unknown. Death was treated as any other
1630: health state: the date of the interview describes the actual state
1631: and not the date of a change in health state. The former idea was
1632: to consider that at each interview the state was recorded
1633: (healthy, disable or death) and IMaCh was corrected; but when we
1634: introduced the exact date of death then we should have modified
1635: the contribution of an exact death to the likelihood. This new
1636: contribution is smaller and very dependent of the step unit
1637: stepm. It is no more the probability to die between last interview
1638: and month of death but the probability to survive from last
1639: interview up to one month before death multiplied by the
1640: probability to die within a month. Thanks to Chris
1641: Jackson for correcting this bug. Former versions increased
1642: mortality artificially. The bad side is that we add another loop
1643: which slows down the processing. The difference can be up to 10%
1644: lower mortality.
1645: */
1646: lli=log(out[s1][s2] - savm[s1][s2]);
1647:
1648:
1649: } else if (s2==-2) {
1650: for (j=1,survp=0. ; j<=nlstate; j++)
1651: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1652: /*survp += out[s1][j]; */
1653: lli= log(survp);
1654: }
1655:
1656: else if (s2==-4) {
1657: for (j=3,survp=0. ; j<=nlstate; j++)
1658: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1659: lli= log(survp);
1660: }
1661:
1662: else if (s2==-5) {
1663: for (j=1,survp=0. ; j<=2; j++)
1664: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1665: lli= log(survp);
1666: }
1667:
1668: else{
1669: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1670: /* 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 */
1671: }
1672: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1673: /*if(lli ==000.0)*/
1674: /*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); */
1675: ipmx +=1;
1676: sw += weight[i];
1677: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1678: } /* end of wave */
1679: } /* end of individual */
1680: } else if(mle==2){
1681: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1682: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1683: for(mi=1; mi<= wav[i]-1; mi++){
1684: for (ii=1;ii<=nlstate+ndeath;ii++)
1685: for (j=1;j<=nlstate+ndeath;j++){
1686: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1687: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1688: }
1689: for(d=0; d<=dh[mi][i]; d++){
1690: newm=savm;
1691: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1692: for (kk=1; kk<=cptcovage;kk++) {
1693: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1694: }
1695: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1696: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1697: savm=oldm;
1698: oldm=newm;
1699: } /* end mult */
1700:
1701: s1=s[mw[mi][i]][i];
1702: s2=s[mw[mi+1][i]][i];
1703: bbh=(double)bh[mi][i]/(double)stepm;
1704: 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 */
1705: ipmx +=1;
1706: sw += weight[i];
1707: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1708: } /* end of wave */
1709: } /* end of individual */
1710: } else if(mle==3){ /* exponential inter-extrapolation */
1711: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1712: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1713: for(mi=1; mi<= wav[i]-1; mi++){
1714: for (ii=1;ii<=nlstate+ndeath;ii++)
1715: for (j=1;j<=nlstate+ndeath;j++){
1716: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1717: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1718: }
1719: for(d=0; d<dh[mi][i]; d++){
1720: newm=savm;
1721: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1722: for (kk=1; kk<=cptcovage;kk++) {
1723: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1724: }
1725: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1726: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1727: savm=oldm;
1728: oldm=newm;
1729: } /* end mult */
1730:
1731: s1=s[mw[mi][i]][i];
1732: s2=s[mw[mi+1][i]][i];
1733: bbh=(double)bh[mi][i]/(double)stepm;
1734: 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 */
1735: ipmx +=1;
1736: sw += weight[i];
1737: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1738: } /* end of wave */
1739: } /* end of individual */
1740: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1741: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1742: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1743: for(mi=1; mi<= wav[i]-1; mi++){
1744: for (ii=1;ii<=nlstate+ndeath;ii++)
1745: for (j=1;j<=nlstate+ndeath;j++){
1746: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1747: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1748: }
1749: for(d=0; d<dh[mi][i]; d++){
1750: newm=savm;
1751: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1752: for (kk=1; kk<=cptcovage;kk++) {
1753: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1754: }
1755:
1756: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1757: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1758: savm=oldm;
1759: oldm=newm;
1760: } /* end mult */
1761:
1762: s1=s[mw[mi][i]][i];
1763: s2=s[mw[mi+1][i]][i];
1764: if( s2 > nlstate){
1765: lli=log(out[s1][s2] - savm[s1][s2]);
1766: }else{
1767: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1768: }
1769: ipmx +=1;
1770: sw += weight[i];
1771: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1772: /* 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]); */
1773: } /* end of wave */
1774: } /* end of individual */
1775: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
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:
1791: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1792: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1793: savm=oldm;
1794: oldm=newm;
1795: } /* end mult */
1796:
1797: s1=s[mw[mi][i]][i];
1798: s2=s[mw[mi+1][i]][i];
1799: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1800: ipmx +=1;
1801: sw += weight[i];
1802: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1803: /*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]);*/
1804: } /* end of wave */
1805: } /* end of individual */
1806: } /* End of if */
1807: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1808: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1809: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1810: return -l;
1811: }
1812:
1813: /*************** log-likelihood *************/
1814: double funcone( double *x)
1815: {
1816: /* Same as likeli but slower because of a lot of printf and if */
1817: int i, ii, j, k, mi, d, kk;
1.131 brouard 1818: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1819: double **out;
1820: double lli; /* Individual log likelihood */
1821: double llt;
1822: int s1, s2;
1823: double bbh, survp;
1824: /*extern weight */
1825: /* We are differentiating ll according to initial status */
1826: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1827: /*for(i=1;i<imx;i++)
1828: printf(" %d\n",s[4][i]);
1829: */
1830: cov[1]=1.;
1831:
1832: for(k=1; k<=nlstate; k++) ll[k]=0.;
1833:
1834: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1835: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1836: for(mi=1; mi<= wav[i]-1; mi++){
1837: for (ii=1;ii<=nlstate+ndeath;ii++)
1838: for (j=1;j<=nlstate+ndeath;j++){
1839: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1840: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1841: }
1842: for(d=0; d<dh[mi][i]; d++){
1843: newm=savm;
1844: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1845: for (kk=1; kk<=cptcovage;kk++) {
1846: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1847: }
1.145 ! brouard 1848: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 1849: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1850: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 ! brouard 1851: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
! 1852: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 1853: savm=oldm;
1854: oldm=newm;
1855: } /* end mult */
1856:
1857: s1=s[mw[mi][i]][i];
1858: s2=s[mw[mi+1][i]][i];
1859: bbh=(double)bh[mi][i]/(double)stepm;
1860: /* bias is positive if real duration
1861: * is higher than the multiple of stepm and negative otherwise.
1862: */
1863: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1864: lli=log(out[s1][s2] - savm[s1][s2]);
1865: } else if (s2==-2) {
1866: for (j=1,survp=0. ; j<=nlstate; j++)
1867: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1868: lli= log(survp);
1869: }else if (mle==1){
1870: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1871: } else if(mle==2){
1872: 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 */
1873: } else if(mle==3){ /* exponential inter-extrapolation */
1874: 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 */
1875: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1876: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 1877: } else{ /* mle=0 back to 1 */
1878: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1879: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 1880: } /* End of if */
1881: ipmx +=1;
1882: sw += weight[i];
1883: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 1884: /*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 1885: if(globpr){
1.141 brouard 1886: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 1887: %11.6f %11.6f %11.6f ", \
1888: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1889: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1890: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1891: llt +=ll[k]*gipmx/gsw;
1892: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1893: }
1894: fprintf(ficresilk," %10.6f\n", -llt);
1895: }
1896: } /* end of wave */
1897: } /* end of individual */
1898: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1899: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1900: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1901: if(globpr==0){ /* First time we count the contributions and weights */
1902: gipmx=ipmx;
1903: gsw=sw;
1904: }
1905: return -l;
1906: }
1907:
1908:
1909: /*************** function likelione ***********/
1910: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1911: {
1912: /* This routine should help understanding what is done with
1913: the selection of individuals/waves and
1914: to check the exact contribution to the likelihood.
1915: Plotting could be done.
1916: */
1917: int k;
1918:
1919: if(*globpri !=0){ /* Just counts and sums, no printings */
1920: strcpy(fileresilk,"ilk");
1921: strcat(fileresilk,fileres);
1922: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1923: printf("Problem with resultfile: %s\n", fileresilk);
1924: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1925: }
1926: 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");
1927: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1928: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1929: for(k=1; k<=nlstate; k++)
1930: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1931: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1932: }
1933:
1934: *fretone=(*funcone)(p);
1935: if(*globpri !=0){
1936: fclose(ficresilk);
1937: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1938: fflush(fichtm);
1939: }
1940: return;
1941: }
1942:
1943:
1944: /*********** Maximum Likelihood Estimation ***************/
1945:
1946: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1947: {
1948: int i,j, iter;
1949: double **xi;
1950: double fret;
1951: double fretone; /* Only one call to likelihood */
1952: /* char filerespow[FILENAMELENGTH];*/
1953: xi=matrix(1,npar,1,npar);
1954: for (i=1;i<=npar;i++)
1955: for (j=1;j<=npar;j++)
1956: xi[i][j]=(i==j ? 1.0 : 0.0);
1957: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1958: strcpy(filerespow,"pow");
1959: strcat(filerespow,fileres);
1960: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1961: printf("Problem with resultfile: %s\n", filerespow);
1962: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1963: }
1964: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1965: for (i=1;i<=nlstate;i++)
1966: for(j=1;j<=nlstate+ndeath;j++)
1967: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1968: fprintf(ficrespow,"\n");
1969:
1970: powell(p,xi,npar,ftol,&iter,&fret,func);
1971:
1972: free_matrix(xi,1,npar,1,npar);
1973: fclose(ficrespow);
1974: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1975: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1976: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1977:
1978: }
1979:
1980: /**** Computes Hessian and covariance matrix ***/
1981: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1982: {
1983: double **a,**y,*x,pd;
1984: double **hess;
1985: int i, j,jk;
1986: int *indx;
1987:
1988: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1989: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1990: void lubksb(double **a, int npar, int *indx, double b[]) ;
1991: void ludcmp(double **a, int npar, int *indx, double *d) ;
1992: double gompertz(double p[]);
1993: hess=matrix(1,npar,1,npar);
1994:
1995: printf("\nCalculation of the hessian matrix. Wait...\n");
1996: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1997: for (i=1;i<=npar;i++){
1998: printf("%d",i);fflush(stdout);
1999: fprintf(ficlog,"%d",i);fflush(ficlog);
2000:
2001: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2002:
2003: /* printf(" %f ",p[i]);
2004: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2005: }
2006:
2007: for (i=1;i<=npar;i++) {
2008: for (j=1;j<=npar;j++) {
2009: if (j>i) {
2010: printf(".%d%d",i,j);fflush(stdout);
2011: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2012: hess[i][j]=hessij(p,delti,i,j,func,npar);
2013:
2014: hess[j][i]=hess[i][j];
2015: /*printf(" %lf ",hess[i][j]);*/
2016: }
2017: }
2018: }
2019: printf("\n");
2020: fprintf(ficlog,"\n");
2021:
2022: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2023: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2024:
2025: a=matrix(1,npar,1,npar);
2026: y=matrix(1,npar,1,npar);
2027: x=vector(1,npar);
2028: indx=ivector(1,npar);
2029: for (i=1;i<=npar;i++)
2030: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2031: ludcmp(a,npar,indx,&pd);
2032:
2033: for (j=1;j<=npar;j++) {
2034: for (i=1;i<=npar;i++) x[i]=0;
2035: x[j]=1;
2036: lubksb(a,npar,indx,x);
2037: for (i=1;i<=npar;i++){
2038: matcov[i][j]=x[i];
2039: }
2040: }
2041:
2042: printf("\n#Hessian matrix#\n");
2043: fprintf(ficlog,"\n#Hessian matrix#\n");
2044: for (i=1;i<=npar;i++) {
2045: for (j=1;j<=npar;j++) {
2046: printf("%.3e ",hess[i][j]);
2047: fprintf(ficlog,"%.3e ",hess[i][j]);
2048: }
2049: printf("\n");
2050: fprintf(ficlog,"\n");
2051: }
2052:
2053: /* Recompute Inverse */
2054: for (i=1;i<=npar;i++)
2055: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2056: ludcmp(a,npar,indx,&pd);
2057:
2058: /* printf("\n#Hessian matrix recomputed#\n");
2059:
2060: for (j=1;j<=npar;j++) {
2061: for (i=1;i<=npar;i++) x[i]=0;
2062: x[j]=1;
2063: lubksb(a,npar,indx,x);
2064: for (i=1;i<=npar;i++){
2065: y[i][j]=x[i];
2066: printf("%.3e ",y[i][j]);
2067: fprintf(ficlog,"%.3e ",y[i][j]);
2068: }
2069: printf("\n");
2070: fprintf(ficlog,"\n");
2071: }
2072: */
2073:
2074: free_matrix(a,1,npar,1,npar);
2075: free_matrix(y,1,npar,1,npar);
2076: free_vector(x,1,npar);
2077: free_ivector(indx,1,npar);
2078: free_matrix(hess,1,npar,1,npar);
2079:
2080:
2081: }
2082:
2083: /*************** hessian matrix ****************/
2084: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2085: {
2086: int i;
2087: int l=1, lmax=20;
2088: double k1,k2;
1.132 brouard 2089: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2090: double res;
2091: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2092: double fx;
2093: int k=0,kmax=10;
2094: double l1;
2095:
2096: fx=func(x);
2097: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 ! brouard 2098: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2099: l1=pow(10,l);
2100: delts=delt;
2101: for(k=1 ; k <kmax; k=k+1){
2102: delt = delta*(l1*k);
2103: p2[theta]=x[theta] +delt;
1.145 ! brouard 2104: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2105: p2[theta]=x[theta]-delt;
2106: k2=func(p2)-fx;
2107: /*res= (k1-2.0*fx+k2)/delt/delt; */
2108: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2109:
1.132 brouard 2110: #ifdef DEBUGHESS
1.126 brouard 2111: 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);
2112: 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);
2113: #endif
2114: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2115: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2116: k=kmax;
2117: }
2118: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2119: k=kmax; l=lmax*10.;
2120: }
2121: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2122: delts=delt;
2123: }
2124: }
2125: }
2126: delti[theta]=delts;
2127: return res;
2128:
2129: }
2130:
2131: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2132: {
2133: int i;
2134: int l=1, l1, lmax=20;
2135: double k1,k2,k3,k4,res,fx;
1.132 brouard 2136: double p2[MAXPARM+1];
1.126 brouard 2137: int k;
2138:
2139: fx=func(x);
2140: for (k=1; k<=2; k++) {
2141: for (i=1;i<=npar;i++) p2[i]=x[i];
2142: p2[thetai]=x[thetai]+delti[thetai]/k;
2143: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2144: k1=func(p2)-fx;
2145:
2146: p2[thetai]=x[thetai]+delti[thetai]/k;
2147: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2148: k2=func(p2)-fx;
2149:
2150: p2[thetai]=x[thetai]-delti[thetai]/k;
2151: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2152: k3=func(p2)-fx;
2153:
2154: p2[thetai]=x[thetai]-delti[thetai]/k;
2155: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2156: k4=func(p2)-fx;
2157: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2158: #ifdef DEBUG
2159: 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);
2160: 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);
2161: #endif
2162: }
2163: return res;
2164: }
2165:
2166: /************** Inverse of matrix **************/
2167: void ludcmp(double **a, int n, int *indx, double *d)
2168: {
2169: int i,imax,j,k;
2170: double big,dum,sum,temp;
2171: double *vv;
2172:
2173: vv=vector(1,n);
2174: *d=1.0;
2175: for (i=1;i<=n;i++) {
2176: big=0.0;
2177: for (j=1;j<=n;j++)
2178: if ((temp=fabs(a[i][j])) > big) big=temp;
2179: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2180: vv[i]=1.0/big;
2181: }
2182: for (j=1;j<=n;j++) {
2183: for (i=1;i<j;i++) {
2184: sum=a[i][j];
2185: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2186: a[i][j]=sum;
2187: }
2188: big=0.0;
2189: for (i=j;i<=n;i++) {
2190: sum=a[i][j];
2191: for (k=1;k<j;k++)
2192: sum -= a[i][k]*a[k][j];
2193: a[i][j]=sum;
2194: if ( (dum=vv[i]*fabs(sum)) >= big) {
2195: big=dum;
2196: imax=i;
2197: }
2198: }
2199: if (j != imax) {
2200: for (k=1;k<=n;k++) {
2201: dum=a[imax][k];
2202: a[imax][k]=a[j][k];
2203: a[j][k]=dum;
2204: }
2205: *d = -(*d);
2206: vv[imax]=vv[j];
2207: }
2208: indx[j]=imax;
2209: if (a[j][j] == 0.0) a[j][j]=TINY;
2210: if (j != n) {
2211: dum=1.0/(a[j][j]);
2212: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2213: }
2214: }
2215: free_vector(vv,1,n); /* Doesn't work */
2216: ;
2217: }
2218:
2219: void lubksb(double **a, int n, int *indx, double b[])
2220: {
2221: int i,ii=0,ip,j;
2222: double sum;
2223:
2224: for (i=1;i<=n;i++) {
2225: ip=indx[i];
2226: sum=b[ip];
2227: b[ip]=b[i];
2228: if (ii)
2229: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2230: else if (sum) ii=i;
2231: b[i]=sum;
2232: }
2233: for (i=n;i>=1;i--) {
2234: sum=b[i];
2235: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2236: b[i]=sum/a[i][i];
2237: }
2238: }
2239:
2240: void pstamp(FILE *fichier)
2241: {
2242: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2243: }
2244:
2245: /************ Frequencies ********************/
2246: 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[])
2247: { /* Some frequencies */
2248:
1.130 brouard 2249: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2250: int first;
2251: double ***freq; /* Frequencies */
2252: double *pp, **prop;
2253: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2254: char fileresp[FILENAMELENGTH];
2255:
2256: pp=vector(1,nlstate);
2257: prop=matrix(1,nlstate,iagemin,iagemax+3);
2258: strcpy(fileresp,"p");
2259: strcat(fileresp,fileres);
2260: if((ficresp=fopen(fileresp,"w"))==NULL) {
2261: printf("Problem with prevalence resultfile: %s\n", fileresp);
2262: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2263: exit(0);
2264: }
2265: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2266: j1=0;
2267:
2268: j=cptcoveff;
2269: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2270:
2271: first=1;
2272:
1.145 ! brouard 2273: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
! 2274: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
! 2275: /* j1++;
! 2276: */
! 2277: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2278: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2279: scanf("%d", i);*/
2280: for (i=-5; i<=nlstate+ndeath; i++)
2281: for (jk=-5; jk<=nlstate+ndeath; jk++)
2282: for(m=iagemin; m <= iagemax+3; m++)
2283: freq[i][jk][m]=0;
1.143 brouard 2284:
2285: for (i=1; i<=nlstate; i++)
2286: for(m=iagemin; m <= iagemax+3; m++)
2287: prop[i][m]=0;
1.126 brouard 2288:
2289: dateintsum=0;
2290: k2cpt=0;
2291: for (i=1; i<=imx; i++) {
2292: bool=1;
1.144 brouard 2293: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2294: for (z1=1; z1<=cptcoveff; z1++)
2295: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 ! brouard 2296: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2297: bool=0;
1.145 ! brouard 2298: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
! 2299: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
! 2300: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2301: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2302: }
1.126 brouard 2303: }
1.144 brouard 2304:
1.126 brouard 2305: if (bool==1){
2306: for(m=firstpass; m<=lastpass; m++){
2307: k2=anint[m][i]+(mint[m][i]/12.);
2308: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2309: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2310: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2311: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2312: if (m<lastpass) {
2313: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2314: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2315: }
2316:
2317: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2318: dateintsum=dateintsum+k2;
2319: k2cpt++;
2320: }
2321: /*}*/
2322: }
2323: }
1.145 ! brouard 2324: } /* end i */
1.126 brouard 2325:
2326: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2327: pstamp(ficresp);
2328: if (cptcovn>0) {
2329: fprintf(ficresp, "\n#********** Variable ");
2330: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2331: fprintf(ficresp, "**********\n#");
1.143 brouard 2332: fprintf(ficlog, "\n#********** Variable ");
2333: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2334: fprintf(ficlog, "**********\n#");
1.126 brouard 2335: }
2336: for(i=1; i<=nlstate;i++)
2337: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2338: fprintf(ficresp, "\n");
2339:
2340: for(i=iagemin; i <= iagemax+3; i++){
2341: if(i==iagemax+3){
2342: fprintf(ficlog,"Total");
2343: }else{
2344: if(first==1){
2345: first=0;
2346: printf("See log file for details...\n");
2347: }
2348: fprintf(ficlog,"Age %d", i);
2349: }
2350: for(jk=1; jk <=nlstate ; jk++){
2351: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2352: pp[jk] += freq[jk][m][i];
2353: }
2354: for(jk=1; jk <=nlstate ; jk++){
2355: for(m=-1, pos=0; m <=0 ; m++)
2356: pos += freq[jk][m][i];
2357: if(pp[jk]>=1.e-10){
2358: if(first==1){
1.132 brouard 2359: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2360: }
2361: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2362: }else{
2363: if(first==1)
2364: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2365: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2366: }
2367: }
2368:
2369: for(jk=1; jk <=nlstate ; jk++){
2370: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2371: pp[jk] += freq[jk][m][i];
2372: }
2373: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2374: pos += pp[jk];
2375: posprop += prop[jk][i];
2376: }
2377: for(jk=1; jk <=nlstate ; jk++){
2378: if(pos>=1.e-5){
2379: if(first==1)
2380: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2381: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2382: }else{
2383: if(first==1)
2384: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2385: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2386: }
2387: if( i <= iagemax){
2388: if(pos>=1.e-5){
2389: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2390: /*probs[i][jk][j1]= pp[jk]/pos;*/
2391: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2392: }
2393: else
2394: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2395: }
2396: }
2397:
2398: for(jk=-1; jk <=nlstate+ndeath; jk++)
2399: for(m=-1; m <=nlstate+ndeath; m++)
2400: if(freq[jk][m][i] !=0 ) {
2401: if(first==1)
2402: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2403: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2404: }
2405: if(i <= iagemax)
2406: fprintf(ficresp,"\n");
2407: if(first==1)
2408: printf("Others in log...\n");
2409: fprintf(ficlog,"\n");
2410: }
1.145 ! brouard 2411: /*}*/
1.126 brouard 2412: }
2413: dateintmean=dateintsum/k2cpt;
2414:
2415: fclose(ficresp);
2416: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2417: free_vector(pp,1,nlstate);
2418: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2419: /* End of Freq */
2420: }
2421:
2422: /************ Prevalence ********************/
2423: 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)
2424: {
2425: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2426: in each health status at the date of interview (if between dateprev1 and dateprev2).
2427: We still use firstpass and lastpass as another selection.
2428: */
2429:
1.130 brouard 2430: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2431: double ***freq; /* Frequencies */
2432: double *pp, **prop;
2433: double pos,posprop;
2434: double y2; /* in fractional years */
2435: int iagemin, iagemax;
1.145 ! brouard 2436: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2437:
2438: iagemin= (int) agemin;
2439: iagemax= (int) agemax;
2440: /*pp=vector(1,nlstate);*/
2441: prop=matrix(1,nlstate,iagemin,iagemax+3);
2442: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2443: j1=0;
2444:
1.145 ! brouard 2445: /*j=cptcoveff;*/
1.126 brouard 2446: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2447:
1.145 ! brouard 2448: first=1;
! 2449: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
! 2450: /*for(i1=1; i1<=ncodemax[k1];i1++){
! 2451: j1++;*/
1.126 brouard 2452:
2453: for (i=1; i<=nlstate; i++)
2454: for(m=iagemin; m <= iagemax+3; m++)
2455: prop[i][m]=0.0;
2456:
2457: for (i=1; i<=imx; i++) { /* Each individual */
2458: bool=1;
2459: if (cptcovn>0) {
2460: for (z1=1; z1<=cptcoveff; z1++)
2461: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2462: bool=0;
2463: }
2464: if (bool==1) {
2465: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2466: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2467: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2468: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2469: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2470: 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);
2471: if (s[m][i]>0 && s[m][i]<=nlstate) {
2472: /*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]]);*/
2473: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2474: prop[s[m][i]][iagemax+3] += weight[i];
2475: }
2476: }
2477: } /* end selection of waves */
2478: }
2479: }
2480: for(i=iagemin; i <= iagemax+3; i++){
2481: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2482: posprop += prop[jk][i];
2483: }
1.145 ! brouard 2484:
1.126 brouard 2485: for(jk=1; jk <=nlstate ; jk++){
2486: if( i <= iagemax){
2487: if(posprop>=1.e-5){
2488: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 ! brouard 2489: } else{
! 2490: if(first==1){
! 2491: first=0;
! 2492: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
! 2493: }
! 2494: }
1.126 brouard 2495: }
2496: }/* end jk */
2497: }/* end i */
1.145 ! brouard 2498: /*} *//* end i1 */
! 2499: } /* end j1 */
1.126 brouard 2500:
2501: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2502: /*free_vector(pp,1,nlstate);*/
2503: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2504: } /* End of prevalence */
2505:
2506: /************* Waves Concatenation ***************/
2507:
2508: 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)
2509: {
2510: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2511: Death is a valid wave (if date is known).
2512: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2513: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2514: and mw[mi+1][i]. dh depends on stepm.
2515: */
2516:
2517: int i, mi, m;
2518: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2519: double sum=0., jmean=0.;*/
2520: int first;
2521: int j, k=0,jk, ju, jl;
2522: double sum=0.;
2523: first=0;
2524: jmin=1e+5;
2525: jmax=-1;
2526: jmean=0.;
2527: for(i=1; i<=imx; i++){
2528: mi=0;
2529: m=firstpass;
2530: while(s[m][i] <= nlstate){
2531: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2532: mw[++mi][i]=m;
2533: if(m >=lastpass)
2534: break;
2535: else
2536: m++;
2537: }/* end while */
2538: if (s[m][i] > nlstate){
2539: mi++; /* Death is another wave */
2540: /* if(mi==0) never been interviewed correctly before death */
2541: /* Only death is a correct wave */
2542: mw[mi][i]=m;
2543: }
2544:
2545: wav[i]=mi;
2546: if(mi==0){
2547: nbwarn++;
2548: if(first==0){
2549: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2550: first=1;
2551: }
2552: if(first==1){
2553: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2554: }
2555: } /* end mi==0 */
2556: } /* End individuals */
2557:
2558: for(i=1; i<=imx; i++){
2559: for(mi=1; mi<wav[i];mi++){
2560: if (stepm <=0)
2561: dh[mi][i]=1;
2562: else{
2563: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2564: if (agedc[i] < 2*AGESUP) {
2565: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2566: if(j==0) j=1; /* Survives at least one month after exam */
2567: else if(j<0){
2568: nberr++;
2569: 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]);
2570: j=1; /* Temporary Dangerous patch */
2571: 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);
2572: 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]);
2573: 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);
2574: }
2575: k=k+1;
2576: if (j >= jmax){
2577: jmax=j;
2578: ijmax=i;
2579: }
2580: if (j <= jmin){
2581: jmin=j;
2582: ijmin=i;
2583: }
2584: sum=sum+j;
2585: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2586: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2587: }
2588: }
2589: else{
2590: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2591: /* 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]); */
2592:
2593: k=k+1;
2594: if (j >= jmax) {
2595: jmax=j;
2596: ijmax=i;
2597: }
2598: else if (j <= jmin){
2599: jmin=j;
2600: ijmin=i;
2601: }
2602: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2603: /*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]);*/
2604: if(j<0){
2605: nberr++;
2606: 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]);
2607: 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]);
2608: }
2609: sum=sum+j;
2610: }
2611: jk= j/stepm;
2612: jl= j -jk*stepm;
2613: ju= j -(jk+1)*stepm;
2614: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2615: if(jl==0){
2616: dh[mi][i]=jk;
2617: bh[mi][i]=0;
2618: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2619: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2620: dh[mi][i]=jk+1;
2621: bh[mi][i]=ju;
2622: }
2623: }else{
2624: if(jl <= -ju){
2625: dh[mi][i]=jk;
2626: bh[mi][i]=jl; /* bias is positive if real duration
2627: * is higher than the multiple of stepm and negative otherwise.
2628: */
2629: }
2630: else{
2631: dh[mi][i]=jk+1;
2632: bh[mi][i]=ju;
2633: }
2634: if(dh[mi][i]==0){
2635: dh[mi][i]=1; /* At least one step */
2636: bh[mi][i]=ju; /* At least one step */
2637: /* 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);*/
2638: }
2639: } /* end if mle */
2640: }
2641: } /* end wave */
2642: }
2643: jmean=sum/k;
2644: 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 2645: 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 2646: }
2647:
2648: /*********** Tricode ****************************/
1.145 ! brouard 2649: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2650: {
1.144 brouard 2651: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2652: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2653: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 ! brouard 2654: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
! 2655: /* nbcode[Tvar[j]][1]=
1.144 brouard 2656: */
1.130 brouard 2657:
1.145 ! brouard 2658: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2659: int modmaxcovj=0; /* Modality max of covariates j */
1.145 ! brouard 2660: int cptcode=0; /* Modality max of covariates j */
! 2661: int modmincovj=0; /* Modality min of covariates j */
! 2662:
! 2663:
1.126 brouard 2664: cptcoveff=0;
2665:
1.145 ! brouard 2666: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2667: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2668:
1.145 ! brouard 2669: /* Loop on covariates without age and products */
! 2670: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
! 2671: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2672: modality of this covariate Vj*/
1.145 ! brouard 2673: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
! 2674: * If product of Vn*Vm, still boolean *:
! 2675: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
! 2676: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
! 2677: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2678: modality of the nth covariate of individual i. */
1.145 ! brouard 2679: if (ij > modmaxcovj)
! 2680: modmaxcovj=ij;
! 2681: else if (ij < modmincovj)
! 2682: modmincovj=ij;
! 2683: if ((ij < -1) && (ij > NCOVMAX)){
! 2684: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
! 2685: exit(1);
! 2686: }else
1.136 brouard 2687: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 ! brouard 2688: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2689: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2690: /* getting the maximum value of the modality of the covariate
2691: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2692: female is 1, then modmaxcovj=1.*/
1.126 brouard 2693: }
1.145 ! brouard 2694: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
! 2695: cptcode=modmaxcovj;
1.137 brouard 2696: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 ! brouard 2697: /*for (i=0; i<=cptcode; i++) {*/
! 2698: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
! 2699: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
! 2700: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
! 2701: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
! 2702: }
! 2703: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
! 2704: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 2705: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2706:
1.136 brouard 2707: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 ! brouard 2708: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
! 2709: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
! 2710: modmincovj=3; modmaxcovj = 7;
! 2711: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
! 2712: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
! 2713: variables V1_1 and V1_2.
! 2714: nbcode[Tvar[j]][ij]=k;
! 2715: nbcode[Tvar[j]][1]=0;
! 2716: nbcode[Tvar[j]][2]=1;
! 2717: nbcode[Tvar[j]][3]=2;
! 2718: */
! 2719: ij=1; /* ij is similar to i but can jumps over null modalities */
! 2720: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
! 2721: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
! 2722: /*recode from 0 */
1.131 brouard 2723: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2724: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2725: k is a modality. If we have model=V1+V1*sex
2726: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2727: ij++;
2728: }
2729: if (ij > ncodemax[j]) break;
1.137 brouard 2730: } /* end of loop on */
2731: } /* end of loop on modality */
2732: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2733:
1.145 ! brouard 2734: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 2735:
1.145 ! brouard 2736: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
! 2737: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
! 2738: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
! 2739: Ndum[ij]++;
! 2740: }
1.126 brouard 2741:
2742: ij=1;
1.145 ! brouard 2743: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
! 2744: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 2745: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 ! brouard 2746: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
! 2747: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 2748: ij++;
1.145 ! brouard 2749: }else
! 2750: Tvaraff[ij]=0;
1.126 brouard 2751: }
1.131 brouard 2752: ij--;
1.144 brouard 2753: cptcoveff=ij; /*Number of total covariates*/
1.145 ! brouard 2754:
1.126 brouard 2755: }
2756:
1.145 ! brouard 2757:
1.126 brouard 2758: /*********** Health Expectancies ****************/
2759:
1.127 brouard 2760: 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 2761:
2762: {
2763: /* Health expectancies, no variances */
2764: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2765: int nhstepma, nstepma; /* Decreasing with age */
2766: double age, agelim, hf;
2767: double ***p3mat;
2768: double eip;
2769:
2770: pstamp(ficreseij);
2771: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2772: fprintf(ficreseij,"# Age");
2773: for(i=1; i<=nlstate;i++){
2774: for(j=1; j<=nlstate;j++){
2775: fprintf(ficreseij," e%1d%1d ",i,j);
2776: }
2777: fprintf(ficreseij," e%1d. ",i);
2778: }
2779: fprintf(ficreseij,"\n");
2780:
2781:
2782: if(estepm < stepm){
2783: printf ("Problem %d lower than %d\n",estepm, stepm);
2784: }
2785: else hstepm=estepm;
2786: /* We compute the life expectancy from trapezoids spaced every estepm months
2787: * This is mainly to measure the difference between two models: for example
2788: * if stepm=24 months pijx are given only every 2 years and by summing them
2789: * we are calculating an estimate of the Life Expectancy assuming a linear
2790: * progression in between and thus overestimating or underestimating according
2791: * to the curvature of the survival function. If, for the same date, we
2792: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2793: * to compare the new estimate of Life expectancy with the same linear
2794: * hypothesis. A more precise result, taking into account a more precise
2795: * curvature will be obtained if estepm is as small as stepm. */
2796:
2797: /* For example we decided to compute the life expectancy with the smallest unit */
2798: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2799: nhstepm is the number of hstepm from age to agelim
2800: nstepm is the number of stepm from age to agelin.
2801: Look at hpijx to understand the reason of that which relies in memory size
2802: and note for a fixed period like estepm months */
2803: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2804: survival function given by stepm (the optimization length). Unfortunately it
2805: means that if the survival funtion is printed only each two years of age and if
2806: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2807: results. So we changed our mind and took the option of the best precision.
2808: */
2809: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2810:
2811: agelim=AGESUP;
2812: /* If stepm=6 months */
2813: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2814: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2815:
2816: /* nhstepm age range expressed in number of stepm */
2817: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2818: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2819: /* if (stepm >= YEARM) hstepm=1;*/
2820: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2821: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2822:
2823: for (age=bage; age<=fage; age ++){
2824: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2825: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2826: /* if (stepm >= YEARM) hstepm=1;*/
2827: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2828:
2829: /* If stepm=6 months */
2830: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2831: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2832:
2833: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2834:
2835: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2836:
2837: printf("%d|",(int)age);fflush(stdout);
2838: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2839:
2840: /* Computing expectancies */
2841: for(i=1; i<=nlstate;i++)
2842: for(j=1; j<=nlstate;j++)
2843: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2844: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2845:
2846: /* 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]);*/
2847:
2848: }
2849:
2850: fprintf(ficreseij,"%3.0f",age );
2851: for(i=1; i<=nlstate;i++){
2852: eip=0;
2853: for(j=1; j<=nlstate;j++){
2854: eip +=eij[i][j][(int)age];
2855: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2856: }
2857: fprintf(ficreseij,"%9.4f", eip );
2858: }
2859: fprintf(ficreseij,"\n");
2860:
2861: }
2862: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2863: printf("\n");
2864: fprintf(ficlog,"\n");
2865:
2866: }
2867:
1.127 brouard 2868: 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 2869:
2870: {
2871: /* Covariances of health expectancies eij and of total life expectancies according
2872: to initial status i, ei. .
2873: */
2874: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2875: int nhstepma, nstepma; /* Decreasing with age */
2876: double age, agelim, hf;
2877: double ***p3matp, ***p3matm, ***varhe;
2878: double **dnewm,**doldm;
2879: double *xp, *xm;
2880: double **gp, **gm;
2881: double ***gradg, ***trgradg;
2882: int theta;
2883:
2884: double eip, vip;
2885:
2886: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2887: xp=vector(1,npar);
2888: xm=vector(1,npar);
2889: dnewm=matrix(1,nlstate*nlstate,1,npar);
2890: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2891:
2892: pstamp(ficresstdeij);
2893: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2894: fprintf(ficresstdeij,"# Age");
2895: for(i=1; i<=nlstate;i++){
2896: for(j=1; j<=nlstate;j++)
2897: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2898: fprintf(ficresstdeij," e%1d. ",i);
2899: }
2900: fprintf(ficresstdeij,"\n");
2901:
2902: pstamp(ficrescveij);
2903: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2904: fprintf(ficrescveij,"# Age");
2905: for(i=1; i<=nlstate;i++)
2906: for(j=1; j<=nlstate;j++){
2907: cptj= (j-1)*nlstate+i;
2908: for(i2=1; i2<=nlstate;i2++)
2909: for(j2=1; j2<=nlstate;j2++){
2910: cptj2= (j2-1)*nlstate+i2;
2911: if(cptj2 <= cptj)
2912: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2913: }
2914: }
2915: fprintf(ficrescveij,"\n");
2916:
2917: if(estepm < stepm){
2918: printf ("Problem %d lower than %d\n",estepm, stepm);
2919: }
2920: else hstepm=estepm;
2921: /* We compute the life expectancy from trapezoids spaced every estepm months
2922: * This is mainly to measure the difference between two models: for example
2923: * if stepm=24 months pijx are given only every 2 years and by summing them
2924: * we are calculating an estimate of the Life Expectancy assuming a linear
2925: * progression in between and thus overestimating or underestimating according
2926: * to the curvature of the survival function. If, for the same date, we
2927: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2928: * to compare the new estimate of Life expectancy with the same linear
2929: * hypothesis. A more precise result, taking into account a more precise
2930: * curvature will be obtained if estepm is as small as stepm. */
2931:
2932: /* For example we decided to compute the life expectancy with the smallest unit */
2933: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2934: nhstepm is the number of hstepm from age to agelim
2935: nstepm is the number of stepm from age to agelin.
2936: Look at hpijx to understand the reason of that which relies in memory size
2937: and note for a fixed period like estepm months */
2938: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2939: survival function given by stepm (the optimization length). Unfortunately it
2940: means that if the survival funtion is printed only each two years of age and if
2941: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2942: results. So we changed our mind and took the option of the best precision.
2943: */
2944: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2945:
2946: /* If stepm=6 months */
2947: /* nhstepm age range expressed in number of stepm */
2948: agelim=AGESUP;
2949: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2950: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2951: /* if (stepm >= YEARM) hstepm=1;*/
2952: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2953:
2954: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2955: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2956: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2957: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2958: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2959: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2960:
2961: for (age=bage; age<=fage; age ++){
2962: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2963: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2964: /* if (stepm >= YEARM) hstepm=1;*/
2965: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2966:
2967: /* If stepm=6 months */
2968: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2969: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2970:
2971: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2972:
2973: /* Computing Variances of health expectancies */
2974: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2975: decrease memory allocation */
2976: for(theta=1; theta <=npar; theta++){
2977: for(i=1; i<=npar; i++){
2978: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2979: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2980: }
2981: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2982: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2983:
2984: for(j=1; j<= nlstate; j++){
2985: for(i=1; i<=nlstate; i++){
2986: for(h=0; h<=nhstepm-1; h++){
2987: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2988: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2989: }
2990: }
2991: }
2992:
2993: for(ij=1; ij<= nlstate*nlstate; ij++)
2994: for(h=0; h<=nhstepm-1; h++){
2995: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2996: }
2997: }/* End theta */
2998:
2999:
3000: for(h=0; h<=nhstepm-1; h++)
3001: for(j=1; j<=nlstate*nlstate;j++)
3002: for(theta=1; theta <=npar; theta++)
3003: trgradg[h][j][theta]=gradg[h][theta][j];
3004:
3005:
3006: for(ij=1;ij<=nlstate*nlstate;ij++)
3007: for(ji=1;ji<=nlstate*nlstate;ji++)
3008: varhe[ij][ji][(int)age] =0.;
3009:
3010: printf("%d|",(int)age);fflush(stdout);
3011: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3012: for(h=0;h<=nhstepm-1;h++){
3013: for(k=0;k<=nhstepm-1;k++){
3014: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3015: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3016: for(ij=1;ij<=nlstate*nlstate;ij++)
3017: for(ji=1;ji<=nlstate*nlstate;ji++)
3018: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3019: }
3020: }
3021:
3022: /* Computing expectancies */
3023: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3024: for(i=1; i<=nlstate;i++)
3025: for(j=1; j<=nlstate;j++)
3026: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3027: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3028:
3029: /* 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]);*/
3030:
3031: }
3032:
3033: fprintf(ficresstdeij,"%3.0f",age );
3034: for(i=1; i<=nlstate;i++){
3035: eip=0.;
3036: vip=0.;
3037: for(j=1; j<=nlstate;j++){
3038: eip += eij[i][j][(int)age];
3039: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3040: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3041: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3042: }
3043: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3044: }
3045: fprintf(ficresstdeij,"\n");
3046:
3047: fprintf(ficrescveij,"%3.0f",age );
3048: for(i=1; i<=nlstate;i++)
3049: for(j=1; j<=nlstate;j++){
3050: cptj= (j-1)*nlstate+i;
3051: for(i2=1; i2<=nlstate;i2++)
3052: for(j2=1; j2<=nlstate;j2++){
3053: cptj2= (j2-1)*nlstate+i2;
3054: if(cptj2 <= cptj)
3055: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3056: }
3057: }
3058: fprintf(ficrescveij,"\n");
3059:
3060: }
3061: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3062: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3063: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3064: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3065: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3066: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3067: printf("\n");
3068: fprintf(ficlog,"\n");
3069:
3070: free_vector(xm,1,npar);
3071: free_vector(xp,1,npar);
3072: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3073: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3074: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3075: }
3076:
3077: /************ Variance ******************/
3078: 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[])
3079: {
3080: /* Variance of health expectancies */
3081: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3082: /* double **newm;*/
3083: double **dnewm,**doldm;
3084: double **dnewmp,**doldmp;
3085: int i, j, nhstepm, hstepm, h, nstepm ;
3086: int k, cptcode;
3087: double *xp;
3088: double **gp, **gm; /* for var eij */
3089: double ***gradg, ***trgradg; /*for var eij */
3090: double **gradgp, **trgradgp; /* for var p point j */
3091: double *gpp, *gmp; /* for var p point j */
3092: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3093: double ***p3mat;
3094: double age,agelim, hf;
3095: double ***mobaverage;
3096: int theta;
3097: char digit[4];
3098: char digitp[25];
3099:
3100: char fileresprobmorprev[FILENAMELENGTH];
3101:
3102: if(popbased==1){
3103: if(mobilav!=0)
3104: strcpy(digitp,"-populbased-mobilav-");
3105: else strcpy(digitp,"-populbased-nomobil-");
3106: }
3107: else
3108: strcpy(digitp,"-stablbased-");
3109:
3110: if (mobilav!=0) {
3111: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3112: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3113: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3114: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3115: }
3116: }
3117:
3118: strcpy(fileresprobmorprev,"prmorprev");
3119: sprintf(digit,"%-d",ij);
3120: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3121: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3122: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3123: strcat(fileresprobmorprev,fileres);
3124: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3125: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3126: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3127: }
3128: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3129:
3130: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3131: pstamp(ficresprobmorprev);
3132: 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);
3133: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3134: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3135: fprintf(ficresprobmorprev," p.%-d SE",j);
3136: for(i=1; i<=nlstate;i++)
3137: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3138: }
3139: fprintf(ficresprobmorprev,"\n");
3140: fprintf(ficgp,"\n# Routine varevsij");
3141: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3142: 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");
3143: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3144: /* } */
3145: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3146: pstamp(ficresvij);
3147: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3148: if(popbased==1)
1.128 brouard 3149: 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 3150: else
3151: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3152: fprintf(ficresvij,"# Age");
3153: for(i=1; i<=nlstate;i++)
3154: for(j=1; j<=nlstate;j++)
3155: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3156: fprintf(ficresvij,"\n");
3157:
3158: xp=vector(1,npar);
3159: dnewm=matrix(1,nlstate,1,npar);
3160: doldm=matrix(1,nlstate,1,nlstate);
3161: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3162: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3163:
3164: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3165: gpp=vector(nlstate+1,nlstate+ndeath);
3166: gmp=vector(nlstate+1,nlstate+ndeath);
3167: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3168:
3169: if(estepm < stepm){
3170: printf ("Problem %d lower than %d\n",estepm, stepm);
3171: }
3172: else hstepm=estepm;
3173: /* For example we decided to compute the life expectancy with the smallest unit */
3174: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3175: nhstepm is the number of hstepm from age to agelim
3176: nstepm is the number of stepm from age to agelin.
1.128 brouard 3177: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3178: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3179: survival function given by stepm (the optimization length). Unfortunately it
3180: means that if the survival funtion is printed every two years of age and if
3181: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3182: results. So we changed our mind and took the option of the best precision.
3183: */
3184: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3185: agelim = AGESUP;
3186: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3187: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3188: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3189: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3190: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3191: gp=matrix(0,nhstepm,1,nlstate);
3192: gm=matrix(0,nhstepm,1,nlstate);
3193:
3194:
3195: for(theta=1; theta <=npar; theta++){
3196: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3197: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3198: }
3199: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3200: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3201:
3202: if (popbased==1) {
3203: if(mobilav ==0){
3204: for(i=1; i<=nlstate;i++)
3205: prlim[i][i]=probs[(int)age][i][ij];
3206: }else{ /* mobilav */
3207: for(i=1; i<=nlstate;i++)
3208: prlim[i][i]=mobaverage[(int)age][i][ij];
3209: }
3210: }
3211:
3212: for(j=1; j<= nlstate; j++){
3213: for(h=0; h<=nhstepm; h++){
3214: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3215: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3216: }
3217: }
3218: /* This for computing probability of death (h=1 means
3219: computed over hstepm matrices product = hstepm*stepm months)
3220: as a weighted average of prlim.
3221: */
3222: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3223: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3224: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3225: }
3226: /* end probability of death */
3227:
3228: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3229: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3230: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3231: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3232:
3233: if (popbased==1) {
3234: if(mobilav ==0){
3235: for(i=1; i<=nlstate;i++)
3236: prlim[i][i]=probs[(int)age][i][ij];
3237: }else{ /* mobilav */
3238: for(i=1; i<=nlstate;i++)
3239: prlim[i][i]=mobaverage[(int)age][i][ij];
3240: }
3241: }
3242:
1.128 brouard 3243: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3244: for(h=0; h<=nhstepm; h++){
3245: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3246: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3247: }
3248: }
3249: /* This for computing probability of death (h=1 means
3250: computed over hstepm matrices product = hstepm*stepm months)
3251: as a weighted average of prlim.
3252: */
3253: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3254: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3255: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3256: }
3257: /* end probability of death */
3258:
3259: for(j=1; j<= nlstate; j++) /* vareij */
3260: for(h=0; h<=nhstepm; h++){
3261: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3262: }
3263:
3264: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3265: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3266: }
3267:
3268: } /* End theta */
3269:
3270: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3271:
3272: for(h=0; h<=nhstepm; h++) /* veij */
3273: for(j=1; j<=nlstate;j++)
3274: for(theta=1; theta <=npar; theta++)
3275: trgradg[h][j][theta]=gradg[h][theta][j];
3276:
3277: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3278: for(theta=1; theta <=npar; theta++)
3279: trgradgp[j][theta]=gradgp[theta][j];
3280:
3281:
3282: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3283: for(i=1;i<=nlstate;i++)
3284: for(j=1;j<=nlstate;j++)
3285: vareij[i][j][(int)age] =0.;
3286:
3287: for(h=0;h<=nhstepm;h++){
3288: for(k=0;k<=nhstepm;k++){
3289: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3290: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3291: for(i=1;i<=nlstate;i++)
3292: for(j=1;j<=nlstate;j++)
3293: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3294: }
3295: }
3296:
3297: /* pptj */
3298: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3299: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3300: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3301: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3302: varppt[j][i]=doldmp[j][i];
3303: /* end ppptj */
3304: /* x centered again */
3305: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3306: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3307:
3308: if (popbased==1) {
3309: if(mobilav ==0){
3310: for(i=1; i<=nlstate;i++)
3311: prlim[i][i]=probs[(int)age][i][ij];
3312: }else{ /* mobilav */
3313: for(i=1; i<=nlstate;i++)
3314: prlim[i][i]=mobaverage[(int)age][i][ij];
3315: }
3316: }
3317:
3318: /* This for computing probability of death (h=1 means
3319: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3320: as a weighted average of prlim.
3321: */
3322: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3323: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3324: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3325: }
3326: /* end probability of death */
3327:
3328: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3329: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3330: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3331: for(i=1; i<=nlstate;i++){
3332: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3333: }
3334: }
3335: fprintf(ficresprobmorprev,"\n");
3336:
3337: fprintf(ficresvij,"%.0f ",age );
3338: for(i=1; i<=nlstate;i++)
3339: for(j=1; j<=nlstate;j++){
3340: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3341: }
3342: fprintf(ficresvij,"\n");
3343: free_matrix(gp,0,nhstepm,1,nlstate);
3344: free_matrix(gm,0,nhstepm,1,nlstate);
3345: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3346: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3347: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3348: } /* End age */
3349: free_vector(gpp,nlstate+1,nlstate+ndeath);
3350: free_vector(gmp,nlstate+1,nlstate+ndeath);
3351: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3352: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 ! brouard 3353: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3354: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3355: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3356: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3357: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3358: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 ! brouard 3359: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
! 3360: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
! 3361: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3362: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3363: 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);
3364: /* 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);
3365: */
3366: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3367: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3368:
3369: free_vector(xp,1,npar);
3370: free_matrix(doldm,1,nlstate,1,nlstate);
3371: free_matrix(dnewm,1,nlstate,1,npar);
3372: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3373: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3374: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3375: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3376: fclose(ficresprobmorprev);
3377: fflush(ficgp);
3378: fflush(fichtm);
3379: } /* end varevsij */
3380:
3381: /************ Variance of prevlim ******************/
3382: 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[])
3383: {
3384: /* Variance of prevalence limit */
3385: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3386: double **newm;
3387: double **dnewm,**doldm;
3388: int i, j, nhstepm, hstepm;
3389: int k, cptcode;
3390: double *xp;
3391: double *gp, *gm;
3392: double **gradg, **trgradg;
3393: double age,agelim;
3394: int theta;
3395:
3396: pstamp(ficresvpl);
3397: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3398: fprintf(ficresvpl,"# Age");
3399: for(i=1; i<=nlstate;i++)
3400: fprintf(ficresvpl," %1d-%1d",i,i);
3401: fprintf(ficresvpl,"\n");
3402:
3403: xp=vector(1,npar);
3404: dnewm=matrix(1,nlstate,1,npar);
3405: doldm=matrix(1,nlstate,1,nlstate);
3406:
3407: hstepm=1*YEARM; /* Every year of age */
3408: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3409: agelim = AGESUP;
3410: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3411: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3412: if (stepm >= YEARM) hstepm=1;
3413: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3414: gradg=matrix(1,npar,1,nlstate);
3415: gp=vector(1,nlstate);
3416: gm=vector(1,nlstate);
3417:
3418: for(theta=1; theta <=npar; theta++){
3419: for(i=1; i<=npar; i++){ /* Computes gradient */
3420: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3421: }
3422: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3423: for(i=1;i<=nlstate;i++)
3424: gp[i] = prlim[i][i];
3425:
3426: for(i=1; i<=npar; i++) /* Computes gradient */
3427: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3428: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3429: for(i=1;i<=nlstate;i++)
3430: gm[i] = prlim[i][i];
3431:
3432: for(i=1;i<=nlstate;i++)
3433: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3434: } /* End theta */
3435:
3436: trgradg =matrix(1,nlstate,1,npar);
3437:
3438: for(j=1; j<=nlstate;j++)
3439: for(theta=1; theta <=npar; theta++)
3440: trgradg[j][theta]=gradg[theta][j];
3441:
3442: for(i=1;i<=nlstate;i++)
3443: varpl[i][(int)age] =0.;
3444: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3445: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3446: for(i=1;i<=nlstate;i++)
3447: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3448:
3449: fprintf(ficresvpl,"%.0f ",age );
3450: for(i=1; i<=nlstate;i++)
3451: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3452: fprintf(ficresvpl,"\n");
3453: free_vector(gp,1,nlstate);
3454: free_vector(gm,1,nlstate);
3455: free_matrix(gradg,1,npar,1,nlstate);
3456: free_matrix(trgradg,1,nlstate,1,npar);
3457: } /* End age */
3458:
3459: free_vector(xp,1,npar);
3460: free_matrix(doldm,1,nlstate,1,npar);
3461: free_matrix(dnewm,1,nlstate,1,nlstate);
3462:
3463: }
3464:
3465: /************ Variance of one-step probabilities ******************/
3466: 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[])
3467: {
3468: int i, j=0, i1, k1, l1, t, tj;
3469: int k2, l2, j1, z1;
3470: int k=0,l, cptcode;
1.145 ! brouard 3471: int first=1, first1, first2;
1.126 brouard 3472: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3473: double **dnewm,**doldm;
3474: double *xp;
3475: double *gp, *gm;
3476: double **gradg, **trgradg;
3477: double **mu;
1.145 ! brouard 3478: double age,agelim, cov[NCOVMAX+1];
1.126 brouard 3479: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3480: int theta;
3481: char fileresprob[FILENAMELENGTH];
3482: char fileresprobcov[FILENAMELENGTH];
3483: char fileresprobcor[FILENAMELENGTH];
3484: double ***varpij;
3485:
3486: strcpy(fileresprob,"prob");
3487: strcat(fileresprob,fileres);
3488: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3489: printf("Problem with resultfile: %s\n", fileresprob);
3490: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3491: }
3492: strcpy(fileresprobcov,"probcov");
3493: strcat(fileresprobcov,fileres);
3494: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3495: printf("Problem with resultfile: %s\n", fileresprobcov);
3496: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3497: }
3498: strcpy(fileresprobcor,"probcor");
3499: strcat(fileresprobcor,fileres);
3500: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3501: printf("Problem with resultfile: %s\n", fileresprobcor);
3502: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3503: }
3504: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3505: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3506: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3507: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3508: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3509: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3510: pstamp(ficresprob);
3511: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3512: fprintf(ficresprob,"# Age");
3513: pstamp(ficresprobcov);
3514: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3515: fprintf(ficresprobcov,"# Age");
3516: pstamp(ficresprobcor);
3517: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3518: fprintf(ficresprobcor,"# Age");
3519:
3520:
3521: for(i=1; i<=nlstate;i++)
3522: for(j=1; j<=(nlstate+ndeath);j++){
3523: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3524: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3525: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3526: }
3527: /* fprintf(ficresprob,"\n");
3528: fprintf(ficresprobcov,"\n");
3529: fprintf(ficresprobcor,"\n");
3530: */
1.131 brouard 3531: xp=vector(1,npar);
1.126 brouard 3532: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3533: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3534: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3535: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3536: first=1;
3537: fprintf(ficgp,"\n# Routine varprob");
3538: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3539: fprintf(fichtm,"\n");
3540:
3541: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3542: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3543: file %s<br>\n",optionfilehtmcov);
3544: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3545: and drawn. It helps understanding how is the covariance between two incidences.\
3546: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3547: 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. \
3548: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3549: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3550: standard deviations wide on each axis. <br>\
3551: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3552: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3553: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3554:
3555: cov[1]=1;
1.145 ! brouard 3556: /* tj=cptcoveff; */
! 3557: tj = (int) pow(2,cptcoveff);
1.126 brouard 3558: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3559: j1=0;
1.145 ! brouard 3560: for(j1=1; j1<=tj;j1++){
! 3561: /*for(i1=1; i1<=ncodemax[t];i1++){ */
! 3562: /*j1++;*/
1.126 brouard 3563: if (cptcovn>0) {
3564: fprintf(ficresprob, "\n#********** Variable ");
3565: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3566: fprintf(ficresprob, "**********\n#\n");
3567: fprintf(ficresprobcov, "\n#********** Variable ");
3568: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3569: fprintf(ficresprobcov, "**********\n#\n");
3570:
3571: fprintf(ficgp, "\n#********** Variable ");
3572: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3573: fprintf(ficgp, "**********\n#\n");
3574:
3575:
3576: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3577: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3578: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3579:
3580: fprintf(ficresprobcor, "\n#********** Variable ");
3581: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3582: fprintf(ficresprobcor, "**********\n#");
3583: }
3584:
1.145 ! brouard 3585: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
! 3586: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
! 3587: gp=vector(1,(nlstate)*(nlstate+ndeath));
! 3588: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3589: for (age=bage; age<=fage; age ++){
3590: cov[2]=age;
3591: for (k=1; k<=cptcovn;k++) {
1.145 ! brouard 3592: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
! 3593: * 1 1 1 1 1
! 3594: * 2 2 1 1 1
! 3595: * 3 1 2 1 1
! 3596: */
! 3597: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3598: }
3599: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3600: for (k=1; k<=cptcovprod;k++)
3601: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3602:
3603:
3604: for(theta=1; theta <=npar; theta++){
3605: for(i=1; i<=npar; i++)
3606: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3607:
3608: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3609:
3610: k=0;
3611: for(i=1; i<= (nlstate); i++){
3612: for(j=1; j<=(nlstate+ndeath);j++){
3613: k=k+1;
3614: gp[k]=pmmij[i][j];
3615: }
3616: }
3617:
3618: for(i=1; i<=npar; i++)
3619: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3620:
3621: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3622: k=0;
3623: for(i=1; i<=(nlstate); i++){
3624: for(j=1; j<=(nlstate+ndeath);j++){
3625: k=k+1;
3626: gm[k]=pmmij[i][j];
3627: }
3628: }
3629:
3630: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3631: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3632: }
3633:
3634: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3635: for(theta=1; theta <=npar; theta++)
3636: trgradg[j][theta]=gradg[theta][j];
3637:
3638: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3639: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3640:
3641: pmij(pmmij,cov,ncovmodel,x,nlstate);
3642:
3643: k=0;
3644: for(i=1; i<=(nlstate); i++){
3645: for(j=1; j<=(nlstate+ndeath);j++){
3646: k=k+1;
3647: mu[k][(int) age]=pmmij[i][j];
3648: }
3649: }
3650: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3651: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3652: varpij[i][j][(int)age] = doldm[i][j];
3653:
3654: /*printf("\n%d ",(int)age);
3655: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3656: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3657: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3658: }*/
3659:
3660: fprintf(ficresprob,"\n%d ",(int)age);
3661: fprintf(ficresprobcov,"\n%d ",(int)age);
3662: fprintf(ficresprobcor,"\n%d ",(int)age);
3663:
3664: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3665: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3666: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3667: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3668: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3669: }
3670: i=0;
3671: for (k=1; k<=(nlstate);k++){
3672: for (l=1; l<=(nlstate+ndeath);l++){
1.145 ! brouard 3673: i++;
1.126 brouard 3674: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3675: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3676: for (j=1; j<=i;j++){
1.145 ! brouard 3677: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3678: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3679: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3680: }
3681: }
3682: }/* end of loop for state */
3683: } /* end of loop for age */
1.145 ! brouard 3684: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3685: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
! 3686: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3687: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
! 3688:
1.126 brouard 3689: /* Confidence intervalle of pij */
3690: /*
1.131 brouard 3691: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3692: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3693: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3694: 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);
3695: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3696: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3697: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3698: */
3699:
3700: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 ! brouard 3701: first1=1;first2=2;
1.126 brouard 3702: for (k2=1; k2<=(nlstate);k2++){
3703: for (l2=1; l2<=(nlstate+ndeath);l2++){
3704: if(l2==k2) continue;
3705: j=(k2-1)*(nlstate+ndeath)+l2;
3706: for (k1=1; k1<=(nlstate);k1++){
3707: for (l1=1; l1<=(nlstate+ndeath);l1++){
3708: if(l1==k1) continue;
3709: i=(k1-1)*(nlstate+ndeath)+l1;
3710: if(i<=j) continue;
3711: for (age=bage; age<=fage; age ++){
3712: if ((int)age %5==0){
3713: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3714: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3715: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3716: mu1=mu[i][(int) age]/stepm*YEARM ;
3717: mu2=mu[j][(int) age]/stepm*YEARM;
3718: c12=cv12/sqrt(v1*v2);
3719: /* Computing eigen value of matrix of covariance */
3720: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3721: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3722: if ((lc2 <0) || (lc1 <0) ){
1.145 ! brouard 3723: if(first2==1){
! 3724: first1=0;
! 3725: printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
! 3726: }
! 3727: fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
! 3728: /* lc1=fabs(lc1); */ /* If we want to have them positive */
! 3729: /* lc2=fabs(lc2); */
1.135 brouard 3730: }
3731:
1.126 brouard 3732: /* Eigen vectors */
3733: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3734: /*v21=sqrt(1.-v11*v11); *//* error */
3735: v21=(lc1-v1)/cv12*v11;
3736: v12=-v21;
3737: v22=v11;
3738: tnalp=v21/v11;
3739: if(first1==1){
3740: first1=0;
3741: 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);
3742: }
3743: 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);
3744: /*printf(fignu*/
3745: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3746: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3747: if(first==1){
3748: first=0;
3749: fprintf(ficgp,"\nset parametric;unset label");
3750: 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);
1.145 ! brouard 3751: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 3752: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3753: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3754: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3755: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3756: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3757: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3758: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3759: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3760: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3761: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3762: 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",\
3763: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3764: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3765: }else{
3766: first=0;
3767: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3768: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3769: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3770: 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",\
3771: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3772: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3773: }/* if first */
3774: } /* age mod 5 */
3775: } /* end loop age */
3776: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3777: first=1;
3778: } /*l12 */
3779: } /* k12 */
3780: } /*l1 */
3781: }/* k1 */
1.145 ! brouard 3782: /* } /* loop covariates */
1.126 brouard 3783: }
3784: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3785: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3786: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3787: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3788: free_vector(xp,1,npar);
3789: fclose(ficresprob);
3790: fclose(ficresprobcov);
3791: fclose(ficresprobcor);
3792: fflush(ficgp);
3793: fflush(fichtmcov);
3794: }
3795:
3796:
3797: /******************* Printing html file ***********/
3798: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3799: int lastpass, int stepm, int weightopt, char model[],\
3800: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3801: int popforecast, int estepm ,\
3802: double jprev1, double mprev1,double anprev1, \
3803: double jprev2, double mprev2,double anprev2){
3804: int jj1, k1, i1, cpt;
3805:
3806: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3807: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3808: </ul>");
3809: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3810: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3811: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3812: fprintf(fichtm,"\
3813: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3814: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3815: fprintf(fichtm,"\
3816: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3817: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3818: fprintf(fichtm,"\
1.128 brouard 3819: - (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 3820: <a href=\"%s\">%s</a> <br>\n",
3821: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3822: fprintf(fichtm,"\
3823: - Population projections by age and states: \
3824: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3825:
3826: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3827:
1.145 ! brouard 3828: m=pow(2,cptcoveff);
1.126 brouard 3829: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3830:
3831: jj1=0;
3832: for(k1=1; k1<=m;k1++){
3833: for(i1=1; i1<=ncodemax[k1];i1++){
3834: jj1++;
3835: if (cptcovn > 0) {
3836: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3837: for (cpt=1; cpt<=cptcoveff;cpt++)
3838: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3839: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3840: }
3841: /* Pij */
1.145 ! brouard 3842: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
! 3843: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 3844: /* Quasi-incidences */
3845: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 ! brouard 3846: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
! 3847: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 3848: /* Period (stable) prevalence in each health state */
3849: for(cpt=1; cpt<nlstate;cpt++){
1.145 ! brouard 3850: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
! 3851: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 3852: }
3853: for(cpt=1; cpt<=nlstate;cpt++) {
3854: 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> \
3855: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3856: }
3857: } /* end i1 */
3858: }/* End k1 */
3859: fprintf(fichtm,"</ul>");
3860:
3861:
3862: fprintf(fichtm,"\
3863: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3864: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3865:
3866: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3867: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3868: fprintf(fichtm,"\
3869: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3870: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3871:
3872: fprintf(fichtm,"\
3873: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3874: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3875: fprintf(fichtm,"\
3876: - 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): \
3877: <a href=\"%s\">%s</a> <br>\n</li>",
3878: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3879: fprintf(fichtm,"\
3880: - (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): \
3881: <a href=\"%s\">%s</a> <br>\n</li>",
3882: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3883: fprintf(fichtm,"\
1.128 brouard 3884: - 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 3885: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3886: fprintf(fichtm,"\
1.128 brouard 3887: - 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",
3888: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3889: fprintf(fichtm,"\
3890: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3891: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3892:
3893: /* if(popforecast==1) fprintf(fichtm,"\n */
3894: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3895: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3896: /* <br>",fileres,fileres,fileres,fileres); */
3897: /* else */
3898: /* 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); */
3899: fflush(fichtm);
3900: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3901:
1.145 ! brouard 3902: m=pow(2,cptcoveff);
1.126 brouard 3903: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3904:
3905: jj1=0;
3906: for(k1=1; k1<=m;k1++){
3907: for(i1=1; i1<=ncodemax[k1];i1++){
3908: jj1++;
3909: if (cptcovn > 0) {
3910: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3911: for (cpt=1; cpt<=cptcoveff;cpt++)
3912: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3913: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3914: }
3915: for(cpt=1; cpt<=nlstate;cpt++) {
3916: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 ! brouard 3917: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
! 3918: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 3919: }
3920: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3921: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3922: true period expectancies (those weighted with period prevalences are also\
3923: drawn in addition to the population based expectancies computed using\
3924: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3925: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3926: } /* end i1 */
3927: }/* End k1 */
3928: fprintf(fichtm,"</ul>");
3929: fflush(fichtm);
3930: }
3931:
3932: /******************* Gnuplot file **************/
3933: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3934:
3935: char dirfileres[132],optfileres[132];
1.130 brouard 3936: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3937: int ng=0;
1.126 brouard 3938: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3939: /* printf("Problem with file %s",optionfilegnuplot); */
3940: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3941: /* } */
3942:
3943: /*#ifdef windows */
3944: fprintf(ficgp,"cd \"%s\" \n",pathc);
3945: /*#endif */
3946: m=pow(2,cptcoveff);
3947:
3948: strcpy(dirfileres,optionfilefiname);
3949: strcpy(optfileres,"vpl");
3950: /* 1eme*/
3951: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 ! brouard 3952: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
! 3953: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
! 3954: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 3955: fprintf(ficgp,"set xlabel \"Age\" \n\
3956: set ylabel \"Probability\" \n\
1.145 ! brouard 3957: set ter png small size 320, 240\n\
1.126 brouard 3958: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3959:
3960: for (i=1; i<= nlstate ; i ++) {
3961: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 3962: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3963: }
1.145 ! brouard 3964: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 3965: for (i=1; i<= nlstate ; i ++) {
3966: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3967: else fprintf(ficgp," \%%*lf (\%%*lf)");
3968: }
1.145 ! brouard 3969: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 3970: for (i=1; i<= nlstate ; i ++) {
3971: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3972: else fprintf(ficgp," \%%*lf (\%%*lf)");
3973: }
1.145 ! brouard 3974: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 3975: }
3976: }
3977: /*2 eme*/
3978:
3979: for (k1=1; k1<= m ; k1 ++) {
3980: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 ! brouard 3981: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 3982:
3983: for (i=1; i<= nlstate+1 ; i ++) {
3984: k=2*i;
3985: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3986: for (j=1; j<= nlstate+1 ; j ++) {
3987: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3988: else fprintf(ficgp," \%%*lf (\%%*lf)");
3989: }
3990: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3991: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3992: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3993: for (j=1; j<= nlstate+1 ; j ++) {
3994: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3995: else fprintf(ficgp," \%%*lf (\%%*lf)");
3996: }
1.145 ! brouard 3997: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 3998: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3999: for (j=1; j<= nlstate+1 ; j ++) {
4000: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4001: else fprintf(ficgp," \%%*lf (\%%*lf)");
4002: }
1.145 ! brouard 4003: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
! 4004: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4005: }
4006: }
4007:
4008: /*3eme*/
4009:
4010: for (k1=1; k1<= m ; k1 ++) {
4011: for (cpt=1; cpt<= nlstate ; cpt ++) {
4012: /* k=2+nlstate*(2*cpt-2); */
4013: k=2+(nlstate+1)*(cpt-1);
4014: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 ! brouard 4015: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4016: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4017: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4018: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4019: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4020: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4021: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4022: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4023:
4024: */
4025: for (i=1; i< nlstate ; i ++) {
4026: 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);
4027: /* 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);*/
4028:
4029: }
4030: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4031: }
4032: }
4033:
4034: /* CV preval stable (period) */
4035: for (k1=1; k1<= m ; k1 ++) {
4036: for (cpt=1; cpt<=nlstate ; cpt ++) {
4037: k=3;
1.145 ! brouard 4038: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4039: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 ! brouard 4040: set ter png small size 320, 240\n\
1.126 brouard 4041: unset log y\n\
4042: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
4043:
4044: for (i=1; i< nlstate ; i ++)
4045: fprintf(ficgp,"+$%d",k+i+1);
4046: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
4047:
4048: l=3+(nlstate+ndeath)*cpt;
4049: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
4050: for (i=1; i< nlstate ; i ++) {
4051: l=3+(nlstate+ndeath)*cpt;
4052: fprintf(ficgp,"+$%d",l+i+1);
4053: }
4054: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
4055: }
4056: }
4057:
4058: /* proba elementaires */
4059: for(i=1,jk=1; i <=nlstate; i++){
4060: for(k=1; k <=(nlstate+ndeath); k++){
4061: if (k != i) {
4062: for(j=1; j <=ncovmodel; j++){
4063: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4064: jk++;
4065: fprintf(ficgp,"\n");
4066: }
4067: }
4068: }
4069: }
1.145 ! brouard 4070: /*goto avoid;*/
1.126 brouard 4071: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4072: for(jk=1; jk <=m; jk++) {
1.145 ! brouard 4073: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4074: if (ng==2)
4075: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4076: else
4077: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 ! brouard 4078: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4079: i=1;
4080: for(k2=1; k2<=nlstate; k2++) {
4081: k3=i;
4082: for(k=1; k<=(nlstate+ndeath); k++) {
4083: if (k != k2){
4084: if(ng==2)
4085: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4086: else
4087: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4088: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4089: for(j=3; j <=ncovmodel; j++) {
1.145 ! brouard 4090: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
! 4091: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
! 4092: /* ij++; */
! 4093: /* } */
! 4094: /* else */
1.126 brouard 4095: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4096: }
4097: fprintf(ficgp,")/(1");
4098:
4099: for(k1=1; k1 <=nlstate; k1++){
4100: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4101: ij=1;
4102: for(j=3; j <=ncovmodel; j++){
1.145 ! brouard 4103: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
! 4104: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
! 4105: /* ij++; */
! 4106: /* } */
! 4107: /* else */
1.126 brouard 4108: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4109: }
4110: fprintf(ficgp,")");
4111: }
4112: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4113: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4114: i=i+ncovmodel;
4115: }
4116: } /* end k */
4117: } /* end k2 */
4118: } /* end jk */
4119: } /* end ng */
1.145 ! brouard 4120: avoid:
1.126 brouard 4121: fflush(ficgp);
4122: } /* end gnuplot */
4123:
4124:
4125: /*************** Moving average **************/
4126: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4127:
4128: int i, cpt, cptcod;
4129: int modcovmax =1;
4130: int mobilavrange, mob;
4131: double age;
4132:
4133: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4134: a covariate has 2 modalities */
4135: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4136:
4137: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4138: if(mobilav==1) mobilavrange=5; /* default */
4139: else mobilavrange=mobilav;
4140: for (age=bage; age<=fage; age++)
4141: for (i=1; i<=nlstate;i++)
4142: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4143: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4144: /* We keep the original values on the extreme ages bage, fage and for
4145: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4146: we use a 5 terms etc. until the borders are no more concerned.
4147: */
4148: for (mob=3;mob <=mobilavrange;mob=mob+2){
4149: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4150: for (i=1; i<=nlstate;i++){
4151: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4152: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4153: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4154: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4155: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4156: }
4157: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4158: }
4159: }
4160: }/* end age */
4161: }/* end mob */
4162: }else return -1;
4163: return 0;
4164: }/* End movingaverage */
4165:
4166:
4167: /************** Forecasting ******************/
4168: 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){
4169: /* proj1, year, month, day of starting projection
4170: agemin, agemax range of age
4171: dateprev1 dateprev2 range of dates during which prevalence is computed
4172: anproj2 year of en of projection (same day and month as proj1).
4173: */
4174: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4175: int *popage;
4176: double agec; /* generic age */
4177: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4178: double *popeffectif,*popcount;
4179: double ***p3mat;
4180: double ***mobaverage;
4181: char fileresf[FILENAMELENGTH];
4182:
4183: agelim=AGESUP;
4184: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4185:
4186: strcpy(fileresf,"f");
4187: strcat(fileresf,fileres);
4188: if((ficresf=fopen(fileresf,"w"))==NULL) {
4189: printf("Problem with forecast resultfile: %s\n", fileresf);
4190: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4191: }
4192: printf("Computing forecasting: result on file '%s' \n", fileresf);
4193: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4194:
4195: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4196:
4197: if (mobilav!=0) {
4198: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4199: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4200: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4201: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4202: }
4203: }
4204:
4205: stepsize=(int) (stepm+YEARM-1)/YEARM;
4206: if (stepm<=12) stepsize=1;
4207: if(estepm < stepm){
4208: printf ("Problem %d lower than %d\n",estepm, stepm);
4209: }
4210: else hstepm=estepm;
4211:
4212: hstepm=hstepm/stepm;
4213: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4214: fractional in yp1 */
4215: anprojmean=yp;
4216: yp2=modf((yp1*12),&yp);
4217: mprojmean=yp;
4218: yp1=modf((yp2*30.5),&yp);
4219: jprojmean=yp;
4220: if(jprojmean==0) jprojmean=1;
4221: if(mprojmean==0) jprojmean=1;
4222:
4223: i1=cptcoveff;
4224: if (cptcovn < 1){i1=1;}
4225:
4226: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4227:
4228: fprintf(ficresf,"#****** Routine prevforecast **\n");
4229:
4230: /* if (h==(int)(YEARM*yearp)){ */
4231: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4232: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4233: k=k+1;
4234: fprintf(ficresf,"\n#******");
4235: for(j=1;j<=cptcoveff;j++) {
4236: 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]]);
4237: }
4238: fprintf(ficresf,"******\n");
4239: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4240: for(j=1; j<=nlstate+ndeath;j++){
4241: for(i=1; i<=nlstate;i++)
4242: fprintf(ficresf," p%d%d",i,j);
4243: fprintf(ficresf," p.%d",j);
4244: }
4245: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4246: fprintf(ficresf,"\n");
4247: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4248:
4249: for (agec=fage; agec>=(ageminpar-1); agec--){
4250: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4251: nhstepm = nhstepm/hstepm;
4252: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4253: oldm=oldms;savm=savms;
4254: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4255:
4256: for (h=0; h<=nhstepm; h++){
4257: if (h*hstepm/YEARM*stepm ==yearp) {
4258: fprintf(ficresf,"\n");
4259: for(j=1;j<=cptcoveff;j++)
4260: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4261: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4262: }
4263: for(j=1; j<=nlstate+ndeath;j++) {
4264: ppij=0.;
4265: for(i=1; i<=nlstate;i++) {
4266: if (mobilav==1)
4267: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4268: else {
4269: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4270: }
4271: if (h*hstepm/YEARM*stepm== yearp) {
4272: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4273: }
4274: } /* end i */
4275: if (h*hstepm/YEARM*stepm==yearp) {
4276: fprintf(ficresf," %.3f", ppij);
4277: }
4278: }/* end j */
4279: } /* end h */
4280: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4281: } /* end agec */
4282: } /* end yearp */
4283: } /* end cptcod */
4284: } /* end cptcov */
4285:
4286: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4287:
4288: fclose(ficresf);
4289: }
4290:
4291: /************** Forecasting *****not tested NB*************/
4292: 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){
4293:
4294: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4295: int *popage;
4296: double calagedatem, agelim, kk1, kk2;
4297: double *popeffectif,*popcount;
4298: double ***p3mat,***tabpop,***tabpopprev;
4299: double ***mobaverage;
4300: char filerespop[FILENAMELENGTH];
4301:
4302: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4303: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4304: agelim=AGESUP;
4305: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4306:
4307: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4308:
4309:
4310: strcpy(filerespop,"pop");
4311: strcat(filerespop,fileres);
4312: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4313: printf("Problem with forecast resultfile: %s\n", filerespop);
4314: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4315: }
4316: printf("Computing forecasting: result on file '%s' \n", filerespop);
4317: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4318:
4319: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4320:
4321: if (mobilav!=0) {
4322: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4323: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4324: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4325: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4326: }
4327: }
4328:
4329: stepsize=(int) (stepm+YEARM-1)/YEARM;
4330: if (stepm<=12) stepsize=1;
4331:
4332: agelim=AGESUP;
4333:
4334: hstepm=1;
4335: hstepm=hstepm/stepm;
4336:
4337: if (popforecast==1) {
4338: if((ficpop=fopen(popfile,"r"))==NULL) {
4339: printf("Problem with population file : %s\n",popfile);exit(0);
4340: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4341: }
4342: popage=ivector(0,AGESUP);
4343: popeffectif=vector(0,AGESUP);
4344: popcount=vector(0,AGESUP);
4345:
4346: i=1;
4347: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4348:
4349: imx=i;
4350: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4351: }
4352:
4353: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4354: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4355: k=k+1;
4356: fprintf(ficrespop,"\n#******");
4357: for(j=1;j<=cptcoveff;j++) {
4358: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4359: }
4360: fprintf(ficrespop,"******\n");
4361: fprintf(ficrespop,"# Age");
4362: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4363: if (popforecast==1) fprintf(ficrespop," [Population]");
4364:
4365: for (cpt=0; cpt<=0;cpt++) {
4366: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4367:
4368: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4369: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4370: nhstepm = nhstepm/hstepm;
4371:
4372: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4373: oldm=oldms;savm=savms;
4374: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4375:
4376: for (h=0; h<=nhstepm; h++){
4377: if (h==(int) (calagedatem+YEARM*cpt)) {
4378: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4379: }
4380: for(j=1; j<=nlstate+ndeath;j++) {
4381: kk1=0.;kk2=0;
4382: for(i=1; i<=nlstate;i++) {
4383: if (mobilav==1)
4384: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4385: else {
4386: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4387: }
4388: }
4389: if (h==(int)(calagedatem+12*cpt)){
4390: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4391: /*fprintf(ficrespop," %.3f", kk1);
4392: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4393: }
4394: }
4395: for(i=1; i<=nlstate;i++){
4396: kk1=0.;
4397: for(j=1; j<=nlstate;j++){
4398: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4399: }
4400: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4401: }
4402:
4403: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4404: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4405: }
4406: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4407: }
4408: }
4409:
4410: /******/
4411:
4412: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4413: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4414: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4415: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4416: nhstepm = nhstepm/hstepm;
4417:
4418: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4419: oldm=oldms;savm=savms;
4420: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4421: for (h=0; h<=nhstepm; h++){
4422: if (h==(int) (calagedatem+YEARM*cpt)) {
4423: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4424: }
4425: for(j=1; j<=nlstate+ndeath;j++) {
4426: kk1=0.;kk2=0;
4427: for(i=1; i<=nlstate;i++) {
4428: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4429: }
4430: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4431: }
4432: }
4433: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4434: }
4435: }
4436: }
4437: }
4438:
4439: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4440:
4441: if (popforecast==1) {
4442: free_ivector(popage,0,AGESUP);
4443: free_vector(popeffectif,0,AGESUP);
4444: free_vector(popcount,0,AGESUP);
4445: }
4446: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4447: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4448: fclose(ficrespop);
4449: } /* End of popforecast */
4450:
4451: int fileappend(FILE *fichier, char *optionfich)
4452: {
4453: if((fichier=fopen(optionfich,"a"))==NULL) {
4454: printf("Problem with file: %s\n", optionfich);
4455: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4456: return (0);
4457: }
4458: fflush(fichier);
4459: return (1);
4460: }
4461:
4462:
4463: /**************** function prwizard **********************/
4464: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4465: {
4466:
4467: /* Wizard to print covariance matrix template */
4468:
4469: char ca[32], cb[32], cc[32];
4470: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4471: int numlinepar;
4472:
4473: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4474: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4475: for(i=1; i <=nlstate; i++){
4476: jj=0;
4477: for(j=1; j <=nlstate+ndeath; j++){
4478: if(j==i) continue;
4479: jj++;
4480: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4481: printf("%1d%1d",i,j);
4482: fprintf(ficparo,"%1d%1d",i,j);
4483: for(k=1; k<=ncovmodel;k++){
4484: /* printf(" %lf",param[i][j][k]); */
4485: /* fprintf(ficparo," %lf",param[i][j][k]); */
4486: printf(" 0.");
4487: fprintf(ficparo," 0.");
4488: }
4489: printf("\n");
4490: fprintf(ficparo,"\n");
4491: }
4492: }
4493: printf("# Scales (for hessian or gradient estimation)\n");
4494: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4495: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4496: for(i=1; i <=nlstate; i++){
4497: jj=0;
4498: for(j=1; j <=nlstate+ndeath; j++){
4499: if(j==i) continue;
4500: jj++;
4501: fprintf(ficparo,"%1d%1d",i,j);
4502: printf("%1d%1d",i,j);
4503: fflush(stdout);
4504: for(k=1; k<=ncovmodel;k++){
4505: /* printf(" %le",delti3[i][j][k]); */
4506: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4507: printf(" 0.");
4508: fprintf(ficparo," 0.");
4509: }
4510: numlinepar++;
4511: printf("\n");
4512: fprintf(ficparo,"\n");
4513: }
4514: }
4515: printf("# Covariance matrix\n");
4516: /* # 121 Var(a12)\n\ */
4517: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4518: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4519: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4520: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4521: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4522: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4523: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4524: fflush(stdout);
4525: fprintf(ficparo,"# Covariance matrix\n");
4526: /* # 121 Var(a12)\n\ */
4527: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4528: /* # ...\n\ */
4529: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4530:
4531: for(itimes=1;itimes<=2;itimes++){
4532: jj=0;
4533: for(i=1; i <=nlstate; i++){
4534: for(j=1; j <=nlstate+ndeath; j++){
4535: if(j==i) continue;
4536: for(k=1; k<=ncovmodel;k++){
4537: jj++;
4538: ca[0]= k+'a'-1;ca[1]='\0';
4539: if(itimes==1){
4540: printf("#%1d%1d%d",i,j,k);
4541: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4542: }else{
4543: printf("%1d%1d%d",i,j,k);
4544: fprintf(ficparo,"%1d%1d%d",i,j,k);
4545: /* printf(" %.5le",matcov[i][j]); */
4546: }
4547: ll=0;
4548: for(li=1;li <=nlstate; li++){
4549: for(lj=1;lj <=nlstate+ndeath; lj++){
4550: if(lj==li) continue;
4551: for(lk=1;lk<=ncovmodel;lk++){
4552: ll++;
4553: if(ll<=jj){
4554: cb[0]= lk +'a'-1;cb[1]='\0';
4555: if(ll<jj){
4556: if(itimes==1){
4557: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4558: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4559: }else{
4560: printf(" 0.");
4561: fprintf(ficparo," 0.");
4562: }
4563: }else{
4564: if(itimes==1){
4565: printf(" Var(%s%1d%1d)",ca,i,j);
4566: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4567: }else{
4568: printf(" 0.");
4569: fprintf(ficparo," 0.");
4570: }
4571: }
4572: }
4573: } /* end lk */
4574: } /* end lj */
4575: } /* end li */
4576: printf("\n");
4577: fprintf(ficparo,"\n");
4578: numlinepar++;
4579: } /* end k*/
4580: } /*end j */
4581: } /* end i */
4582: } /* end itimes */
4583:
4584: } /* end of prwizard */
4585: /******************* Gompertz Likelihood ******************************/
4586: double gompertz(double x[])
4587: {
4588: double A,B,L=0.0,sump=0.,num=0.;
4589: int i,n=0; /* n is the size of the sample */
4590:
4591: for (i=0;i<=imx-1 ; i++) {
4592: sump=sump+weight[i];
4593: /* sump=sump+1;*/
4594: num=num+1;
4595: }
4596:
4597:
4598: /* for (i=0; i<=imx; i++)
4599: 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]);*/
4600:
4601: for (i=1;i<=imx ; i++)
4602: {
4603: if (cens[i] == 1 && wav[i]>1)
4604: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4605:
4606: if (cens[i] == 0 && wav[i]>1)
4607: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4608: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4609:
4610: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4611: if (wav[i] > 1 ) { /* ??? */
4612: L=L+A*weight[i];
4613: /* 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]);*/
4614: }
4615: }
4616:
4617: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4618:
4619: return -2*L*num/sump;
4620: }
4621:
1.136 brouard 4622: #ifdef GSL
4623: /******************* Gompertz_f Likelihood ******************************/
4624: double gompertz_f(const gsl_vector *v, void *params)
4625: {
4626: double A,B,LL=0.0,sump=0.,num=0.;
4627: double *x= (double *) v->data;
4628: int i,n=0; /* n is the size of the sample */
4629:
4630: for (i=0;i<=imx-1 ; i++) {
4631: sump=sump+weight[i];
4632: /* sump=sump+1;*/
4633: num=num+1;
4634: }
4635:
4636:
4637: /* for (i=0; i<=imx; i++)
4638: 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]);*/
4639: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4640: for (i=1;i<=imx ; i++)
4641: {
4642: if (cens[i] == 1 && wav[i]>1)
4643: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4644:
4645: if (cens[i] == 0 && wav[i]>1)
4646: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4647: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4648:
4649: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4650: if (wav[i] > 1 ) { /* ??? */
4651: LL=LL+A*weight[i];
4652: /* 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]);*/
4653: }
4654: }
4655:
4656: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4657: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4658:
4659: return -2*LL*num/sump;
4660: }
4661: #endif
4662:
1.126 brouard 4663: /******************* Printing html file ***********/
4664: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4665: int lastpass, int stepm, int weightopt, char model[],\
4666: int imx, double p[],double **matcov,double agemortsup){
4667: int i,k;
4668:
4669: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4670: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4671: for (i=1;i<=2;i++)
4672: 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]));
4673: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4674: fprintf(fichtm,"</ul>");
4675:
4676: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4677:
4678: 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>");
4679:
4680: for (k=agegomp;k<(agemortsup-2);k++)
4681: 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]);
4682:
4683:
4684: fflush(fichtm);
4685: }
4686:
4687: /******************* Gnuplot file **************/
4688: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4689:
4690: char dirfileres[132],optfileres[132];
4691: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4692: int ng;
4693:
4694:
4695: /*#ifdef windows */
4696: fprintf(ficgp,"cd \"%s\" \n",pathc);
4697: /*#endif */
4698:
4699:
4700: strcpy(dirfileres,optionfilefiname);
4701: strcpy(optfileres,"vpl");
4702: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4703: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 ! brouard 4704: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
! 4705: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 4706: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4707:
4708: }
4709:
1.136 brouard 4710: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4711: {
1.126 brouard 4712:
1.136 brouard 4713: /*-------- data file ----------*/
4714: FILE *fic;
4715: char dummy[]=" ";
4716: int i, j, n;
4717: int linei, month, year,iout;
4718: char line[MAXLINE], linetmp[MAXLINE];
4719: char stra[80], strb[80];
4720: char *stratrunc;
4721: int lstra;
1.126 brouard 4722:
4723:
1.136 brouard 4724: if((fic=fopen(datafile,"r"))==NULL) {
4725: printf("Problem while opening datafile: %s\n", datafile);return 1;
4726: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4727: }
1.126 brouard 4728:
1.136 brouard 4729: i=1;
4730: linei=0;
4731: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4732: linei=linei+1;
4733: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4734: if(line[j] == '\t')
4735: line[j] = ' ';
4736: }
4737: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4738: ;
4739: };
4740: line[j+1]=0; /* Trims blanks at end of line */
4741: if(line[0]=='#'){
4742: fprintf(ficlog,"Comment line\n%s\n",line);
4743: printf("Comment line\n%s\n",line);
4744: continue;
4745: }
4746: trimbb(linetmp,line); /* Trims multiple blanks in line */
4747: for (j=0; line[j]!='\0';j++){
4748: line[j]=linetmp[j];
4749: }
4750:
1.126 brouard 4751:
1.136 brouard 4752: for (j=maxwav;j>=1;j--){
1.137 brouard 4753: cutv(stra, strb, line, ' ');
1.136 brouard 4754: if(strb[0]=='.') { /* Missing status */
4755: lval=-1;
4756: }else{
4757: errno=0;
4758: lval=strtol(strb,&endptr,10);
4759: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4760: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4761: 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);
4762: 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 4763: return 1;
4764: }
4765: }
4766: s[j][i]=lval;
4767:
4768: strcpy(line,stra);
4769: cutv(stra, strb,line,' ');
4770: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4771: }
1.145 ! brouard 4772: else if(iout=sscanf(strb,"%s.",dummy) != 0){
1.136 brouard 4773: month=99;
4774: year=9999;
4775: }else{
1.141 brouard 4776: 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);
4777: 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 4778: return 1;
4779: }
4780: anint[j][i]= (double) year;
4781: mint[j][i]= (double)month;
4782: strcpy(line,stra);
4783: } /* ENd Waves */
4784:
4785: cutv(stra, strb,line,' ');
4786: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4787: }
4788: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4789: month=99;
4790: year=9999;
4791: }else{
1.141 brouard 4792: 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);
4793: 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 4794: return 1;
4795: }
4796: andc[i]=(double) year;
4797: moisdc[i]=(double) month;
4798: strcpy(line,stra);
4799:
4800: cutv(stra, strb,line,' ');
4801: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4802: }
1.145 ! brouard 4803: else if(iout=sscanf(strb,"%s.", dummy) != 0){
1.136 brouard 4804: month=99;
4805: year=9999;
4806: }else{
1.141 brouard 4807: 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);
4808: 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 4809: return 1;
4810: }
4811: if (year==9999) {
1.141 brouard 4812: 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);
4813: 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 4814: return 1;
1.126 brouard 4815:
1.136 brouard 4816: }
4817: annais[i]=(double)(year);
4818: moisnais[i]=(double)(month);
4819: strcpy(line,stra);
4820:
4821: cutv(stra, strb,line,' ');
4822: errno=0;
4823: dval=strtod(strb,&endptr);
4824: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4825: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4826: 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 4827: fflush(ficlog);
4828: return 1;
4829: }
4830: weight[i]=dval;
4831: strcpy(line,stra);
4832:
4833: for (j=ncovcol;j>=1;j--){
4834: cutv(stra, strb,line,' ');
4835: if(strb[0]=='.') { /* Missing status */
4836: lval=-1;
4837: }else{
4838: errno=0;
4839: lval=strtol(strb,&endptr,10);
4840: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4841: 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);
4842: 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 4843: return 1;
4844: }
4845: }
4846: if(lval <-1 || lval >1){
1.141 brouard 4847: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4848: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4849: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4850: For example, for multinomial values like 1, 2 and 3,\n \
4851: build V1=0 V2=0 for the reference value (1),\n \
4852: V1=1 V2=0 for (2) \n \
4853: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4854: output of IMaCh is often meaningless.\n \
4855: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 4856: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4857: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4858: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4859: For example, for multinomial values like 1, 2 and 3,\n \
4860: build V1=0 V2=0 for the reference value (1),\n \
4861: V1=1 V2=0 for (2) \n \
4862: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4863: output of IMaCh is often meaningless.\n \
4864: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4865: return 1;
4866: }
4867: covar[j][i]=(double)(lval);
4868: strcpy(line,stra);
4869: }
4870: lstra=strlen(stra);
4871:
4872: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4873: stratrunc = &(stra[lstra-9]);
4874: num[i]=atol(stratrunc);
4875: }
4876: else
4877: num[i]=atol(stra);
4878: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4879: 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;}*/
4880:
4881: i=i+1;
4882: } /* End loop reading data */
1.126 brouard 4883:
1.136 brouard 4884: *imax=i-1; /* Number of individuals */
4885: fclose(fic);
4886:
4887: return (0);
4888: endread:
4889: printf("Exiting readdata: ");
4890: fclose(fic);
4891: return (1);
1.126 brouard 4892:
4893:
4894:
1.136 brouard 4895: }
1.145 ! brouard 4896: void removespace(char *str) {
! 4897: char *p1 = str, *p2 = str;
! 4898: do
! 4899: while (*p2 == ' ')
! 4900: p2++;
! 4901: while (*p1++ = *p2++);
! 4902: }
! 4903:
! 4904: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
! 4905: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
! 4906: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
! 4907: * - cptcovn or number of covariates k of the models excluding age*products =6
! 4908: * - cptcovage number of covariates with age*products =2
! 4909: * - cptcovs number of simple covariates
! 4910: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
! 4911: * which is a new column after the 9 (ncovcol) variables.
! 4912: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
! 4913: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
! 4914: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
! 4915: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
! 4916: */
1.136 brouard 4917: {
1.145 ! brouard 4918: int i, j, k, ks;
1.136 brouard 4919: int i1, j1, k1, k2;
4920: char modelsav[80];
1.145 ! brouard 4921: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 4922:
1.145 ! brouard 4923: /*removespace(model);*/
1.136 brouard 4924: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 ! brouard 4925: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
! 4926: j=nbocc(model,'+'); /**< j=Number of '+' */
! 4927: j1=nbocc(model,'*'); /**< j1=Number of '*' */
! 4928: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
! 4929: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
! 4930: /* including age products which are counted in cptcovage.
! 4931: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
! 4932: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
! 4933: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 4934: strcpy(modelsav,model);
1.137 brouard 4935: if (strstr(model,"AGE") !=0){
4936: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4937: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 4938: return 1;
4939: }
1.141 brouard 4940: if (strstr(model,"v") !=0){
4941: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4942: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4943: return 1;
4944: }
1.136 brouard 4945:
1.145 ! brouard 4946: /* Design
! 4947: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
! 4948: * < ncovcol=8 >
! 4949: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
! 4950: * k= 1 2 3 4 5 6 7 8
! 4951: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
! 4952: * covar[k,i], value of kth covariate if not including age for individual i:
! 4953: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
! 4954: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
! 4955: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
! 4956: * Tage[++cptcovage]=k
! 4957: * if products, new covar are created after ncovcol with k1
! 4958: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
! 4959: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
! 4960: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
! 4961: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 4962: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
! 4963: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
! 4964: * < ncovcol=8 >
! 4965: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
! 4966: * k= 1 2 3 4 5 6 7 8 9 10 11 12
! 4967: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
! 4968: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 4969: * p Tprod[1]@2={ 6, 5}
! 4970: *p Tvard[1][1]@4= {7, 8, 5, 6}
! 4971: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
! 4972: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
! 4973: *How to reorganize?
! 4974: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
! 4975: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
! 4976: * {2, 1, 4, 8, 5, 6, 3, 7}
! 4977: * Struct []
! 4978: */
! 4979:
1.136 brouard 4980: /* This loop fills the array Tvar from the string 'model'.*/
4981: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 4982: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
4983: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
4984: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
4985: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
4986: /* k=1 Tvar[1]=2 (from V2) */
4987: /* k=5 Tvar[5] */
4988: /* for (k=1; k<=cptcovn;k++) { */
4989: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
4990: /* } */
4991: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 ! brouard 4992: /*
! 4993: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
! 4994: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
! 4995: Tvar[k]=0;
! 4996: cptcovage=0;
! 4997: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
! 4998: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
! 4999: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5000: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5001: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5002: /*scanf("%d",i);*/
1.145 ! brouard 5003: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
! 5004: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 5005: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
! 5006: /* covar is not filled and then is empty */
1.136 brouard 5007: cptcovprod--;
1.145 ! brouard 5008: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
! 5009: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5010: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5011: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5012: /*printf("stre=%s ", stre);*/
1.137 brouard 5013: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5014: cptcovprod--;
1.145 ! brouard 5015: cutl(stre,strb,strc,'V');
1.136 brouard 5016: Tvar[k]=atoi(stre);
5017: cptcovage++;
5018: Tage[cptcovage]=k;
1.137 brouard 5019: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5020: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 ! brouard 5021: cptcovn++;
! 5022: cptcovprodnoage++;k1++;
! 5023: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 5024: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5025: because this model-covariate is a construction we invent a new column
5026: ncovcol + k1
5027: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5028: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 ! brouard 5029: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5030: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 ! brouard 5031: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
! 5032: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
! 5033: k2=k2+2;
! 5034: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
! 5035: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5036: for (i=1; i<=lastobs;i++){
5037: /* Computes the new covariate which is a product of
1.145 ! brouard 5038: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5039: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5040: }
5041: } /* End age is not in the model */
5042: } /* End if model includes a product */
1.136 brouard 5043: else { /* no more sum */
5044: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5045: /* scanf("%d",i);*/
1.145 ! brouard 5046: cutl(strd,strc,strb,'V');
! 5047: ks++; /**< Number of simple covariates */
! 5048: cptcovn++;
! 5049: Tvar[k]=atoi(strd);
1.136 brouard 5050: }
1.137 brouard 5051: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5052: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5053: scanf("%d",i);*/
5054: } /* end of loop + */
5055: } /* end model */
5056:
5057: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5058: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5059:
5060: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5061: printf("cptcovprod=%d ", cptcovprod);
5062: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5063:
5064: scanf("%d ",i);*/
5065:
5066:
1.137 brouard 5067: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.136 brouard 5068: endread:
5069: printf("Exiting decodemodel: ");
5070: return (1);
5071: }
5072:
5073: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5074: {
5075: int i, m;
5076:
5077: for (i=1; i<=imx; i++) {
5078: for(m=2; (m<= maxwav); m++) {
5079: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5080: anint[m][i]=9999;
5081: s[m][i]=-1;
5082: }
5083: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5084: *nberr++;
5085: 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);
5086: 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);
5087: s[m][i]=-1;
5088: }
5089: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5090: *nberr++;
5091: 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]);
5092: 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]);
5093: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5094: }
5095: }
5096: }
5097:
5098: for (i=1; i<=imx; i++) {
5099: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5100: for(m=firstpass; (m<= lastpass); m++){
5101: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5102: if (s[m][i] >= nlstate+1) {
5103: if(agedc[i]>0)
5104: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5105: agev[m][i]=agedc[i];
5106: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5107: else {
5108: if ((int)andc[i]!=9999){
5109: nbwarn++;
5110: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5111: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5112: agev[m][i]=-1;
5113: }
5114: }
5115: }
5116: else if(s[m][i] !=9){ /* Standard case, age in fractional
5117: years but with the precision of a month */
5118: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5119: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5120: agev[m][i]=1;
5121: else if(agev[m][i] < *agemin){
5122: *agemin=agev[m][i];
5123: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5124: }
5125: else if(agev[m][i] >*agemax){
5126: *agemax=agev[m][i];
1.139 brouard 5127: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
1.136 brouard 5128: }
5129: /*agev[m][i]=anint[m][i]-annais[i];*/
5130: /* agev[m][i] = age[i]+2*m;*/
5131: }
5132: else { /* =9 */
5133: agev[m][i]=1;
5134: s[m][i]=-1;
5135: }
5136: }
5137: else /*= 0 Unknown */
5138: agev[m][i]=1;
5139: }
5140:
5141: }
5142: for (i=1; i<=imx; i++) {
5143: for(m=firstpass; (m<=lastpass); m++){
5144: if (s[m][i] > (nlstate+ndeath)) {
5145: *nberr++;
5146: 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);
5147: 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);
5148: return 1;
5149: }
5150: }
5151: }
5152:
5153: /*for (i=1; i<=imx; i++){
5154: for (m=firstpass; (m<lastpass); m++){
5155: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5156: }
5157:
5158: }*/
5159:
5160:
1.139 brouard 5161: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5162: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5163:
5164: return (0);
5165: endread:
5166: printf("Exiting calandcheckages: ");
5167: return (1);
5168: }
5169:
5170:
5171: /***********************************************/
5172: /**************** Main Program *****************/
5173: /***********************************************/
5174:
5175: int main(int argc, char *argv[])
5176: {
5177: #ifdef GSL
5178: const gsl_multimin_fminimizer_type *T;
5179: size_t iteri = 0, it;
5180: int rval = GSL_CONTINUE;
5181: int status = GSL_SUCCESS;
5182: double ssval;
5183: #endif
5184: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5185: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5186: int linei, month, year,iout;
5187: int jj, ll, li, lj, lk, imk;
5188: int numlinepar=0; /* Current linenumber of parameter file */
5189: int itimes;
5190: int NDIM=2;
5191: int vpopbased=0;
5192:
5193: char ca[32], cb[32], cc[32];
5194: /* FILE *fichtm; *//* Html File */
5195: /* FILE *ficgp;*/ /*Gnuplot File */
5196: struct stat info;
5197: double agedeb, agefin,hf;
5198: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5199:
5200: double fret;
5201: double **xi,tmp,delta;
5202:
5203: double dum; /* Dummy variable */
5204: double ***p3mat;
5205: double ***mobaverage;
5206: int *indx;
5207: char line[MAXLINE], linepar[MAXLINE];
5208: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5209: char pathr[MAXLINE], pathimach[MAXLINE];
5210: char **bp, *tok, *val; /* pathtot */
5211: int firstobs=1, lastobs=10;
5212: int sdeb, sfin; /* Status at beginning and end */
5213: int c, h , cpt,l;
5214: int ju,jl, mi;
5215: int i1,j1, jk,aa,bb, stepsize, ij;
5216: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5217: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5218: int mobilav=0,popforecast=0;
5219: int hstepm, nhstepm;
5220: int agemortsup;
5221: float sumlpop=0.;
5222: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5223: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5224:
5225: double bage, fage, age, agelim, agebase;
5226: double ftolpl=FTOL;
5227: double **prlim;
5228: double ***param; /* Matrix of parameters */
5229: double *p;
5230: double **matcov; /* Matrix of covariance */
5231: double ***delti3; /* Scale */
5232: double *delti; /* Scale */
5233: double ***eij, ***vareij;
5234: double **varpl; /* Variances of prevalence limits by age */
5235: double *epj, vepp;
5236: double kk1, kk2;
5237: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5238: double **ximort;
1.145 ! brouard 5239: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5240: int *dcwave;
5241:
5242: char z[1]="c", occ;
5243:
5244: /*char *strt;*/
5245: char strtend[80];
1.126 brouard 5246:
5247: long total_usecs;
5248:
5249: /* setlocale (LC_ALL, ""); */
5250: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5251: /* textdomain (PACKAGE); */
5252: /* setlocale (LC_CTYPE, ""); */
5253: /* setlocale (LC_MESSAGES, ""); */
5254:
5255: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5256: (void) gettimeofday(&start_time,&tzp);
5257: curr_time=start_time;
5258: tm = *localtime(&start_time.tv_sec);
5259: tmg = *gmtime(&start_time.tv_sec);
5260: strcpy(strstart,asctime(&tm));
5261:
5262: /* printf("Localtime (at start)=%s",strstart); */
5263: /* tp.tv_sec = tp.tv_sec +86400; */
5264: /* tm = *localtime(&start_time.tv_sec); */
5265: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5266: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5267: /* tmg.tm_hour=tmg.tm_hour + 1; */
5268: /* tp.tv_sec = mktime(&tmg); */
5269: /* strt=asctime(&tmg); */
5270: /* printf("Time(after) =%s",strstart); */
5271: /* (void) time (&time_value);
5272: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5273: * tm = *localtime(&time_value);
5274: * strstart=asctime(&tm);
5275: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5276: */
5277:
5278: nberr=0; /* Number of errors and warnings */
5279: nbwarn=0;
5280: getcwd(pathcd, size);
5281:
5282: printf("\n%s\n%s",version,fullversion);
5283: if(argc <=1){
5284: printf("\nEnter the parameter file name: ");
5285: fgets(pathr,FILENAMELENGTH,stdin);
5286: i=strlen(pathr);
5287: if(pathr[i-1]=='\n')
5288: pathr[i-1]='\0';
5289: for (tok = pathr; tok != NULL; ){
5290: printf("Pathr |%s|\n",pathr);
5291: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5292: printf("val= |%s| pathr=%s\n",val,pathr);
5293: strcpy (pathtot, val);
5294: if(pathr[0] == '\0') break; /* Dirty */
5295: }
5296: }
5297: else{
5298: strcpy(pathtot,argv[1]);
5299: }
5300: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5301: /*cygwin_split_path(pathtot,path,optionfile);
5302: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5303: /* cutv(path,optionfile,pathtot,'\\');*/
5304:
5305: /* Split argv[0], imach program to get pathimach */
5306: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5307: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5308: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5309: /* strcpy(pathimach,argv[0]); */
5310: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5311: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5312: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5313: chdir(path); /* Can be a relative path */
5314: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5315: printf("Current directory %s!\n",pathcd);
5316: strcpy(command,"mkdir ");
5317: strcat(command,optionfilefiname);
5318: if((outcmd=system(command)) != 0){
5319: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5320: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5321: /* fclose(ficlog); */
5322: /* exit(1); */
5323: }
5324: /* if((imk=mkdir(optionfilefiname))<0){ */
5325: /* perror("mkdir"); */
5326: /* } */
5327:
5328: /*-------- arguments in the command line --------*/
5329:
5330: /* Log file */
5331: strcat(filelog, optionfilefiname);
5332: strcat(filelog,".log"); /* */
5333: if((ficlog=fopen(filelog,"w"))==NULL) {
5334: printf("Problem with logfile %s\n",filelog);
5335: goto end;
5336: }
5337: fprintf(ficlog,"Log filename:%s\n",filelog);
5338: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5339: fprintf(ficlog,"\nEnter the parameter file name: \n");
5340: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5341: path=%s \n\
5342: optionfile=%s\n\
5343: optionfilext=%s\n\
5344: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5345:
5346: printf("Local time (at start):%s",strstart);
5347: fprintf(ficlog,"Local time (at start): %s",strstart);
5348: fflush(ficlog);
5349: /* (void) gettimeofday(&curr_time,&tzp); */
5350: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5351:
5352: /* */
5353: strcpy(fileres,"r");
5354: strcat(fileres, optionfilefiname);
5355: strcat(fileres,".txt"); /* Other files have txt extension */
5356:
5357: /*---------arguments file --------*/
5358:
5359: if((ficpar=fopen(optionfile,"r"))==NULL) {
5360: printf("Problem with optionfile %s\n",optionfile);
5361: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5362: fflush(ficlog);
5363: goto end;
5364: }
5365:
5366:
5367:
5368: strcpy(filereso,"o");
5369: strcat(filereso,fileres);
5370: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5371: printf("Problem with Output resultfile: %s\n", filereso);
5372: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5373: fflush(ficlog);
5374: goto end;
5375: }
5376:
5377: /* Reads comments: lines beginning with '#' */
5378: numlinepar=0;
5379: while((c=getc(ficpar))=='#' && c!= EOF){
5380: ungetc(c,ficpar);
5381: fgets(line, MAXLINE, ficpar);
5382: numlinepar++;
1.141 brouard 5383: fputs(line,stdout);
1.126 brouard 5384: fputs(line,ficparo);
5385: fputs(line,ficlog);
5386: }
5387: ungetc(c,ficpar);
5388:
5389: 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);
5390: numlinepar++;
5391: 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);
5392: 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);
5393: 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);
5394: fflush(ficlog);
5395: while((c=getc(ficpar))=='#' && c!= EOF){
5396: ungetc(c,ficpar);
5397: fgets(line, MAXLINE, ficpar);
5398: numlinepar++;
1.141 brouard 5399: fputs(line, stdout);
5400: //puts(line);
1.126 brouard 5401: fputs(line,ficparo);
5402: fputs(line,ficlog);
5403: }
5404: ungetc(c,ficpar);
5405:
5406:
1.145 ! brouard 5407: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5408: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5409: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5410: v1+v2*age+v2*v3 makes cptcovn = 3
5411: */
5412: if (strlen(model)>1)
1.145 ! brouard 5413: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
! 5414: else
! 5415: ncovmodel=2;
1.126 brouard 5416: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5417: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5418: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5419: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5420: 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);
5421: 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);
5422: fflush(stdout);
5423: fclose (ficlog);
5424: goto end;
5425: }
1.126 brouard 5426: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5427: delti=delti3[1][1];
5428: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5429: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5430: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5431: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5432: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5433: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5434: fclose (ficparo);
5435: fclose (ficlog);
5436: goto end;
5437: exit(0);
5438: }
5439: else if(mle==-3) {
5440: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5441: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5442: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5443: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5444: matcov=matrix(1,npar,1,npar);
5445: }
5446: else{
1.145 ! brouard 5447: /* Read guessed parameters */
1.126 brouard 5448: /* Reads comments: lines beginning with '#' */
5449: while((c=getc(ficpar))=='#' && c!= EOF){
5450: ungetc(c,ficpar);
5451: fgets(line, MAXLINE, ficpar);
5452: numlinepar++;
1.141 brouard 5453: fputs(line,stdout);
1.126 brouard 5454: fputs(line,ficparo);
5455: fputs(line,ficlog);
5456: }
5457: ungetc(c,ficpar);
5458:
5459: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5460: for(i=1; i <=nlstate; i++){
5461: j=0;
5462: for(jj=1; jj <=nlstate+ndeath; jj++){
5463: if(jj==i) continue;
5464: j++;
5465: fscanf(ficpar,"%1d%1d",&i1,&j1);
5466: if ((i1 != i) && (j1 != j)){
5467: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5468: It might be a problem of design; if ncovcol and the model are correct\n \
5469: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5470: exit(1);
5471: }
5472: fprintf(ficparo,"%1d%1d",i1,j1);
5473: if(mle==1)
5474: printf("%1d%1d",i,j);
5475: fprintf(ficlog,"%1d%1d",i,j);
5476: for(k=1; k<=ncovmodel;k++){
5477: fscanf(ficpar," %lf",¶m[i][j][k]);
5478: if(mle==1){
5479: printf(" %lf",param[i][j][k]);
5480: fprintf(ficlog," %lf",param[i][j][k]);
5481: }
5482: else
5483: fprintf(ficlog," %lf",param[i][j][k]);
5484: fprintf(ficparo," %lf",param[i][j][k]);
5485: }
5486: fscanf(ficpar,"\n");
5487: numlinepar++;
5488: if(mle==1)
5489: printf("\n");
5490: fprintf(ficlog,"\n");
5491: fprintf(ficparo,"\n");
5492: }
5493: }
5494: fflush(ficlog);
5495:
1.145 ! brouard 5496: /* Reads scales values */
1.126 brouard 5497: p=param[1][1];
5498:
5499: /* Reads comments: lines beginning with '#' */
5500: while((c=getc(ficpar))=='#' && c!= EOF){
5501: ungetc(c,ficpar);
5502: fgets(line, MAXLINE, ficpar);
5503: numlinepar++;
1.141 brouard 5504: fputs(line,stdout);
1.126 brouard 5505: fputs(line,ficparo);
5506: fputs(line,ficlog);
5507: }
5508: ungetc(c,ficpar);
5509:
5510: for(i=1; i <=nlstate; i++){
5511: for(j=1; j <=nlstate+ndeath-1; j++){
5512: fscanf(ficpar,"%1d%1d",&i1,&j1);
5513: if ((i1-i)*(j1-j)!=0){
5514: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5515: exit(1);
5516: }
5517: printf("%1d%1d",i,j);
5518: fprintf(ficparo,"%1d%1d",i1,j1);
5519: fprintf(ficlog,"%1d%1d",i1,j1);
5520: for(k=1; k<=ncovmodel;k++){
5521: fscanf(ficpar,"%le",&delti3[i][j][k]);
5522: printf(" %le",delti3[i][j][k]);
5523: fprintf(ficparo," %le",delti3[i][j][k]);
5524: fprintf(ficlog," %le",delti3[i][j][k]);
5525: }
5526: fscanf(ficpar,"\n");
5527: numlinepar++;
5528: printf("\n");
5529: fprintf(ficparo,"\n");
5530: fprintf(ficlog,"\n");
5531: }
5532: }
5533: fflush(ficlog);
5534:
1.145 ! brouard 5535: /* Reads covariance matrix */
1.126 brouard 5536: delti=delti3[1][1];
5537:
5538:
5539: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5540:
5541: /* Reads comments: lines beginning with '#' */
5542: while((c=getc(ficpar))=='#' && c!= EOF){
5543: ungetc(c,ficpar);
5544: fgets(line, MAXLINE, ficpar);
5545: numlinepar++;
1.141 brouard 5546: fputs(line,stdout);
1.126 brouard 5547: fputs(line,ficparo);
5548: fputs(line,ficlog);
5549: }
5550: ungetc(c,ficpar);
5551:
5552: matcov=matrix(1,npar,1,npar);
1.131 brouard 5553: for(i=1; i <=npar; i++)
5554: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5555:
1.126 brouard 5556: for(i=1; i <=npar; i++){
1.145 ! brouard 5557: fscanf(ficpar,"%s",str);
1.126 brouard 5558: if(mle==1)
5559: printf("%s",str);
5560: fprintf(ficlog,"%s",str);
5561: fprintf(ficparo,"%s",str);
5562: for(j=1; j <=i; j++){
5563: fscanf(ficpar," %le",&matcov[i][j]);
5564: if(mle==1){
5565: printf(" %.5le",matcov[i][j]);
5566: }
5567: fprintf(ficlog," %.5le",matcov[i][j]);
5568: fprintf(ficparo," %.5le",matcov[i][j]);
5569: }
5570: fscanf(ficpar,"\n");
5571: numlinepar++;
5572: if(mle==1)
5573: printf("\n");
5574: fprintf(ficlog,"\n");
5575: fprintf(ficparo,"\n");
5576: }
5577: for(i=1; i <=npar; i++)
5578: for(j=i+1;j<=npar;j++)
5579: matcov[i][j]=matcov[j][i];
5580:
5581: if(mle==1)
5582: printf("\n");
5583: fprintf(ficlog,"\n");
5584:
5585: fflush(ficlog);
5586:
5587: /*-------- Rewriting parameter file ----------*/
5588: strcpy(rfileres,"r"); /* "Rparameterfile */
5589: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5590: strcat(rfileres,"."); /* */
5591: strcat(rfileres,optionfilext); /* Other files have txt extension */
5592: if((ficres =fopen(rfileres,"w"))==NULL) {
5593: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5594: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5595: }
5596: fprintf(ficres,"#%s\n",version);
5597: } /* End of mle != -3 */
5598:
5599:
5600: n= lastobs;
5601: num=lvector(1,n);
5602: moisnais=vector(1,n);
5603: annais=vector(1,n);
5604: moisdc=vector(1,n);
5605: andc=vector(1,n);
5606: agedc=vector(1,n);
5607: cod=ivector(1,n);
5608: weight=vector(1,n);
5609: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5610: mint=matrix(1,maxwav,1,n);
5611: anint=matrix(1,maxwav,1,n);
1.131 brouard 5612: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5613: tab=ivector(1,NCOVMAX);
1.144 brouard 5614: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5615:
1.136 brouard 5616: /* Reads data from file datafile */
5617: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5618: goto end;
5619:
5620: /* Calculation of the number of parameters from char model */
1.137 brouard 5621: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5622: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5623: k=3 V4 Tvar[k=3]= 4 (from V4)
5624: k=2 V1 Tvar[k=2]= 1 (from V1)
5625: k=1 Tvar[1]=2 (from V2)
5626: */
5627: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5628: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5629: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5630: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5631: */
5632: /* For model-covariate k tells which data-covariate to use but
5633: because this model-covariate is a construction we invent a new column
5634: ncovcol + k1
5635: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5636: Tvar[3=V1*V4]=4+1 etc */
1.145 ! brouard 5637: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 5638: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5639: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5640: */
1.145 ! brouard 5641: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
! 5642: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 5643: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5644: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 ! brouard 5645: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 5646: 4 covariates (3 plus signs)
5647: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5648: */
1.136 brouard 5649:
5650: if(decodemodel(model, lastobs) == 1)
5651: goto end;
5652:
1.137 brouard 5653: if((double)(lastobs-imx)/(double)imx > 1.10){
5654: nbwarn++;
5655: 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);
5656: 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);
5657: }
1.136 brouard 5658: /* if(mle==1){*/
1.137 brouard 5659: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5660: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 5661: }
5662:
5663: /*-calculation of age at interview from date of interview and age at death -*/
5664: agev=matrix(1,maxwav,1,imx);
5665:
5666: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5667: goto end;
5668:
1.126 brouard 5669:
1.136 brouard 5670: agegomp=(int)agemin;
5671: free_vector(moisnais,1,n);
5672: free_vector(annais,1,n);
1.126 brouard 5673: /* free_matrix(mint,1,maxwav,1,n);
5674: free_matrix(anint,1,maxwav,1,n);*/
5675: free_vector(moisdc,1,n);
5676: free_vector(andc,1,n);
1.145 ! brouard 5677: /* */
! 5678:
1.126 brouard 5679: wav=ivector(1,imx);
5680: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5681: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5682: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5683:
5684: /* Concatenates waves */
5685: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 ! brouard 5686: /* */
! 5687:
1.126 brouard 5688: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5689:
5690: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5691: ncodemax[1]=1;
1.145 ! brouard 5692: Ndum =ivector(-1,NCOVMAX);
! 5693: if (ncovmodel > 2)
! 5694: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
! 5695:
! 5696: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
! 5697: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
! 5698: h=0;
! 5699:
! 5700:
! 5701: /*if (cptcovn > 0) */
1.126 brouard 5702:
1.145 ! brouard 5703:
1.126 brouard 5704: m=pow(2,cptcoveff);
5705:
1.131 brouard 5706: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 5707: 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 */
5708: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5709: 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 5710: h++;
1.141 brouard 5711: if (h>m)
1.136 brouard 5712: h=1;
1.144 brouard 5713: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 5714: * h 1 2 3 4
5715: *______________________________
5716: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5717: * 2 2 1 1 1
5718: * 3 i=2 1 2 1 1
5719: * 4 2 2 1 1
5720: * 5 i=3 1 i=2 1 2 1
5721: * 6 2 1 2 1
5722: * 7 i=4 1 2 2 1
5723: * 8 2 2 2 1
5724: * 9 i=5 1 i=3 1 i=2 1 1
5725: * 10 2 1 1 1
5726: * 11 i=6 1 2 1 1
5727: * 12 2 2 1 1
5728: * 13 i=7 1 i=4 1 2 1
5729: * 14 2 1 2 1
5730: * 15 i=8 1 2 2 1
5731: * 16 2 2 2 1
5732: */
1.141 brouard 5733: codtab[h][k]=j;
1.145 ! brouard 5734: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 5735: 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 5736: }
5737: }
5738: }
5739: }
5740: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5741: codtab[1][2]=1;codtab[2][2]=2; */
5742: /* for(i=1; i <=m ;i++){
5743: for(k=1; k <=cptcovn; k++){
1.131 brouard 5744: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5745: }
5746: printf("\n");
5747: }
5748: scanf("%d",i);*/
1.145 ! brouard 5749:
! 5750: free_ivector(Ndum,-1,NCOVMAX);
! 5751:
! 5752:
1.126 brouard 5753:
5754: /*------------ gnuplot -------------*/
5755: strcpy(optionfilegnuplot,optionfilefiname);
5756: if(mle==-3)
5757: strcat(optionfilegnuplot,"-mort");
5758: strcat(optionfilegnuplot,".gp");
5759:
5760: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5761: printf("Problem with file %s",optionfilegnuplot);
5762: }
5763: else{
5764: fprintf(ficgp,"\n# %s\n", version);
5765: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 5766: //fprintf(ficgp,"set missing 'NaNq'\n");
5767: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 5768: }
5769: /* fclose(ficgp);*/
5770: /*--------- index.htm --------*/
5771:
5772: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5773: if(mle==-3)
5774: strcat(optionfilehtm,"-mort");
5775: strcat(optionfilehtm,".htm");
5776: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 5777: printf("Problem with %s \n",optionfilehtm);
5778: exit(0);
1.126 brouard 5779: }
5780:
5781: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5782: strcat(optionfilehtmcov,"-cov.htm");
5783: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5784: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5785: }
5786: else{
5787: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5788: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5789: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5790: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5791: }
5792:
5793: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5794: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5795: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5796: \n\
5797: <hr size=\"2\" color=\"#EC5E5E\">\
5798: <ul><li><h4>Parameter files</h4>\n\
5799: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5800: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5801: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5802: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5803: - Date and time at start: %s</ul>\n",\
5804: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5805: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5806: fileres,fileres,\
5807: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5808: fflush(fichtm);
5809:
5810: strcpy(pathr,path);
5811: strcat(pathr,optionfilefiname);
5812: chdir(optionfilefiname); /* Move to directory named optionfile */
5813:
5814: /* Calculates basic frequencies. Computes observed prevalence at single age
5815: and prints on file fileres'p'. */
5816: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5817:
5818: fprintf(fichtm,"\n");
5819: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5820: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5821: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5822: imx,agemin,agemax,jmin,jmax,jmean);
5823: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5824: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5825: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5826: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5827: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5828:
5829:
5830: /* For Powell, parameters are in a vector p[] starting at p[1]
5831: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5832: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5833:
5834: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5835:
5836: if (mle==-3){
1.136 brouard 5837: ximort=matrix(1,NDIM,1,NDIM);
5838: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 5839: cens=ivector(1,n);
5840: ageexmed=vector(1,n);
5841: agecens=vector(1,n);
5842: dcwave=ivector(1,n);
5843:
5844: for (i=1; i<=imx; i++){
5845: dcwave[i]=-1;
5846: for (m=firstpass; m<=lastpass; m++)
5847: if (s[m][i]>nlstate) {
5848: dcwave[i]=m;
5849: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5850: break;
5851: }
5852: }
5853:
5854: for (i=1; i<=imx; i++) {
5855: if (wav[i]>0){
5856: ageexmed[i]=agev[mw[1][i]][i];
5857: j=wav[i];
5858: agecens[i]=1.;
5859:
5860: if (ageexmed[i]> 1 && wav[i] > 0){
5861: agecens[i]=agev[mw[j][i]][i];
5862: cens[i]= 1;
5863: }else if (ageexmed[i]< 1)
5864: cens[i]= -1;
5865: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5866: cens[i]=0 ;
5867: }
5868: else cens[i]=-1;
5869: }
5870:
5871: for (i=1;i<=NDIM;i++) {
5872: for (j=1;j<=NDIM;j++)
5873: ximort[i][j]=(i == j ? 1.0 : 0.0);
5874: }
5875:
1.145 ! brouard 5876: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 5877: /*printf("%lf %lf", p[1], p[2]);*/
5878:
5879:
1.136 brouard 5880: #ifdef GSL
5881: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5882: #elsedef
1.126 brouard 5883: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 5884: #endif
1.126 brouard 5885: strcpy(filerespow,"pow-mort");
5886: strcat(filerespow,fileres);
5887: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5888: printf("Problem with resultfile: %s\n", filerespow);
5889: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5890: }
1.136 brouard 5891: #ifdef GSL
5892: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5893: #elsedef
1.126 brouard 5894: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 5895: #endif
1.126 brouard 5896: /* for (i=1;i<=nlstate;i++)
5897: for(j=1;j<=nlstate+ndeath;j++)
5898: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5899: */
5900: fprintf(ficrespow,"\n");
1.136 brouard 5901: #ifdef GSL
5902: /* gsl starts here */
5903: T = gsl_multimin_fminimizer_nmsimplex;
5904: gsl_multimin_fminimizer *sfm = NULL;
5905: gsl_vector *ss, *x;
5906: gsl_multimin_function minex_func;
5907:
5908: /* Initial vertex size vector */
5909: ss = gsl_vector_alloc (NDIM);
5910:
5911: if (ss == NULL){
5912: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5913: }
5914: /* Set all step sizes to 1 */
5915: gsl_vector_set_all (ss, 0.001);
5916:
5917: /* Starting point */
1.126 brouard 5918:
1.136 brouard 5919: x = gsl_vector_alloc (NDIM);
5920:
5921: if (x == NULL){
5922: gsl_vector_free(ss);
5923: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5924: }
5925:
5926: /* Initialize method and iterate */
5927: /* p[1]=0.0268; p[NDIM]=0.083; */
5928: /* gsl_vector_set(x, 0, 0.0268); */
5929: /* gsl_vector_set(x, 1, 0.083); */
5930: gsl_vector_set(x, 0, p[1]);
5931: gsl_vector_set(x, 1, p[2]);
5932:
5933: minex_func.f = &gompertz_f;
5934: minex_func.n = NDIM;
5935: minex_func.params = (void *)&p; /* ??? */
5936:
5937: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5938: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5939:
5940: printf("Iterations beginning .....\n\n");
5941: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5942:
5943: iteri=0;
5944: while (rval == GSL_CONTINUE){
5945: iteri++;
5946: status = gsl_multimin_fminimizer_iterate(sfm);
5947:
5948: if (status) printf("error: %s\n", gsl_strerror (status));
5949: fflush(0);
5950:
5951: if (status)
5952: break;
5953:
5954: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5955: ssval = gsl_multimin_fminimizer_size (sfm);
5956:
5957: if (rval == GSL_SUCCESS)
5958: printf ("converged to a local maximum at\n");
5959:
5960: printf("%5d ", iteri);
5961: for (it = 0; it < NDIM; it++){
5962: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
5963: }
5964: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
5965: }
5966:
5967: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
5968:
5969: gsl_vector_free(x); /* initial values */
5970: gsl_vector_free(ss); /* inital step size */
5971: for (it=0; it<NDIM; it++){
5972: p[it+1]=gsl_vector_get(sfm->x,it);
5973: fprintf(ficrespow," %.12lf", p[it]);
5974: }
5975: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
5976: #endif
5977: #ifdef POWELL
5978: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5979: #endif
1.126 brouard 5980: fclose(ficrespow);
5981:
5982: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5983:
5984: for(i=1; i <=NDIM; i++)
5985: for(j=i+1;j<=NDIM;j++)
5986: matcov[i][j]=matcov[j][i];
5987:
5988: printf("\nCovariance matrix\n ");
5989: for(i=1; i <=NDIM; i++) {
5990: for(j=1;j<=NDIM;j++){
5991: printf("%f ",matcov[i][j]);
5992: }
5993: printf("\n ");
5994: }
5995:
5996: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5997: for (i=1;i<=NDIM;i++)
5998: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5999:
6000: lsurv=vector(1,AGESUP);
6001: lpop=vector(1,AGESUP);
6002: tpop=vector(1,AGESUP);
6003: lsurv[agegomp]=100000;
6004:
6005: for (k=agegomp;k<=AGESUP;k++) {
6006: agemortsup=k;
6007: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6008: }
6009:
6010: for (k=agegomp;k<agemortsup;k++)
6011: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6012:
6013: for (k=agegomp;k<agemortsup;k++){
6014: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6015: sumlpop=sumlpop+lpop[k];
6016: }
6017:
6018: tpop[agegomp]=sumlpop;
6019: for (k=agegomp;k<(agemortsup-3);k++){
6020: /* tpop[k+1]=2;*/
6021: tpop[k+1]=tpop[k]-lpop[k];
6022: }
6023:
6024:
6025: printf("\nAge lx qx dx Lx Tx e(x)\n");
6026: for (k=agegomp;k<(agemortsup-2);k++)
6027: 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]);
6028:
6029:
6030: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6031: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6032:
6033: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6034: stepm, weightopt,\
6035: model,imx,p,matcov,agemortsup);
6036:
6037: free_vector(lsurv,1,AGESUP);
6038: free_vector(lpop,1,AGESUP);
6039: free_vector(tpop,1,AGESUP);
1.136 brouard 6040: #ifdef GSL
6041: free_ivector(cens,1,n);
6042: free_vector(agecens,1,n);
6043: free_ivector(dcwave,1,n);
6044: free_matrix(ximort,1,NDIM,1,NDIM);
6045: #endif
1.126 brouard 6046: } /* Endof if mle==-3 */
6047:
6048: else{ /* For mle >=1 */
1.132 brouard 6049: globpr=0;/* debug */
6050: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6051: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6052: for (k=1; k<=npar;k++)
6053: printf(" %d %8.5f",k,p[k]);
6054: printf("\n");
6055: globpr=1; /* to print the contributions */
6056: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6057: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6058: for (k=1; k<=npar;k++)
6059: printf(" %d %8.5f",k,p[k]);
6060: printf("\n");
6061: if(mle>=1){ /* Could be 1 or 2 */
6062: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6063: }
6064:
6065: /*--------- results files --------------*/
6066: 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);
6067:
6068:
6069: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6070: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6071: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6072: for(i=1,jk=1; i <=nlstate; i++){
6073: for(k=1; k <=(nlstate+ndeath); k++){
6074: if (k != i) {
6075: printf("%d%d ",i,k);
6076: fprintf(ficlog,"%d%d ",i,k);
6077: fprintf(ficres,"%1d%1d ",i,k);
6078: for(j=1; j <=ncovmodel; j++){
6079: printf("%lf ",p[jk]);
6080: fprintf(ficlog,"%lf ",p[jk]);
6081: fprintf(ficres,"%lf ",p[jk]);
6082: jk++;
6083: }
6084: printf("\n");
6085: fprintf(ficlog,"\n");
6086: fprintf(ficres,"\n");
6087: }
6088: }
6089: }
6090: if(mle!=0){
6091: /* Computing hessian and covariance matrix */
6092: ftolhess=ftol; /* Usually correct */
6093: hesscov(matcov, p, npar, delti, ftolhess, func);
6094: }
6095: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6096: printf("# Scales (for hessian or gradient estimation)\n");
6097: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6098: for(i=1,jk=1; i <=nlstate; i++){
6099: for(j=1; j <=nlstate+ndeath; j++){
6100: if (j!=i) {
6101: fprintf(ficres,"%1d%1d",i,j);
6102: printf("%1d%1d",i,j);
6103: fprintf(ficlog,"%1d%1d",i,j);
6104: for(k=1; k<=ncovmodel;k++){
6105: printf(" %.5e",delti[jk]);
6106: fprintf(ficlog," %.5e",delti[jk]);
6107: fprintf(ficres," %.5e",delti[jk]);
6108: jk++;
6109: }
6110: printf("\n");
6111: fprintf(ficlog,"\n");
6112: fprintf(ficres,"\n");
6113: }
6114: }
6115: }
6116:
6117: 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");
6118: if(mle>=1)
6119: 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");
6120: 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");
6121: /* # 121 Var(a12)\n\ */
6122: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6123: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6124: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6125: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6126: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6127: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6128: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6129:
6130:
6131: /* Just to have a covariance matrix which will be more understandable
6132: even is we still don't want to manage dictionary of variables
6133: */
6134: for(itimes=1;itimes<=2;itimes++){
6135: jj=0;
6136: for(i=1; i <=nlstate; i++){
6137: for(j=1; j <=nlstate+ndeath; j++){
6138: if(j==i) continue;
6139: for(k=1; k<=ncovmodel;k++){
6140: jj++;
6141: ca[0]= k+'a'-1;ca[1]='\0';
6142: if(itimes==1){
6143: if(mle>=1)
6144: printf("#%1d%1d%d",i,j,k);
6145: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6146: fprintf(ficres,"#%1d%1d%d",i,j,k);
6147: }else{
6148: if(mle>=1)
6149: printf("%1d%1d%d",i,j,k);
6150: fprintf(ficlog,"%1d%1d%d",i,j,k);
6151: fprintf(ficres,"%1d%1d%d",i,j,k);
6152: }
6153: ll=0;
6154: for(li=1;li <=nlstate; li++){
6155: for(lj=1;lj <=nlstate+ndeath; lj++){
6156: if(lj==li) continue;
6157: for(lk=1;lk<=ncovmodel;lk++){
6158: ll++;
6159: if(ll<=jj){
6160: cb[0]= lk +'a'-1;cb[1]='\0';
6161: if(ll<jj){
6162: if(itimes==1){
6163: if(mle>=1)
6164: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6165: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6166: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6167: }else{
6168: if(mle>=1)
6169: printf(" %.5e",matcov[jj][ll]);
6170: fprintf(ficlog," %.5e",matcov[jj][ll]);
6171: fprintf(ficres," %.5e",matcov[jj][ll]);
6172: }
6173: }else{
6174: if(itimes==1){
6175: if(mle>=1)
6176: printf(" Var(%s%1d%1d)",ca,i,j);
6177: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6178: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6179: }else{
6180: if(mle>=1)
6181: printf(" %.5e",matcov[jj][ll]);
6182: fprintf(ficlog," %.5e",matcov[jj][ll]);
6183: fprintf(ficres," %.5e",matcov[jj][ll]);
6184: }
6185: }
6186: }
6187: } /* end lk */
6188: } /* end lj */
6189: } /* end li */
6190: if(mle>=1)
6191: printf("\n");
6192: fprintf(ficlog,"\n");
6193: fprintf(ficres,"\n");
6194: numlinepar++;
6195: } /* end k*/
6196: } /*end j */
6197: } /* end i */
6198: } /* end itimes */
6199:
6200: fflush(ficlog);
6201: fflush(ficres);
6202:
6203: while((c=getc(ficpar))=='#' && c!= EOF){
6204: ungetc(c,ficpar);
6205: fgets(line, MAXLINE, ficpar);
1.141 brouard 6206: fputs(line,stdout);
1.126 brouard 6207: fputs(line,ficparo);
6208: }
6209: ungetc(c,ficpar);
6210:
6211: estepm=0;
6212: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6213: if (estepm==0 || estepm < stepm) estepm=stepm;
6214: if (fage <= 2) {
6215: bage = ageminpar;
6216: fage = agemaxpar;
6217: }
6218:
6219: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6220: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6221: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6222:
6223: while((c=getc(ficpar))=='#' && c!= EOF){
6224: ungetc(c,ficpar);
6225: fgets(line, MAXLINE, ficpar);
1.141 brouard 6226: fputs(line,stdout);
1.126 brouard 6227: fputs(line,ficparo);
6228: }
6229: ungetc(c,ficpar);
6230:
6231: 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);
6232: 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);
6233: 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);
6234: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6235: 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);
6236:
6237: while((c=getc(ficpar))=='#' && c!= EOF){
6238: ungetc(c,ficpar);
6239: fgets(line, MAXLINE, ficpar);
1.141 brouard 6240: fputs(line,stdout);
1.126 brouard 6241: fputs(line,ficparo);
6242: }
6243: ungetc(c,ficpar);
6244:
6245:
6246: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6247: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6248:
6249: fscanf(ficpar,"pop_based=%d\n",&popbased);
6250: fprintf(ficparo,"pop_based=%d\n",popbased);
6251: fprintf(ficres,"pop_based=%d\n",popbased);
6252:
6253: while((c=getc(ficpar))=='#' && c!= EOF){
6254: ungetc(c,ficpar);
6255: fgets(line, MAXLINE, ficpar);
1.141 brouard 6256: fputs(line,stdout);
1.126 brouard 6257: fputs(line,ficparo);
6258: }
6259: ungetc(c,ficpar);
6260:
6261: 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);
6262: 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);
6263: 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);
6264: 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);
6265: 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);
6266: /* day and month of proj2 are not used but only year anproj2.*/
6267:
6268:
6269:
1.145 ! brouard 6270: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
! 6271: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6272:
6273: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6274: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6275:
6276: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6277: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6278: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6279:
6280: /*------------ free_vector -------------*/
6281: /* chdir(path); */
6282:
6283: free_ivector(wav,1,imx);
6284: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6285: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6286: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6287: free_lvector(num,1,n);
6288: free_vector(agedc,1,n);
6289: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6290: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6291: fclose(ficparo);
6292: fclose(ficres);
6293:
6294:
6295: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 ! brouard 6296: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6297: fclose(ficrespl);
6298:
1.145 ! brouard 6299: #ifdef FREEEXIT2
! 6300: #include "freeexit2.h"
! 6301: #endif
! 6302:
1.126 brouard 6303: /*------------- h Pij x at various ages ------------*/
1.145 ! brouard 6304: #include "hpijx.h"
! 6305: fclose(ficrespij);
1.126 brouard 6306:
1.145 ! brouard 6307: /*-------------- Variance of one-step probabilities---*/
! 6308: k=1;
1.126 brouard 6309: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6310:
6311:
6312: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6313: for(i=1;i<=AGESUP;i++)
6314: for(j=1;j<=NCOVMAX;j++)
6315: for(k=1;k<=NCOVMAX;k++)
6316: probs[i][j][k]=0.;
6317:
6318: /*---------- Forecasting ------------------*/
6319: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6320: if(prevfcast==1){
6321: /* if(stepm ==1){*/
6322: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6323: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6324: /* } */
6325: /* else{ */
6326: /* erreur=108; */
6327: /* 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); */
6328: /* 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); */
6329: /* } */
6330: }
6331:
6332:
1.127 brouard 6333: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6334:
6335: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6336: /* 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",\
6337: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6338: */
1.126 brouard 6339:
1.127 brouard 6340: if (mobilav!=0) {
6341: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6342: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6343: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6344: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6345: }
1.126 brouard 6346: }
6347:
6348:
1.127 brouard 6349: /*---------- Health expectancies, no variances ------------*/
6350:
1.126 brouard 6351: strcpy(filerese,"e");
6352: strcat(filerese,fileres);
6353: if((ficreseij=fopen(filerese,"w"))==NULL) {
6354: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6355: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6356: }
6357: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6358: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 ! brouard 6359: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6360: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6361:
! 6362: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6363: fprintf(ficreseij,"\n#****** ");
6364: for(j=1;j<=cptcoveff;j++) {
6365: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6366: }
6367: fprintf(ficreseij,"******\n");
6368:
6369: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6370: oldm=oldms;savm=savms;
6371: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6372:
6373: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 ! brouard 6374: /*}*/
1.127 brouard 6375: }
6376: fclose(ficreseij);
6377:
6378:
6379: /*---------- Health expectancies and variances ------------*/
6380:
6381:
6382: strcpy(filerest,"t");
6383: strcat(filerest,fileres);
6384: if((ficrest=fopen(filerest,"w"))==NULL) {
6385: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6386: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6387: }
6388: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6389: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6390:
1.126 brouard 6391:
6392: strcpy(fileresstde,"stde");
6393: strcat(fileresstde,fileres);
6394: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6395: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6396: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6397: }
6398: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6399: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6400:
6401: strcpy(filerescve,"cve");
6402: strcat(filerescve,fileres);
6403: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6404: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6405: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6406: }
6407: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6408: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6409:
6410: strcpy(fileresv,"v");
6411: strcat(fileresv,fileres);
6412: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6413: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6414: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6415: }
6416: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6417: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6418:
1.145 ! brouard 6419: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6420: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6421:
! 6422: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 6423: fprintf(ficrest,"\n#****** ");
1.126 brouard 6424: for(j=1;j<=cptcoveff;j++)
6425: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6426: fprintf(ficrest,"******\n");
6427:
6428: fprintf(ficresstdeij,"\n#****** ");
6429: fprintf(ficrescveij,"\n#****** ");
6430: for(j=1;j<=cptcoveff;j++) {
6431: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6432: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6433: }
6434: fprintf(ficresstdeij,"******\n");
6435: fprintf(ficrescveij,"******\n");
6436:
6437: fprintf(ficresvij,"\n#****** ");
6438: for(j=1;j<=cptcoveff;j++)
6439: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6440: fprintf(ficresvij,"******\n");
6441:
6442: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6443: oldm=oldms;savm=savms;
1.127 brouard 6444: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 ! brouard 6445: /*
! 6446: */
! 6447: /* goto endfree; */
1.126 brouard 6448:
6449: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6450: pstamp(ficrest);
1.145 ! brouard 6451:
! 6452:
1.128 brouard 6453: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 ! brouard 6454: oldm=oldms;savm=savms; /* Segmentation fault */
! 6455: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
! 6456: 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 ");
1.128 brouard 6457: if(vpopbased==1)
6458: 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);
6459: else
6460: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6461: fprintf(ficrest,"# Age e.. (std) ");
6462: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6463: fprintf(ficrest,"\n");
1.126 brouard 6464:
1.128 brouard 6465: epj=vector(1,nlstate+1);
6466: for(age=bage; age <=fage ;age++){
6467: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6468: if (vpopbased==1) {
6469: if(mobilav ==0){
6470: for(i=1; i<=nlstate;i++)
6471: prlim[i][i]=probs[(int)age][i][k];
6472: }else{ /* mobilav */
6473: for(i=1; i<=nlstate;i++)
6474: prlim[i][i]=mobaverage[(int)age][i][k];
6475: }
1.126 brouard 6476: }
6477:
1.128 brouard 6478: fprintf(ficrest," %4.0f",age);
6479: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6480: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6481: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6482: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6483: }
6484: epj[nlstate+1] +=epj[j];
1.126 brouard 6485: }
6486:
1.128 brouard 6487: for(i=1, vepp=0.;i <=nlstate;i++)
6488: for(j=1;j <=nlstate;j++)
6489: vepp += vareij[i][j][(int)age];
6490: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6491: for(j=1;j <=nlstate;j++){
6492: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6493: }
6494: fprintf(ficrest,"\n");
1.126 brouard 6495: }
6496: }
6497: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6498: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6499: free_vector(epj,1,nlstate+1);
1.145 ! brouard 6500: /*}*/
1.126 brouard 6501: }
6502: free_vector(weight,1,n);
1.145 ! brouard 6503: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6504: free_imatrix(s,1,maxwav+1,1,n);
6505: free_matrix(anint,1,maxwav,1,n);
6506: free_matrix(mint,1,maxwav,1,n);
6507: free_ivector(cod,1,n);
6508: free_ivector(tab,1,NCOVMAX);
6509: fclose(ficresstdeij);
6510: fclose(ficrescveij);
6511: fclose(ficresvij);
6512: fclose(ficrest);
6513: fclose(ficpar);
6514:
6515: /*------- Variance of period (stable) prevalence------*/
6516:
6517: strcpy(fileresvpl,"vpl");
6518: strcat(fileresvpl,fileres);
6519: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6520: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6521: exit(0);
6522: }
6523: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6524:
1.145 ! brouard 6525: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
! 6526: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
! 6527:
! 6528: for (k=1; k <= (int) pow(2,cptcoveff); k++){
! 6529: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6530: for(j=1;j<=cptcoveff;j++)
6531: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6532: fprintf(ficresvpl,"******\n");
6533:
6534: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6535: oldm=oldms;savm=savms;
6536: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6537: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 ! brouard 6538: /*}*/
1.126 brouard 6539: }
6540:
6541: fclose(ficresvpl);
6542:
6543: /*---------- End : free ----------------*/
6544: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6545: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6546: } /* mle==-3 arrives here for freeing */
1.131 brouard 6547: endfree:
1.141 brouard 6548: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6549: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6550: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6551: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6552: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6553: free_matrix(covar,0,NCOVMAX,1,n);
6554: free_matrix(matcov,1,npar,1,npar);
6555: /*free_vector(delti,1,npar);*/
6556: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6557: free_matrix(agev,1,maxwav,1,imx);
6558: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6559:
1.145 ! brouard 6560: free_ivector(ncodemax,1,NCOVMAX);
! 6561: free_ivector(Tvar,1,NCOVMAX);
! 6562: free_ivector(Tprod,1,NCOVMAX);
! 6563: free_ivector(Tvaraff,1,NCOVMAX);
! 6564: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 6565:
6566: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6567: free_imatrix(codtab,1,100,1,10);
6568: fflush(fichtm);
6569: fflush(ficgp);
6570:
6571:
6572: if((nberr >0) || (nbwarn>0)){
6573: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6574: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6575: }else{
6576: printf("End of Imach\n");
6577: fprintf(ficlog,"End of Imach\n");
6578: }
6579: printf("See log file on %s\n",filelog);
6580: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6581: (void) gettimeofday(&end_time,&tzp);
6582: tm = *localtime(&end_time.tv_sec);
6583: tmg = *gmtime(&end_time.tv_sec);
6584: strcpy(strtend,asctime(&tm));
6585: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6586: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6587: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6588:
1.141 brouard 6589: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6590: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.141 brouard 6591: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6592: /* printf("Total time was %d uSec.\n", total_usecs);*/
6593: /* if(fileappend(fichtm,optionfilehtm)){ */
6594: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6595: fclose(fichtm);
6596: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6597: fclose(fichtmcov);
6598: fclose(ficgp);
6599: fclose(ficlog);
6600: /*------ End -----------*/
6601:
6602:
6603: printf("Before Current directory %s!\n",pathcd);
6604: if(chdir(pathcd) != 0)
6605: printf("Can't move to directory %s!\n",path);
6606: if(getcwd(pathcd,MAXLINE) > 0)
6607: printf("Current directory %s!\n",pathcd);
6608: /*strcat(plotcmd,CHARSEPARATOR);*/
6609: sprintf(plotcmd,"gnuplot");
6610: #ifndef UNIX
6611: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6612: #endif
6613: if(!stat(plotcmd,&info)){
6614: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6615: if(!stat(getenv("GNUPLOTBIN"),&info)){
6616: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6617: }else
6618: strcpy(pplotcmd,plotcmd);
6619: #ifdef UNIX
6620: strcpy(plotcmd,GNUPLOTPROGRAM);
6621: if(!stat(plotcmd,&info)){
6622: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6623: }else
6624: strcpy(pplotcmd,plotcmd);
6625: #endif
6626: }else
6627: strcpy(pplotcmd,plotcmd);
6628:
6629: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6630: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6631:
6632: if((outcmd=system(plotcmd)) != 0){
6633: printf("\n Problem with gnuplot\n");
6634: }
6635: printf(" Wait...");
6636: while (z[0] != 'q') {
6637: /* chdir(path); */
6638: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6639: scanf("%s",z);
6640: /* if (z[0] == 'c') system("./imach"); */
6641: if (z[0] == 'e') {
6642: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6643: system(optionfilehtm);
6644: }
6645: else if (z[0] == 'g') system(plotcmd);
6646: else if (z[0] == 'q') exit(0);
6647: }
6648: end:
6649: while (z[0] != 'q') {
6650: printf("\nType q for exiting: ");
6651: scanf("%s",z);
6652: }
6653: }
6654:
6655:
6656:
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