1: /* $Id: imach.c,v 1.160 2014/09/02 09:24:05 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.160 2014/09/02 09:24:05 brouard
5: *** empty log message ***
6:
7: Revision 1.159 2014/09/01 10:34:10 brouard
8: Summary: WIN32
9: Author: Brouard
10:
11: Revision 1.158 2014/08/27 17:11:51 brouard
12: *** empty log message ***
13:
14: Revision 1.157 2014/08/27 16:26:55 brouard
15: Summary: Preparing windows Visual studio version
16: Author: Brouard
17:
18: In order to compile on Visual studio, time.h is now correct and time_t
19: and tm struct should be used. difftime should be used but sometimes I
20: just make the differences in raw time format (time(&now).
21: Trying to suppress #ifdef LINUX
22: Add xdg-open for __linux in order to open default browser.
23:
24: Revision 1.156 2014/08/25 20:10:10 brouard
25: *** empty log message ***
26:
27: Revision 1.155 2014/08/25 18:32:34 brouard
28: Summary: New compile, minor changes
29: Author: Brouard
30:
31: Revision 1.154 2014/06/20 17:32:08 brouard
32: Summary: Outputs now all graphs of convergence to period prevalence
33:
34: Revision 1.153 2014/06/20 16:45:46 brouard
35: Summary: If 3 live state, convergence to period prevalence on same graph
36: Author: Brouard
37:
38: Revision 1.152 2014/06/18 17:54:09 brouard
39: Summary: open browser, use gnuplot on same dir than imach if not found in the path
40:
41: Revision 1.151 2014/06/18 16:43:30 brouard
42: *** empty log message ***
43:
44: Revision 1.150 2014/06/18 16:42:35 brouard
45: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
46: Author: brouard
47:
48: Revision 1.149 2014/06/18 15:51:14 brouard
49: Summary: Some fixes in parameter files errors
50: Author: Nicolas Brouard
51:
52: Revision 1.148 2014/06/17 17:38:48 brouard
53: Summary: Nothing new
54: Author: Brouard
55:
56: Just a new packaging for OS/X version 0.98nS
57:
58: Revision 1.147 2014/06/16 10:33:11 brouard
59: *** empty log message ***
60:
61: Revision 1.146 2014/06/16 10:20:28 brouard
62: Summary: Merge
63: Author: Brouard
64:
65: Merge, before building revised version.
66:
67: Revision 1.145 2014/06/10 21:23:15 brouard
68: Summary: Debugging with valgrind
69: Author: Nicolas Brouard
70:
71: Lot of changes in order to output the results with some covariates
72: After the Edimburgh REVES conference 2014, it seems mandatory to
73: improve the code.
74: No more memory valgrind error but a lot has to be done in order to
75: continue the work of splitting the code into subroutines.
76: Also, decodemodel has been improved. Tricode is still not
77: optimal. nbcode should be improved. Documentation has been added in
78: the source code.
79:
80: Revision 1.143 2014/01/26 09:45:38 brouard
81: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
82:
83: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
84: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
85:
86: Revision 1.142 2014/01/26 03:57:36 brouard
87: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
88:
89: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
90:
91: Revision 1.141 2014/01/26 02:42:01 brouard
92: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
93:
94: Revision 1.140 2011/09/02 10:37:54 brouard
95: Summary: times.h is ok with mingw32 now.
96:
97: Revision 1.139 2010/06/14 07:50:17 brouard
98: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
99: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
100:
101: Revision 1.138 2010/04/30 18:19:40 brouard
102: *** empty log message ***
103:
104: Revision 1.137 2010/04/29 18:11:38 brouard
105: (Module): Checking covariates for more complex models
106: than V1+V2. A lot of change to be done. Unstable.
107:
108: Revision 1.136 2010/04/26 20:30:53 brouard
109: (Module): merging some libgsl code. Fixing computation
110: of likelione (using inter/intrapolation if mle = 0) in order to
111: get same likelihood as if mle=1.
112: Some cleaning of code and comments added.
113:
114: Revision 1.135 2009/10/29 15:33:14 brouard
115: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
116:
117: Revision 1.134 2009/10/29 13:18:53 brouard
118: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
119:
120: Revision 1.133 2009/07/06 10:21:25 brouard
121: just nforces
122:
123: Revision 1.132 2009/07/06 08:22:05 brouard
124: Many tings
125:
126: Revision 1.131 2009/06/20 16:22:47 brouard
127: Some dimensions resccaled
128:
129: Revision 1.130 2009/05/26 06:44:34 brouard
130: (Module): Max Covariate is now set to 20 instead of 8. A
131: lot of cleaning with variables initialized to 0. Trying to make
132: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
133:
134: Revision 1.129 2007/08/31 13:49:27 lievre
135: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
136:
137: Revision 1.128 2006/06/30 13:02:05 brouard
138: (Module): Clarifications on computing e.j
139:
140: Revision 1.127 2006/04/28 18:11:50 brouard
141: (Module): Yes the sum of survivors was wrong since
142: imach-114 because nhstepm was no more computed in the age
143: loop. Now we define nhstepma in the age loop.
144: (Module): In order to speed up (in case of numerous covariates) we
145: compute health expectancies (without variances) in a first step
146: and then all the health expectancies with variances or standard
147: deviation (needs data from the Hessian matrices) which slows the
148: computation.
149: In the future we should be able to stop the program is only health
150: expectancies and graph are needed without standard deviations.
151:
152: Revision 1.126 2006/04/28 17:23:28 brouard
153: (Module): Yes the sum of survivors was wrong since
154: imach-114 because nhstepm was no more computed in the age
155: loop. Now we define nhstepma in the age loop.
156: Version 0.98h
157:
158: Revision 1.125 2006/04/04 15:20:31 lievre
159: Errors in calculation of health expectancies. Age was not initialized.
160: Forecasting file added.
161:
162: Revision 1.124 2006/03/22 17:13:53 lievre
163: Parameters are printed with %lf instead of %f (more numbers after the comma).
164: The log-likelihood is printed in the log file
165:
166: Revision 1.123 2006/03/20 10:52:43 brouard
167: * imach.c (Module): <title> changed, corresponds to .htm file
168: name. <head> headers where missing.
169:
170: * imach.c (Module): Weights can have a decimal point as for
171: English (a comma might work with a correct LC_NUMERIC environment,
172: otherwise the weight is truncated).
173: Modification of warning when the covariates values are not 0 or
174: 1.
175: Version 0.98g
176:
177: Revision 1.122 2006/03/20 09:45:41 brouard
178: (Module): Weights can have a decimal point as for
179: English (a comma might work with a correct LC_NUMERIC environment,
180: otherwise the weight is truncated).
181: Modification of warning when the covariates values are not 0 or
182: 1.
183: Version 0.98g
184:
185: Revision 1.121 2006/03/16 17:45:01 lievre
186: * imach.c (Module): Comments concerning covariates added
187:
188: * imach.c (Module): refinements in the computation of lli if
189: status=-2 in order to have more reliable computation if stepm is
190: not 1 month. Version 0.98f
191:
192: Revision 1.120 2006/03/16 15:10:38 lievre
193: (Module): refinements in the computation of lli if
194: status=-2 in order to have more reliable computation if stepm is
195: not 1 month. Version 0.98f
196:
197: Revision 1.119 2006/03/15 17:42:26 brouard
198: (Module): Bug if status = -2, the loglikelihood was
199: computed as likelihood omitting the logarithm. Version O.98e
200:
201: Revision 1.118 2006/03/14 18:20:07 brouard
202: (Module): varevsij Comments added explaining the second
203: table of variances if popbased=1 .
204: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
205: (Module): Function pstamp added
206: (Module): Version 0.98d
207:
208: Revision 1.117 2006/03/14 17:16:22 brouard
209: (Module): varevsij Comments added explaining the second
210: table of variances if popbased=1 .
211: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
212: (Module): Function pstamp added
213: (Module): Version 0.98d
214:
215: Revision 1.116 2006/03/06 10:29:27 brouard
216: (Module): Variance-covariance wrong links and
217: varian-covariance of ej. is needed (Saito).
218:
219: Revision 1.115 2006/02/27 12:17:45 brouard
220: (Module): One freematrix added in mlikeli! 0.98c
221:
222: Revision 1.114 2006/02/26 12:57:58 brouard
223: (Module): Some improvements in processing parameter
224: filename with strsep.
225:
226: Revision 1.113 2006/02/24 14:20:24 brouard
227: (Module): Memory leaks checks with valgrind and:
228: datafile was not closed, some imatrix were not freed and on matrix
229: allocation too.
230:
231: Revision 1.112 2006/01/30 09:55:26 brouard
232: (Module): Back to gnuplot.exe instead of wgnuplot.exe
233:
234: Revision 1.111 2006/01/25 20:38:18 brouard
235: (Module): Lots of cleaning and bugs added (Gompertz)
236: (Module): Comments can be added in data file. Missing date values
237: can be a simple dot '.'.
238:
239: Revision 1.110 2006/01/25 00:51:50 brouard
240: (Module): Lots of cleaning and bugs added (Gompertz)
241:
242: Revision 1.109 2006/01/24 19:37:15 brouard
243: (Module): Comments (lines starting with a #) are allowed in data.
244:
245: Revision 1.108 2006/01/19 18:05:42 lievre
246: Gnuplot problem appeared...
247: To be fixed
248:
249: Revision 1.107 2006/01/19 16:20:37 brouard
250: Test existence of gnuplot in imach path
251:
252: Revision 1.106 2006/01/19 13:24:36 brouard
253: Some cleaning and links added in html output
254:
255: Revision 1.105 2006/01/05 20:23:19 lievre
256: *** empty log message ***
257:
258: Revision 1.104 2005/09/30 16:11:43 lievre
259: (Module): sump fixed, loop imx fixed, and simplifications.
260: (Module): If the status is missing at the last wave but we know
261: that the person is alive, then we can code his/her status as -2
262: (instead of missing=-1 in earlier versions) and his/her
263: contributions to the likelihood is 1 - Prob of dying from last
264: health status (= 1-p13= p11+p12 in the easiest case of somebody in
265: the healthy state at last known wave). Version is 0.98
266:
267: Revision 1.103 2005/09/30 15:54:49 lievre
268: (Module): sump fixed, loop imx fixed, and simplifications.
269:
270: Revision 1.102 2004/09/15 17:31:30 brouard
271: Add the possibility to read data file including tab characters.
272:
273: Revision 1.101 2004/09/15 10:38:38 brouard
274: Fix on curr_time
275:
276: Revision 1.100 2004/07/12 18:29:06 brouard
277: Add version for Mac OS X. Just define UNIX in Makefile
278:
279: Revision 1.99 2004/06/05 08:57:40 brouard
280: *** empty log message ***
281:
282: Revision 1.98 2004/05/16 15:05:56 brouard
283: New version 0.97 . First attempt to estimate force of mortality
284: directly from the data i.e. without the need of knowing the health
285: state at each age, but using a Gompertz model: log u =a + b*age .
286: This is the basic analysis of mortality and should be done before any
287: other analysis, in order to test if the mortality estimated from the
288: cross-longitudinal survey is different from the mortality estimated
289: from other sources like vital statistic data.
290:
291: The same imach parameter file can be used but the option for mle should be -3.
292:
293: Agnès, who wrote this part of the code, tried to keep most of the
294: former routines in order to include the new code within the former code.
295:
296: The output is very simple: only an estimate of the intercept and of
297: the slope with 95% confident intervals.
298:
299: Current limitations:
300: A) Even if you enter covariates, i.e. with the
301: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
302: B) There is no computation of Life Expectancy nor Life Table.
303:
304: Revision 1.97 2004/02/20 13:25:42 lievre
305: Version 0.96d. Population forecasting command line is (temporarily)
306: suppressed.
307:
308: Revision 1.96 2003/07/15 15:38:55 brouard
309: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
310: rewritten within the same printf. Workaround: many printfs.
311:
312: Revision 1.95 2003/07/08 07:54:34 brouard
313: * imach.c (Repository):
314: (Repository): Using imachwizard code to output a more meaningful covariance
315: matrix (cov(a12,c31) instead of numbers.
316:
317: Revision 1.94 2003/06/27 13:00:02 brouard
318: Just cleaning
319:
320: Revision 1.93 2003/06/25 16:33:55 brouard
321: (Module): On windows (cygwin) function asctime_r doesn't
322: exist so I changed back to asctime which exists.
323: (Module): Version 0.96b
324:
325: Revision 1.92 2003/06/25 16:30:45 brouard
326: (Module): On windows (cygwin) function asctime_r doesn't
327: exist so I changed back to asctime which exists.
328:
329: Revision 1.91 2003/06/25 15:30:29 brouard
330: * imach.c (Repository): Duplicated warning errors corrected.
331: (Repository): Elapsed time after each iteration is now output. It
332: helps to forecast when convergence will be reached. Elapsed time
333: is stamped in powell. We created a new html file for the graphs
334: concerning matrix of covariance. It has extension -cov.htm.
335:
336: Revision 1.90 2003/06/24 12:34:15 brouard
337: (Module): Some bugs corrected for windows. Also, when
338: mle=-1 a template is output in file "or"mypar.txt with the design
339: of the covariance matrix to be input.
340:
341: Revision 1.89 2003/06/24 12:30:52 brouard
342: (Module): Some bugs corrected for windows. Also, when
343: mle=-1 a template is output in file "or"mypar.txt with the design
344: of the covariance matrix to be input.
345:
346: Revision 1.88 2003/06/23 17:54:56 brouard
347: * 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.
348:
349: Revision 1.87 2003/06/18 12:26:01 brouard
350: Version 0.96
351:
352: Revision 1.86 2003/06/17 20:04:08 brouard
353: (Module): Change position of html and gnuplot routines and added
354: routine fileappend.
355:
356: Revision 1.85 2003/06/17 13:12:43 brouard
357: * imach.c (Repository): Check when date of death was earlier that
358: current date of interview. It may happen when the death was just
359: prior to the death. In this case, dh was negative and likelihood
360: was wrong (infinity). We still send an "Error" but patch by
361: assuming that the date of death was just one stepm after the
362: interview.
363: (Repository): Because some people have very long ID (first column)
364: we changed int to long in num[] and we added a new lvector for
365: memory allocation. But we also truncated to 8 characters (left
366: truncation)
367: (Repository): No more line truncation errors.
368:
369: Revision 1.84 2003/06/13 21:44:43 brouard
370: * imach.c (Repository): Replace "freqsummary" at a correct
371: place. It differs from routine "prevalence" which may be called
372: many times. Probs is memory consuming and must be used with
373: parcimony.
374: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
375:
376: Revision 1.83 2003/06/10 13:39:11 lievre
377: *** empty log message ***
378:
379: Revision 1.82 2003/06/05 15:57:20 brouard
380: Add log in imach.c and fullversion number is now printed.
381:
382: */
383: /*
384: Interpolated Markov Chain
385:
386: Short summary of the programme:
387:
388: This program computes Healthy Life Expectancies from
389: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
390: first survey ("cross") where individuals from different ages are
391: interviewed on their health status or degree of disability (in the
392: case of a health survey which is our main interest) -2- at least a
393: second wave of interviews ("longitudinal") which measure each change
394: (if any) in individual health status. Health expectancies are
395: computed from the time spent in each health state according to a
396: model. More health states you consider, more time is necessary to reach the
397: Maximum Likelihood of the parameters involved in the model. The
398: simplest model is the multinomial logistic model where pij is the
399: probability to be observed in state j at the second wave
400: conditional to be observed in state i at the first wave. Therefore
401: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
402: 'age' is age and 'sex' is a covariate. If you want to have a more
403: complex model than "constant and age", you should modify the program
404: where the markup *Covariates have to be included here again* invites
405: you to do it. More covariates you add, slower the
406: convergence.
407:
408: The advantage of this computer programme, compared to a simple
409: multinomial logistic model, is clear when the delay between waves is not
410: identical for each individual. Also, if a individual missed an
411: intermediate interview, the information is lost, but taken into
412: account using an interpolation or extrapolation.
413:
414: hPijx is the probability to be observed in state i at age x+h
415: conditional to the observed state i at age x. The delay 'h' can be
416: split into an exact number (nh*stepm) of unobserved intermediate
417: states. This elementary transition (by month, quarter,
418: semester or year) is modelled as a multinomial logistic. The hPx
419: matrix is simply the matrix product of nh*stepm elementary matrices
420: and the contribution of each individual to the likelihood is simply
421: hPijx.
422:
423: Also this programme outputs the covariance matrix of the parameters but also
424: of the life expectancies. It also computes the period (stable) prevalence.
425:
426: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
427: Institut national d'études démographiques, Paris.
428: This software have been partly granted by Euro-REVES, a concerted action
429: from the European Union.
430: It is copyrighted identically to a GNU software product, ie programme and
431: software can be distributed freely for non commercial use. Latest version
432: can be accessed at http://euroreves.ined.fr/imach .
433:
434: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
435: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
436:
437: **********************************************************************/
438: /*
439: main
440: read parameterfile
441: read datafile
442: concatwav
443: freqsummary
444: if (mle >= 1)
445: mlikeli
446: print results files
447: if mle==1
448: computes hessian
449: read end of parameter file: agemin, agemax, bage, fage, estepm
450: begin-prev-date,...
451: open gnuplot file
452: open html file
453: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
454: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
455: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
456: freexexit2 possible for memory heap.
457:
458: h Pij x | pij_nom ficrestpij
459: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
460: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
461: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
462:
463: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
464: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
465: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
466: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
467: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
468:
469: forecasting if prevfcast==1 prevforecast call prevalence()
470: health expectancies
471: Variance-covariance of DFLE
472: prevalence()
473: movingaverage()
474: varevsij()
475: if popbased==1 varevsij(,popbased)
476: total life expectancies
477: Variance of period (stable) prevalence
478: end
479: */
480:
481:
482:
483:
484: #include <math.h>
485: #include <stdio.h>
486: #include <stdlib.h>
487: #include <string.h>
488:
489: #ifdef _WIN32
490: #include <io.h>
491: #else
492: #include <unistd.h>
493: #endif
494:
495: #include <limits.h>
496: #include <sys/types.h>
497: #include <sys/stat.h>
498: #include <errno.h>
499: /* extern int errno; */
500:
501: /* #ifdef LINUX */
502: /* #include <time.h> */
503: /* #include "timeval.h" */
504: /* #else */
505: /* #include <sys/time.h> */
506: /* #endif */
507:
508: #include <time.h>
509:
510: #ifdef GSL
511: #include <gsl/gsl_errno.h>
512: #include <gsl/gsl_multimin.h>
513: #endif
514:
515: /* #include <libintl.h> */
516: /* #define _(String) gettext (String) */
517:
518: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
519:
520: #define GNUPLOTPROGRAM "gnuplot"
521: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
522: #define FILENAMELENGTH 132
523:
524: #define GLOCK_ERROR_NOPATH -1 /* empty path */
525: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
526:
527: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
528: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
529:
530: #define NINTERVMAX 8
531: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
532: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
533: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
534: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
535: #define MAXN 20000
536: #define YEARM 12. /**< Number of months per year */
537: #define AGESUP 130
538: #define AGEBASE 40
539: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
540: #ifdef _WIN32
541: #define DIRSEPARATOR '\\'
542: #define CHARSEPARATOR "\\"
543: #define ODIRSEPARATOR '/'
544: #else
545: #define DIRSEPARATOR '/'
546: #define CHARSEPARATOR "/"
547: #define ODIRSEPARATOR '\\'
548: #endif
549:
550: /* $Id: imach.c,v 1.160 2014/09/02 09:24:05 brouard Exp $ */
551: /* $State: Exp $ */
552:
553: char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
554: char fullversion[]="$Revision: 1.160 $ $Date: 2014/09/02 09:24:05 $";
555: char strstart[80];
556: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
557: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
558: int nvar=0, nforce=0; /* Number of variables, number of forces */
559: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
560: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
561: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
562: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
563: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
564: int cptcovprodnoage=0; /**< Number of covariate products without age */
565: int cptcoveff=0; /* Total number of covariates to vary for printing results */
566: int cptcov=0; /* Working variable */
567: int npar=NPARMAX;
568: int nlstate=2; /* Number of live states */
569: int ndeath=1; /* Number of dead states */
570: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
571: int popbased=0;
572:
573: int *wav; /* Number of waves for this individuual 0 is possible */
574: int maxwav=0; /* Maxim number of waves */
575: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
576: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
577: int gipmx=0, gsw=0; /* Global variables on the number of contributions
578: to the likelihood and the sum of weights (done by funcone)*/
579: int mle=1, weightopt=0;
580: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
581: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
582: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
583: * wave mi and wave mi+1 is not an exact multiple of stepm. */
584: double jmean=1; /* Mean space between 2 waves */
585: double **matprod2(); /* test */
586: double **oldm, **newm, **savm; /* Working pointers to matrices */
587: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
588: /*FILE *fic ; */ /* Used in readdata only */
589: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
590: FILE *ficlog, *ficrespow;
591: int globpr=0; /* Global variable for printing or not */
592: double fretone; /* Only one call to likelihood */
593: long ipmx=0; /* Number of contributions */
594: double sw; /* Sum of weights */
595: char filerespow[FILENAMELENGTH];
596: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
597: FILE *ficresilk;
598: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
599: FILE *ficresprobmorprev;
600: FILE *fichtm, *fichtmcov; /* Html File */
601: FILE *ficreseij;
602: char filerese[FILENAMELENGTH];
603: FILE *ficresstdeij;
604: char fileresstde[FILENAMELENGTH];
605: FILE *ficrescveij;
606: char filerescve[FILENAMELENGTH];
607: FILE *ficresvij;
608: char fileresv[FILENAMELENGTH];
609: FILE *ficresvpl;
610: char fileresvpl[FILENAMELENGTH];
611: char title[MAXLINE];
612: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
613: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
614: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
615: char command[FILENAMELENGTH];
616: int outcmd=0;
617:
618: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
619:
620: char filelog[FILENAMELENGTH]; /* Log file */
621: char filerest[FILENAMELENGTH];
622: char fileregp[FILENAMELENGTH];
623: char popfile[FILENAMELENGTH];
624:
625: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
626:
627: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
628: /* struct timezone tzp; */
629: /* extern int gettimeofday(); */
630: struct tm tml, *gmtime(), *localtime();
631:
632: extern time_t time();
633:
634: struct tm start_time, end_time, curr_time, last_time, forecast_time;
635: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
636: struct tm tm;
637:
638: char strcurr[80], strfor[80];
639:
640: char *endptr;
641: long lval;
642: double dval;
643:
644: #define NR_END 1
645: #define FREE_ARG char*
646: #define FTOL 1.0e-10
647:
648: #define NRANSI
649: #define ITMAX 200
650:
651: #define TOL 2.0e-4
652:
653: #define CGOLD 0.3819660
654: #define ZEPS 1.0e-10
655: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
656:
657: #define GOLD 1.618034
658: #define GLIMIT 100.0
659: #define TINY 1.0e-20
660:
661: static double maxarg1,maxarg2;
662: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
663: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
664:
665: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
666: #define rint(a) floor(a+0.5)
667:
668: static double sqrarg;
669: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
670: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
671: int agegomp= AGEGOMP;
672:
673: int imx;
674: int stepm=1;
675: /* Stepm, step in month: minimum step interpolation*/
676:
677: int estepm;
678: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
679:
680: int m,nb;
681: long *num;
682: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
683: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
684: double **pmmij, ***probs;
685: double *ageexmed,*agecens;
686: double dateintmean=0;
687:
688: double *weight;
689: int **s; /* Status */
690: double *agedc;
691: double **covar; /**< covar[j,i], value of jth covariate for individual i,
692: * covar=matrix(0,NCOVMAX,1,n);
693: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
694: double idx;
695: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
696: int *Ndum; /** Freq of modality (tricode */
697: int **codtab; /**< codtab=imatrix(1,100,1,10); */
698: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
699: double *lsurv, *lpop, *tpop;
700:
701: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
702: double ftolhess; /**< Tolerance for computing hessian */
703:
704: /**************** split *************************/
705: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
706: {
707: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
708: the name of the file (name), its extension only (ext) and its first part of the name (finame)
709: */
710: char *ss; /* pointer */
711: int l1, l2; /* length counters */
712:
713: l1 = strlen(path ); /* length of path */
714: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
715: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
716: if ( ss == NULL ) { /* no directory, so determine current directory */
717: strcpy( name, path ); /* we got the fullname name because no directory */
718: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
719: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
720: /* get current working directory */
721: /* extern char* getcwd ( char *buf , int len);*/
722: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
723: return( GLOCK_ERROR_GETCWD );
724: }
725: /* got dirc from getcwd*/
726: printf(" DIRC = %s \n",dirc);
727: } else { /* strip direcotry from path */
728: ss++; /* after this, the filename */
729: l2 = strlen( ss ); /* length of filename */
730: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
731: strcpy( name, ss ); /* save file name */
732: strncpy( dirc, path, l1 - l2 ); /* now the directory */
733: dirc[l1-l2] = 0; /* add zero */
734: printf(" DIRC2 = %s \n",dirc);
735: }
736: /* We add a separator at the end of dirc if not exists */
737: l1 = strlen( dirc ); /* length of directory */
738: if( dirc[l1-1] != DIRSEPARATOR ){
739: dirc[l1] = DIRSEPARATOR;
740: dirc[l1+1] = 0;
741: printf(" DIRC3 = %s \n",dirc);
742: }
743: ss = strrchr( name, '.' ); /* find last / */
744: if (ss >0){
745: ss++;
746: strcpy(ext,ss); /* save extension */
747: l1= strlen( name);
748: l2= strlen(ss)+1;
749: strncpy( finame, name, l1-l2);
750: finame[l1-l2]= 0;
751: }
752:
753: return( 0 ); /* we're done */
754: }
755:
756:
757: /******************************************/
758:
759: void replace_back_to_slash(char *s, char*t)
760: {
761: int i;
762: int lg=0;
763: i=0;
764: lg=strlen(t);
765: for(i=0; i<= lg; i++) {
766: (s[i] = t[i]);
767: if (t[i]== '\\') s[i]='/';
768: }
769: }
770:
771: char *trimbb(char *out, char *in)
772: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
773: char *s;
774: s=out;
775: while (*in != '\0'){
776: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
777: in++;
778: }
779: *out++ = *in++;
780: }
781: *out='\0';
782: return s;
783: }
784:
785: char *cutl(char *blocc, char *alocc, char *in, char occ)
786: {
787: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
788: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
789: gives blocc="abcdef2ghi" and alocc="j".
790: If occ is not found blocc is null and alocc is equal to in. Returns blocc
791: */
792: char *s, *t;
793: t=in;s=in;
794: while ((*in != occ) && (*in != '\0')){
795: *alocc++ = *in++;
796: }
797: if( *in == occ){
798: *(alocc)='\0';
799: s=++in;
800: }
801:
802: if (s == t) {/* occ not found */
803: *(alocc-(in-s))='\0';
804: in=s;
805: }
806: while ( *in != '\0'){
807: *blocc++ = *in++;
808: }
809:
810: *blocc='\0';
811: return t;
812: }
813: char *cutv(char *blocc, char *alocc, char *in, char occ)
814: {
815: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
816: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
817: gives blocc="abcdef2ghi" and alocc="j".
818: If occ is not found blocc is null and alocc is equal to in. Returns alocc
819: */
820: char *s, *t;
821: t=in;s=in;
822: while (*in != '\0'){
823: while( *in == occ){
824: *blocc++ = *in++;
825: s=in;
826: }
827: *blocc++ = *in++;
828: }
829: if (s == t) /* occ not found */
830: *(blocc-(in-s))='\0';
831: else
832: *(blocc-(in-s)-1)='\0';
833: in=s;
834: while ( *in != '\0'){
835: *alocc++ = *in++;
836: }
837:
838: *alocc='\0';
839: return s;
840: }
841:
842: int nbocc(char *s, char occ)
843: {
844: int i,j=0;
845: int lg=20;
846: i=0;
847: lg=strlen(s);
848: for(i=0; i<= lg; i++) {
849: if (s[i] == occ ) j++;
850: }
851: return j;
852: }
853:
854: /* void cutv(char *u,char *v, char*t, char occ) */
855: /* { */
856: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
857: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
858: /* gives u="abcdef2ghi" and v="j" *\/ */
859: /* int i,lg,j,p=0; */
860: /* i=0; */
861: /* lg=strlen(t); */
862: /* for(j=0; j<=lg-1; j++) { */
863: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
864: /* } */
865:
866: /* for(j=0; j<p; j++) { */
867: /* (u[j] = t[j]); */
868: /* } */
869: /* u[p]='\0'; */
870:
871: /* for(j=0; j<= lg; j++) { */
872: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
873: /* } */
874: /* } */
875:
876: #ifdef _WIN32
877: char * strsep(char **pp, const char *delim)
878: {
879: char *p, *q;
880:
881: if ((p = *pp) == NULL)
882: return 0;
883: if ((q = strpbrk (p, delim)) != NULL)
884: {
885: *pp = q + 1;
886: *q = '\0';
887: }
888: else
889: *pp = 0;
890: return p;
891: }
892: #endif
893:
894: /********************** nrerror ********************/
895:
896: void nrerror(char error_text[])
897: {
898: fprintf(stderr,"ERREUR ...\n");
899: fprintf(stderr,"%s\n",error_text);
900: exit(EXIT_FAILURE);
901: }
902: /*********************** vector *******************/
903: double *vector(int nl, int nh)
904: {
905: double *v;
906: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
907: if (!v) nrerror("allocation failure in vector");
908: return v-nl+NR_END;
909: }
910:
911: /************************ free vector ******************/
912: void free_vector(double*v, int nl, int nh)
913: {
914: free((FREE_ARG)(v+nl-NR_END));
915: }
916:
917: /************************ivector *******************************/
918: int *ivector(long nl,long nh)
919: {
920: int *v;
921: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
922: if (!v) nrerror("allocation failure in ivector");
923: return v-nl+NR_END;
924: }
925:
926: /******************free ivector **************************/
927: void free_ivector(int *v, long nl, long nh)
928: {
929: free((FREE_ARG)(v+nl-NR_END));
930: }
931:
932: /************************lvector *******************************/
933: long *lvector(long nl,long nh)
934: {
935: long *v;
936: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
937: if (!v) nrerror("allocation failure in ivector");
938: return v-nl+NR_END;
939: }
940:
941: /******************free lvector **************************/
942: void free_lvector(long *v, long nl, long nh)
943: {
944: free((FREE_ARG)(v+nl-NR_END));
945: }
946:
947: /******************* imatrix *******************************/
948: int **imatrix(long nrl, long nrh, long ncl, long nch)
949: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
950: {
951: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
952: int **m;
953:
954: /* allocate pointers to rows */
955: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
956: if (!m) nrerror("allocation failure 1 in matrix()");
957: m += NR_END;
958: m -= nrl;
959:
960:
961: /* allocate rows and set pointers to them */
962: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
963: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
964: m[nrl] += NR_END;
965: m[nrl] -= ncl;
966:
967: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
968:
969: /* return pointer to array of pointers to rows */
970: return m;
971: }
972:
973: /****************** free_imatrix *************************/
974: void free_imatrix(m,nrl,nrh,ncl,nch)
975: int **m;
976: long nch,ncl,nrh,nrl;
977: /* free an int matrix allocated by imatrix() */
978: {
979: free((FREE_ARG) (m[nrl]+ncl-NR_END));
980: free((FREE_ARG) (m+nrl-NR_END));
981: }
982:
983: /******************* matrix *******************************/
984: double **matrix(long nrl, long nrh, long ncl, long nch)
985: {
986: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
987: double **m;
988:
989: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
990: if (!m) nrerror("allocation failure 1 in matrix()");
991: m += NR_END;
992: m -= nrl;
993:
994: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
995: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
996: m[nrl] += NR_END;
997: m[nrl] -= ncl;
998:
999: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1000: return m;
1001: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1002: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1003: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1004: */
1005: }
1006:
1007: /*************************free matrix ************************/
1008: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1009: {
1010: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1011: free((FREE_ARG)(m+nrl-NR_END));
1012: }
1013:
1014: /******************* ma3x *******************************/
1015: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1016: {
1017: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1018: double ***m;
1019:
1020: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1021: if (!m) nrerror("allocation failure 1 in matrix()");
1022: m += NR_END;
1023: m -= nrl;
1024:
1025: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1026: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1027: m[nrl] += NR_END;
1028: m[nrl] -= ncl;
1029:
1030: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1031:
1032: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1033: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1034: m[nrl][ncl] += NR_END;
1035: m[nrl][ncl] -= nll;
1036: for (j=ncl+1; j<=nch; j++)
1037: m[nrl][j]=m[nrl][j-1]+nlay;
1038:
1039: for (i=nrl+1; i<=nrh; i++) {
1040: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1041: for (j=ncl+1; j<=nch; j++)
1042: m[i][j]=m[i][j-1]+nlay;
1043: }
1044: return m;
1045: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1046: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1047: */
1048: }
1049:
1050: /*************************free ma3x ************************/
1051: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1052: {
1053: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1054: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1055: free((FREE_ARG)(m+nrl-NR_END));
1056: }
1057:
1058: /*************** function subdirf ***********/
1059: char *subdirf(char fileres[])
1060: {
1061: /* Caution optionfilefiname is hidden */
1062: strcpy(tmpout,optionfilefiname);
1063: strcat(tmpout,"/"); /* Add to the right */
1064: strcat(tmpout,fileres);
1065: return tmpout;
1066: }
1067:
1068: /*************** function subdirf2 ***********/
1069: char *subdirf2(char fileres[], char *preop)
1070: {
1071:
1072: /* Caution optionfilefiname is hidden */
1073: strcpy(tmpout,optionfilefiname);
1074: strcat(tmpout,"/");
1075: strcat(tmpout,preop);
1076: strcat(tmpout,fileres);
1077: return tmpout;
1078: }
1079:
1080: /*************** function subdirf3 ***********/
1081: char *subdirf3(char fileres[], char *preop, char *preop2)
1082: {
1083:
1084: /* Caution optionfilefiname is hidden */
1085: strcpy(tmpout,optionfilefiname);
1086: strcat(tmpout,"/");
1087: strcat(tmpout,preop);
1088: strcat(tmpout,preop2);
1089: strcat(tmpout,fileres);
1090: return tmpout;
1091: }
1092:
1093: /***************** f1dim *************************/
1094: extern int ncom;
1095: extern double *pcom,*xicom;
1096: extern double (*nrfunc)(double []);
1097:
1098: double f1dim(double x)
1099: {
1100: int j;
1101: double f;
1102: double *xt;
1103:
1104: xt=vector(1,ncom);
1105: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1106: f=(*nrfunc)(xt);
1107: free_vector(xt,1,ncom);
1108: return f;
1109: }
1110:
1111: /*****************brent *************************/
1112: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1113: {
1114: int iter;
1115: double a,b,d,etemp;
1116: double fu=0,fv,fw,fx;
1117: double ftemp;
1118: double p,q,r,tol1,tol2,u,v,w,x,xm;
1119: double e=0.0;
1120:
1121: a=(ax < cx ? ax : cx);
1122: b=(ax > cx ? ax : cx);
1123: x=w=v=bx;
1124: fw=fv=fx=(*f)(x);
1125: for (iter=1;iter<=ITMAX;iter++) {
1126: xm=0.5*(a+b);
1127: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1128: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1129: printf(".");fflush(stdout);
1130: fprintf(ficlog,".");fflush(ficlog);
1131: #ifdef DEBUG
1132: 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);
1133: 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);
1134: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1135: #endif
1136: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1137: *xmin=x;
1138: return fx;
1139: }
1140: ftemp=fu;
1141: if (fabs(e) > tol1) {
1142: r=(x-w)*(fx-fv);
1143: q=(x-v)*(fx-fw);
1144: p=(x-v)*q-(x-w)*r;
1145: q=2.0*(q-r);
1146: if (q > 0.0) p = -p;
1147: q=fabs(q);
1148: etemp=e;
1149: e=d;
1150: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1151: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1152: else {
1153: d=p/q;
1154: u=x+d;
1155: if (u-a < tol2 || b-u < tol2)
1156: d=SIGN(tol1,xm-x);
1157: }
1158: } else {
1159: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1160: }
1161: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1162: fu=(*f)(u);
1163: if (fu <= fx) {
1164: if (u >= x) a=x; else b=x;
1165: SHFT(v,w,x,u)
1166: SHFT(fv,fw,fx,fu)
1167: } else {
1168: if (u < x) a=u; else b=u;
1169: if (fu <= fw || w == x) {
1170: v=w;
1171: w=u;
1172: fv=fw;
1173: fw=fu;
1174: } else if (fu <= fv || v == x || v == w) {
1175: v=u;
1176: fv=fu;
1177: }
1178: }
1179: }
1180: nrerror("Too many iterations in brent");
1181: *xmin=x;
1182: return fx;
1183: }
1184:
1185: /****************** mnbrak ***********************/
1186:
1187: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1188: double (*func)(double))
1189: {
1190: double ulim,u,r,q, dum;
1191: double fu;
1192:
1193: *fa=(*func)(*ax);
1194: *fb=(*func)(*bx);
1195: if (*fb > *fa) {
1196: SHFT(dum,*ax,*bx,dum)
1197: SHFT(dum,*fb,*fa,dum)
1198: }
1199: *cx=(*bx)+GOLD*(*bx-*ax);
1200: *fc=(*func)(*cx);
1201: while (*fb > *fc) {
1202: r=(*bx-*ax)*(*fb-*fc);
1203: q=(*bx-*cx)*(*fb-*fa);
1204: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1205: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1206: ulim=(*bx)+GLIMIT*(*cx-*bx);
1207: if ((*bx-u)*(u-*cx) > 0.0) {
1208: fu=(*func)(u);
1209: } else if ((*cx-u)*(u-ulim) > 0.0) {
1210: fu=(*func)(u);
1211: if (fu < *fc) {
1212: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1213: SHFT(*fb,*fc,fu,(*func)(u))
1214: }
1215: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1216: u=ulim;
1217: fu=(*func)(u);
1218: } else {
1219: u=(*cx)+GOLD*(*cx-*bx);
1220: fu=(*func)(u);
1221: }
1222: SHFT(*ax,*bx,*cx,u)
1223: SHFT(*fa,*fb,*fc,fu)
1224: }
1225: }
1226:
1227: /*************** linmin ************************/
1228:
1229: int ncom;
1230: double *pcom,*xicom;
1231: double (*nrfunc)(double []);
1232:
1233: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1234: {
1235: double brent(double ax, double bx, double cx,
1236: double (*f)(double), double tol, double *xmin);
1237: double f1dim(double x);
1238: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1239: double *fc, double (*func)(double));
1240: int j;
1241: double xx,xmin,bx,ax;
1242: double fx,fb,fa;
1243:
1244: ncom=n;
1245: pcom=vector(1,n);
1246: xicom=vector(1,n);
1247: nrfunc=func;
1248: for (j=1;j<=n;j++) {
1249: pcom[j]=p[j];
1250: xicom[j]=xi[j];
1251: }
1252: ax=0.0;
1253: xx=1.0;
1254: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1255: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1256: #ifdef DEBUG
1257: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1258: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1259: #endif
1260: for (j=1;j<=n;j++) {
1261: xi[j] *= xmin;
1262: p[j] += xi[j];
1263: }
1264: free_vector(xicom,1,n);
1265: free_vector(pcom,1,n);
1266: }
1267:
1268: char *asc_diff_time(long time_sec, char ascdiff[])
1269: {
1270: long sec_left, days, hours, minutes;
1271: days = (time_sec) / (60*60*24);
1272: sec_left = (time_sec) % (60*60*24);
1273: hours = (sec_left) / (60*60) ;
1274: sec_left = (sec_left) %(60*60);
1275: minutes = (sec_left) /60;
1276: sec_left = (sec_left) % (60);
1277: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1278: return ascdiff;
1279: }
1280:
1281: /*************** powell ************************/
1282: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1283: double (*func)(double []))
1284: {
1285: void linmin(double p[], double xi[], int n, double *fret,
1286: double (*func)(double []));
1287: int i,ibig,j;
1288: double del,t,*pt,*ptt,*xit;
1289: double fp,fptt;
1290: double *xits;
1291: int niterf, itmp;
1292:
1293: pt=vector(1,n);
1294: ptt=vector(1,n);
1295: xit=vector(1,n);
1296: xits=vector(1,n);
1297: *fret=(*func)(p);
1298: for (j=1;j<=n;j++) pt[j]=p[j];
1299: rcurr_time = time(NULL);
1300: for (*iter=1;;++(*iter)) {
1301: fp=(*fret);
1302: ibig=0;
1303: del=0.0;
1304: rlast_time=rcurr_time;
1305: /* (void) gettimeofday(&curr_time,&tzp); */
1306: rcurr_time = time(NULL);
1307: curr_time = *localtime(&rcurr_time);
1308: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1309: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1310: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1311: for (i=1;i<=n;i++) {
1312: printf(" %d %.12f",i, p[i]);
1313: fprintf(ficlog," %d %.12lf",i, p[i]);
1314: fprintf(ficrespow," %.12lf", p[i]);
1315: }
1316: printf("\n");
1317: fprintf(ficlog,"\n");
1318: fprintf(ficrespow,"\n");fflush(ficrespow);
1319: if(*iter <=3){
1320: tml = *localtime(&rcurr_time);
1321: strcpy(strcurr,asctime(&tml));
1322: /* asctime_r(&tm,strcurr); */
1323: rforecast_time=rcurr_time;
1324: itmp = strlen(strcurr);
1325: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1326: strcurr[itmp-1]='\0';
1327: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1328: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1329: for(niterf=10;niterf<=30;niterf+=10){
1330: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1331: forecast_time = *localtime(&rforecast_time);
1332: /* asctime_r(&tmf,strfor); */
1333: strcpy(strfor,asctime(&forecast_time));
1334: itmp = strlen(strfor);
1335: if(strfor[itmp-1]=='\n')
1336: strfor[itmp-1]='\0';
1337: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1338: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1339: }
1340: }
1341: for (i=1;i<=n;i++) {
1342: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1343: fptt=(*fret);
1344: #ifdef DEBUG
1345: printf("fret=%lf \n",*fret);
1346: fprintf(ficlog,"fret=%lf \n",*fret);
1347: #endif
1348: printf("%d",i);fflush(stdout);
1349: fprintf(ficlog,"%d",i);fflush(ficlog);
1350: linmin(p,xit,n,fret,func);
1351: if (fabs(fptt-(*fret)) > del) {
1352: del=fabs(fptt-(*fret));
1353: ibig=i;
1354: }
1355: #ifdef DEBUG
1356: printf("%d %.12e",i,(*fret));
1357: fprintf(ficlog,"%d %.12e",i,(*fret));
1358: for (j=1;j<=n;j++) {
1359: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1360: printf(" x(%d)=%.12e",j,xit[j]);
1361: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1362: }
1363: for(j=1;j<=n;j++) {
1364: printf(" p=%.12e",p[j]);
1365: fprintf(ficlog," p=%.12e",p[j]);
1366: }
1367: printf("\n");
1368: fprintf(ficlog,"\n");
1369: #endif
1370: }
1371: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1372: #ifdef DEBUG
1373: int k[2],l;
1374: k[0]=1;
1375: k[1]=-1;
1376: printf("Max: %.12e",(*func)(p));
1377: fprintf(ficlog,"Max: %.12e",(*func)(p));
1378: for (j=1;j<=n;j++) {
1379: printf(" %.12e",p[j]);
1380: fprintf(ficlog," %.12e",p[j]);
1381: }
1382: printf("\n");
1383: fprintf(ficlog,"\n");
1384: for(l=0;l<=1;l++) {
1385: for (j=1;j<=n;j++) {
1386: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1387: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1388: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1389: }
1390: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1391: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1392: }
1393: #endif
1394:
1395:
1396: free_vector(xit,1,n);
1397: free_vector(xits,1,n);
1398: free_vector(ptt,1,n);
1399: free_vector(pt,1,n);
1400: return;
1401: }
1402: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1403: for (j=1;j<=n;j++) {
1404: ptt[j]=2.0*p[j]-pt[j];
1405: xit[j]=p[j]-pt[j];
1406: pt[j]=p[j];
1407: }
1408: fptt=(*func)(ptt);
1409: if (fptt < fp) {
1410: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1411: if (t < 0.0) {
1412: linmin(p,xit,n,fret,func);
1413: for (j=1;j<=n;j++) {
1414: xi[j][ibig]=xi[j][n];
1415: xi[j][n]=xit[j];
1416: }
1417: #ifdef DEBUG
1418: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1419: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1420: for(j=1;j<=n;j++){
1421: printf(" %.12e",xit[j]);
1422: fprintf(ficlog," %.12e",xit[j]);
1423: }
1424: printf("\n");
1425: fprintf(ficlog,"\n");
1426: #endif
1427: }
1428: }
1429: }
1430: }
1431:
1432: /**** Prevalence limit (stable or period prevalence) ****************/
1433:
1434: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1435: {
1436: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1437: matrix by transitions matrix until convergence is reached */
1438:
1439: int i, ii,j,k;
1440: double min, max, maxmin, maxmax,sumnew=0.;
1441: /* double **matprod2(); */ /* test */
1442: double **out, cov[NCOVMAX+1], **pmij();
1443: double **newm;
1444: double agefin, delaymax=50 ; /* Max number of years to converge */
1445:
1446: for (ii=1;ii<=nlstate+ndeath;ii++)
1447: for (j=1;j<=nlstate+ndeath;j++){
1448: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1449: }
1450:
1451: cov[1]=1.;
1452:
1453: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1454: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1455: newm=savm;
1456: /* Covariates have to be included here again */
1457: cov[2]=agefin;
1458:
1459: for (k=1; k<=cptcovn;k++) {
1460: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1461: /*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]]);*/
1462: }
1463: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1464: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1465: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1466:
1467: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1468: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1469: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1470: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1471: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1472: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1473:
1474: savm=oldm;
1475: oldm=newm;
1476: maxmax=0.;
1477: for(j=1;j<=nlstate;j++){
1478: min=1.;
1479: max=0.;
1480: for(i=1; i<=nlstate; i++) {
1481: sumnew=0;
1482: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1483: prlim[i][j]= newm[i][j]/(1-sumnew);
1484: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1485: max=FMAX(max,prlim[i][j]);
1486: min=FMIN(min,prlim[i][j]);
1487: }
1488: maxmin=max-min;
1489: maxmax=FMAX(maxmax,maxmin);
1490: }
1491: if(maxmax < ftolpl){
1492: return prlim;
1493: }
1494: }
1495: }
1496:
1497: /*************** transition probabilities ***************/
1498:
1499: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1500: {
1501: /* According to parameters values stored in x and the covariate's values stored in cov,
1502: computes the probability to be observed in state j being in state i by appying the
1503: model to the ncovmodel covariates (including constant and age).
1504: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1505: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1506: ncth covariate in the global vector x is given by the formula:
1507: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1508: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1509: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1510: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1511: Outputs ps[i][j] the probability to be observed in j being in j according to
1512: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1513: */
1514: double s1, lnpijopii;
1515: /*double t34;*/
1516: int i,j,j1, nc, ii, jj;
1517:
1518: for(i=1; i<= nlstate; i++){
1519: for(j=1; j<i;j++){
1520: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1521: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1522: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1523: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1524: }
1525: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1526: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1527: }
1528: for(j=i+1; j<=nlstate+ndeath;j++){
1529: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1530: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1531: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1532: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1533: }
1534: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1535: }
1536: }
1537:
1538: for(i=1; i<= nlstate; i++){
1539: s1=0;
1540: for(j=1; j<i; j++){
1541: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1542: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1543: }
1544: for(j=i+1; j<=nlstate+ndeath; j++){
1545: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1546: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1547: }
1548: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1549: ps[i][i]=1./(s1+1.);
1550: /* Computing other pijs */
1551: for(j=1; j<i; j++)
1552: ps[i][j]= exp(ps[i][j])*ps[i][i];
1553: for(j=i+1; j<=nlstate+ndeath; j++)
1554: ps[i][j]= exp(ps[i][j])*ps[i][i];
1555: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1556: } /* end i */
1557:
1558: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1559: for(jj=1; jj<= nlstate+ndeath; jj++){
1560: ps[ii][jj]=0;
1561: ps[ii][ii]=1;
1562: }
1563: }
1564:
1565:
1566: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1567: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1568: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1569: /* } */
1570: /* printf("\n "); */
1571: /* } */
1572: /* printf("\n ");printf("%lf ",cov[2]);*/
1573: /*
1574: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1575: goto end;*/
1576: return ps;
1577: }
1578:
1579: /**************** Product of 2 matrices ******************/
1580:
1581: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1582: {
1583: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1584: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1585: /* in, b, out are matrice of pointers which should have been initialized
1586: before: only the contents of out is modified. The function returns
1587: a pointer to pointers identical to out */
1588: int i, j, k;
1589: for(i=nrl; i<= nrh; i++)
1590: for(k=ncolol; k<=ncoloh; k++){
1591: out[i][k]=0.;
1592: for(j=ncl; j<=nch; j++)
1593: out[i][k] +=in[i][j]*b[j][k];
1594: }
1595: return out;
1596: }
1597:
1598:
1599: /************* Higher Matrix Product ***************/
1600:
1601: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1602: {
1603: /* Computes the transition matrix starting at age 'age' over
1604: 'nhstepm*hstepm*stepm' months (i.e. until
1605: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1606: nhstepm*hstepm matrices.
1607: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1608: (typically every 2 years instead of every month which is too big
1609: for the memory).
1610: Model is determined by parameters x and covariates have to be
1611: included manually here.
1612:
1613: */
1614:
1615: int i, j, d, h, k;
1616: double **out, cov[NCOVMAX+1];
1617: double **newm;
1618:
1619: /* Hstepm could be zero and should return the unit matrix */
1620: for (i=1;i<=nlstate+ndeath;i++)
1621: for (j=1;j<=nlstate+ndeath;j++){
1622: oldm[i][j]=(i==j ? 1.0 : 0.0);
1623: po[i][j][0]=(i==j ? 1.0 : 0.0);
1624: }
1625: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1626: for(h=1; h <=nhstepm; h++){
1627: for(d=1; d <=hstepm; d++){
1628: newm=savm;
1629: /* Covariates have to be included here again */
1630: cov[1]=1.;
1631: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1632: for (k=1; k<=cptcovn;k++)
1633: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1634: for (k=1; k<=cptcovage;k++)
1635: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1636: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1637: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1638:
1639:
1640: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1641: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1642: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1643: pmij(pmmij,cov,ncovmodel,x,nlstate));
1644: savm=oldm;
1645: oldm=newm;
1646: }
1647: for(i=1; i<=nlstate+ndeath; i++)
1648: for(j=1;j<=nlstate+ndeath;j++) {
1649: po[i][j][h]=newm[i][j];
1650: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1651: }
1652: /*printf("h=%d ",h);*/
1653: } /* end h */
1654: /* printf("\n H=%d \n",h); */
1655: return po;
1656: }
1657:
1658:
1659: /*************** log-likelihood *************/
1660: double func( double *x)
1661: {
1662: int i, ii, j, k, mi, d, kk;
1663: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1664: double **out;
1665: double sw; /* Sum of weights */
1666: double lli; /* Individual log likelihood */
1667: int s1, s2;
1668: double bbh, survp;
1669: long ipmx;
1670: /*extern weight */
1671: /* We are differentiating ll according to initial status */
1672: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1673: /*for(i=1;i<imx;i++)
1674: printf(" %d\n",s[4][i]);
1675: */
1676: cov[1]=1.;
1677:
1678: for(k=1; k<=nlstate; k++) ll[k]=0.;
1679:
1680: if(mle==1){
1681: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1682: /* Computes the values of the ncovmodel covariates of the model
1683: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1684: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1685: to be observed in j being in i according to the model.
1686: */
1687: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1688: cov[2+k]=covar[Tvar[k]][i];
1689: }
1690: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1691: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1692: has been calculated etc */
1693: for(mi=1; mi<= wav[i]-1; mi++){
1694: for (ii=1;ii<=nlstate+ndeath;ii++)
1695: for (j=1;j<=nlstate+ndeath;j++){
1696: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1697: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1698: }
1699: for(d=0; d<dh[mi][i]; d++){
1700: newm=savm;
1701: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1702: for (kk=1; kk<=cptcovage;kk++) {
1703: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1704: }
1705: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1706: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1707: savm=oldm;
1708: oldm=newm;
1709: } /* end mult */
1710:
1711: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1712: /* But now since version 0.9 we anticipate for bias at large stepm.
1713: * If stepm is larger than one month (smallest stepm) and if the exact delay
1714: * (in months) between two waves is not a multiple of stepm, we rounded to
1715: * the nearest (and in case of equal distance, to the lowest) interval but now
1716: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1717: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1718: * probability in order to take into account the bias as a fraction of the way
1719: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1720: * -stepm/2 to stepm/2 .
1721: * For stepm=1 the results are the same as for previous versions of Imach.
1722: * For stepm > 1 the results are less biased than in previous versions.
1723: */
1724: s1=s[mw[mi][i]][i];
1725: s2=s[mw[mi+1][i]][i];
1726: bbh=(double)bh[mi][i]/(double)stepm;
1727: /* bias bh is positive if real duration
1728: * is higher than the multiple of stepm and negative otherwise.
1729: */
1730: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1731: if( s2 > nlstate){
1732: /* i.e. if s2 is a death state and if the date of death is known
1733: then the contribution to the likelihood is the probability to
1734: die between last step unit time and current step unit time,
1735: which is also equal to probability to die before dh
1736: minus probability to die before dh-stepm .
1737: In version up to 0.92 likelihood was computed
1738: as if date of death was unknown. Death was treated as any other
1739: health state: the date of the interview describes the actual state
1740: and not the date of a change in health state. The former idea was
1741: to consider that at each interview the state was recorded
1742: (healthy, disable or death) and IMaCh was corrected; but when we
1743: introduced the exact date of death then we should have modified
1744: the contribution of an exact death to the likelihood. This new
1745: contribution is smaller and very dependent of the step unit
1746: stepm. It is no more the probability to die between last interview
1747: and month of death but the probability to survive from last
1748: interview up to one month before death multiplied by the
1749: probability to die within a month. Thanks to Chris
1750: Jackson for correcting this bug. Former versions increased
1751: mortality artificially. The bad side is that we add another loop
1752: which slows down the processing. The difference can be up to 10%
1753: lower mortality.
1754: */
1755: lli=log(out[s1][s2] - savm[s1][s2]);
1756:
1757:
1758: } else if (s2==-2) {
1759: for (j=1,survp=0. ; j<=nlstate; j++)
1760: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1761: /*survp += out[s1][j]; */
1762: lli= log(survp);
1763: }
1764:
1765: else if (s2==-4) {
1766: for (j=3,survp=0. ; j<=nlstate; j++)
1767: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1768: lli= log(survp);
1769: }
1770:
1771: else if (s2==-5) {
1772: for (j=1,survp=0. ; j<=2; j++)
1773: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1774: lli= log(survp);
1775: }
1776:
1777: else{
1778: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1779: /* 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 */
1780: }
1781: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1782: /*if(lli ==000.0)*/
1783: /*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); */
1784: ipmx +=1;
1785: sw += weight[i];
1786: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1787: } /* end of wave */
1788: } /* end of individual */
1789: } else if(mle==2){
1790: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1791: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1792: for(mi=1; mi<= wav[i]-1; mi++){
1793: for (ii=1;ii<=nlstate+ndeath;ii++)
1794: for (j=1;j<=nlstate+ndeath;j++){
1795: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1796: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1797: }
1798: for(d=0; d<=dh[mi][i]; d++){
1799: newm=savm;
1800: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1801: for (kk=1; kk<=cptcovage;kk++) {
1802: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1803: }
1804: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1805: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1806: savm=oldm;
1807: oldm=newm;
1808: } /* end mult */
1809:
1810: s1=s[mw[mi][i]][i];
1811: s2=s[mw[mi+1][i]][i];
1812: bbh=(double)bh[mi][i]/(double)stepm;
1813: 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 */
1814: ipmx +=1;
1815: sw += weight[i];
1816: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1817: } /* end of wave */
1818: } /* end of individual */
1819: } else if(mle==3){ /* exponential inter-extrapolation */
1820: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1821: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1822: for(mi=1; mi<= wav[i]-1; mi++){
1823: for (ii=1;ii<=nlstate+ndeath;ii++)
1824: for (j=1;j<=nlstate+ndeath;j++){
1825: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1826: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1827: }
1828: for(d=0; d<dh[mi][i]; d++){
1829: newm=savm;
1830: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1831: for (kk=1; kk<=cptcovage;kk++) {
1832: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1833: }
1834: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1835: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1836: savm=oldm;
1837: oldm=newm;
1838: } /* end mult */
1839:
1840: s1=s[mw[mi][i]][i];
1841: s2=s[mw[mi+1][i]][i];
1842: bbh=(double)bh[mi][i]/(double)stepm;
1843: 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 */
1844: ipmx +=1;
1845: sw += weight[i];
1846: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1847: } /* end of wave */
1848: } /* end of individual */
1849: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1850: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1851: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1852: for(mi=1; mi<= wav[i]-1; mi++){
1853: for (ii=1;ii<=nlstate+ndeath;ii++)
1854: for (j=1;j<=nlstate+ndeath;j++){
1855: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1856: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1857: }
1858: for(d=0; d<dh[mi][i]; d++){
1859: newm=savm;
1860: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1861: for (kk=1; kk<=cptcovage;kk++) {
1862: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1863: }
1864:
1865: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1866: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1867: savm=oldm;
1868: oldm=newm;
1869: } /* end mult */
1870:
1871: s1=s[mw[mi][i]][i];
1872: s2=s[mw[mi+1][i]][i];
1873: if( s2 > nlstate){
1874: lli=log(out[s1][s2] - savm[s1][s2]);
1875: }else{
1876: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1877: }
1878: ipmx +=1;
1879: sw += weight[i];
1880: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1881: /* 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]); */
1882: } /* end of wave */
1883: } /* end of individual */
1884: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1885: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1886: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1887: for(mi=1; mi<= wav[i]-1; mi++){
1888: for (ii=1;ii<=nlstate+ndeath;ii++)
1889: for (j=1;j<=nlstate+ndeath;j++){
1890: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1891: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1892: }
1893: for(d=0; d<dh[mi][i]; d++){
1894: newm=savm;
1895: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1896: for (kk=1; kk<=cptcovage;kk++) {
1897: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1898: }
1899:
1900: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1901: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1902: savm=oldm;
1903: oldm=newm;
1904: } /* end mult */
1905:
1906: s1=s[mw[mi][i]][i];
1907: s2=s[mw[mi+1][i]][i];
1908: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1909: ipmx +=1;
1910: sw += weight[i];
1911: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1912: /*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]);*/
1913: } /* end of wave */
1914: } /* end of individual */
1915: } /* End of if */
1916: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1917: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1918: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1919: return -l;
1920: }
1921:
1922: /*************** log-likelihood *************/
1923: double funcone( double *x)
1924: {
1925: /* Same as likeli but slower because of a lot of printf and if */
1926: int i, ii, j, k, mi, d, kk;
1927: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1928: double **out;
1929: double lli; /* Individual log likelihood */
1930: double llt;
1931: int s1, s2;
1932: double bbh, survp;
1933: /*extern weight */
1934: /* We are differentiating ll according to initial status */
1935: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1936: /*for(i=1;i<imx;i++)
1937: printf(" %d\n",s[4][i]);
1938: */
1939: cov[1]=1.;
1940:
1941: for(k=1; k<=nlstate; k++) ll[k]=0.;
1942:
1943: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1944: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1945: for(mi=1; mi<= wav[i]-1; mi++){
1946: for (ii=1;ii<=nlstate+ndeath;ii++)
1947: for (j=1;j<=nlstate+ndeath;j++){
1948: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1949: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1950: }
1951: for(d=0; d<dh[mi][i]; d++){
1952: newm=savm;
1953: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1954: for (kk=1; kk<=cptcovage;kk++) {
1955: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1956: }
1957: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1958: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1959: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1960: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1961: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1962: savm=oldm;
1963: oldm=newm;
1964: } /* end mult */
1965:
1966: s1=s[mw[mi][i]][i];
1967: s2=s[mw[mi+1][i]][i];
1968: bbh=(double)bh[mi][i]/(double)stepm;
1969: /* bias is positive if real duration
1970: * is higher than the multiple of stepm and negative otherwise.
1971: */
1972: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1973: lli=log(out[s1][s2] - savm[s1][s2]);
1974: } else if (s2==-2) {
1975: for (j=1,survp=0. ; j<=nlstate; j++)
1976: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1977: lli= log(survp);
1978: }else if (mle==1){
1979: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1980: } else if(mle==2){
1981: 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 */
1982: } else if(mle==3){ /* exponential inter-extrapolation */
1983: 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 */
1984: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1985: lli=log(out[s1][s2]); /* Original formula */
1986: } else{ /* mle=0 back to 1 */
1987: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1988: /*lli=log(out[s1][s2]); */ /* Original formula */
1989: } /* End of if */
1990: ipmx +=1;
1991: sw += weight[i];
1992: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1993: /*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]); */
1994: if(globpr){
1995: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1996: %11.6f %11.6f %11.6f ", \
1997: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1998: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1999: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2000: llt +=ll[k]*gipmx/gsw;
2001: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2002: }
2003: fprintf(ficresilk," %10.6f\n", -llt);
2004: }
2005: } /* end of wave */
2006: } /* end of individual */
2007: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2008: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2009: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2010: if(globpr==0){ /* First time we count the contributions and weights */
2011: gipmx=ipmx;
2012: gsw=sw;
2013: }
2014: return -l;
2015: }
2016:
2017:
2018: /*************** function likelione ***********/
2019: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2020: {
2021: /* This routine should help understanding what is done with
2022: the selection of individuals/waves and
2023: to check the exact contribution to the likelihood.
2024: Plotting could be done.
2025: */
2026: int k;
2027:
2028: if(*globpri !=0){ /* Just counts and sums, no printings */
2029: strcpy(fileresilk,"ilk");
2030: strcat(fileresilk,fileres);
2031: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2032: printf("Problem with resultfile: %s\n", fileresilk);
2033: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2034: }
2035: 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");
2036: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2037: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2038: for(k=1; k<=nlstate; k++)
2039: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2040: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2041: }
2042:
2043: *fretone=(*funcone)(p);
2044: if(*globpri !=0){
2045: fclose(ficresilk);
2046: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2047: fflush(fichtm);
2048: }
2049: return;
2050: }
2051:
2052:
2053: /*********** Maximum Likelihood Estimation ***************/
2054:
2055: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2056: {
2057: int i,j, iter;
2058: double **xi;
2059: double fret;
2060: double fretone; /* Only one call to likelihood */
2061: /* char filerespow[FILENAMELENGTH];*/
2062: xi=matrix(1,npar,1,npar);
2063: for (i=1;i<=npar;i++)
2064: for (j=1;j<=npar;j++)
2065: xi[i][j]=(i==j ? 1.0 : 0.0);
2066: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2067: strcpy(filerespow,"pow");
2068: strcat(filerespow,fileres);
2069: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2070: printf("Problem with resultfile: %s\n", filerespow);
2071: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2072: }
2073: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2074: for (i=1;i<=nlstate;i++)
2075: for(j=1;j<=nlstate+ndeath;j++)
2076: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2077: fprintf(ficrespow,"\n");
2078:
2079: powell(p,xi,npar,ftol,&iter,&fret,func);
2080:
2081: free_matrix(xi,1,npar,1,npar);
2082: fclose(ficrespow);
2083: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2084: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2085: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2086:
2087: }
2088:
2089: /**** Computes Hessian and covariance matrix ***/
2090: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2091: {
2092: double **a,**y,*x,pd;
2093: double **hess;
2094: int i, j,jk;
2095: int *indx;
2096:
2097: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2098: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2099: void lubksb(double **a, int npar, int *indx, double b[]) ;
2100: void ludcmp(double **a, int npar, int *indx, double *d) ;
2101: double gompertz(double p[]);
2102: hess=matrix(1,npar,1,npar);
2103:
2104: printf("\nCalculation of the hessian matrix. Wait...\n");
2105: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2106: for (i=1;i<=npar;i++){
2107: printf("%d",i);fflush(stdout);
2108: fprintf(ficlog,"%d",i);fflush(ficlog);
2109:
2110: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2111:
2112: /* printf(" %f ",p[i]);
2113: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2114: }
2115:
2116: for (i=1;i<=npar;i++) {
2117: for (j=1;j<=npar;j++) {
2118: if (j>i) {
2119: printf(".%d%d",i,j);fflush(stdout);
2120: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2121: hess[i][j]=hessij(p,delti,i,j,func,npar);
2122:
2123: hess[j][i]=hess[i][j];
2124: /*printf(" %lf ",hess[i][j]);*/
2125: }
2126: }
2127: }
2128: printf("\n");
2129: fprintf(ficlog,"\n");
2130:
2131: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2132: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2133:
2134: a=matrix(1,npar,1,npar);
2135: y=matrix(1,npar,1,npar);
2136: x=vector(1,npar);
2137: indx=ivector(1,npar);
2138: for (i=1;i<=npar;i++)
2139: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2140: ludcmp(a,npar,indx,&pd);
2141:
2142: for (j=1;j<=npar;j++) {
2143: for (i=1;i<=npar;i++) x[i]=0;
2144: x[j]=1;
2145: lubksb(a,npar,indx,x);
2146: for (i=1;i<=npar;i++){
2147: matcov[i][j]=x[i];
2148: }
2149: }
2150:
2151: printf("\n#Hessian matrix#\n");
2152: fprintf(ficlog,"\n#Hessian matrix#\n");
2153: for (i=1;i<=npar;i++) {
2154: for (j=1;j<=npar;j++) {
2155: printf("%.3e ",hess[i][j]);
2156: fprintf(ficlog,"%.3e ",hess[i][j]);
2157: }
2158: printf("\n");
2159: fprintf(ficlog,"\n");
2160: }
2161:
2162: /* Recompute Inverse */
2163: for (i=1;i<=npar;i++)
2164: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2165: ludcmp(a,npar,indx,&pd);
2166:
2167: /* printf("\n#Hessian matrix recomputed#\n");
2168:
2169: for (j=1;j<=npar;j++) {
2170: for (i=1;i<=npar;i++) x[i]=0;
2171: x[j]=1;
2172: lubksb(a,npar,indx,x);
2173: for (i=1;i<=npar;i++){
2174: y[i][j]=x[i];
2175: printf("%.3e ",y[i][j]);
2176: fprintf(ficlog,"%.3e ",y[i][j]);
2177: }
2178: printf("\n");
2179: fprintf(ficlog,"\n");
2180: }
2181: */
2182:
2183: free_matrix(a,1,npar,1,npar);
2184: free_matrix(y,1,npar,1,npar);
2185: free_vector(x,1,npar);
2186: free_ivector(indx,1,npar);
2187: free_matrix(hess,1,npar,1,npar);
2188:
2189:
2190: }
2191:
2192: /*************** hessian matrix ****************/
2193: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2194: {
2195: int i;
2196: int l=1, lmax=20;
2197: double k1,k2;
2198: double p2[MAXPARM+1]; /* identical to x */
2199: double res;
2200: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2201: double fx;
2202: int k=0,kmax=10;
2203: double l1;
2204:
2205: fx=func(x);
2206: for (i=1;i<=npar;i++) p2[i]=x[i];
2207: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2208: l1=pow(10,l);
2209: delts=delt;
2210: for(k=1 ; k <kmax; k=k+1){
2211: delt = delta*(l1*k);
2212: p2[theta]=x[theta] +delt;
2213: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2214: p2[theta]=x[theta]-delt;
2215: k2=func(p2)-fx;
2216: /*res= (k1-2.0*fx+k2)/delt/delt; */
2217: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2218:
2219: #ifdef DEBUGHESS
2220: 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);
2221: 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);
2222: #endif
2223: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2224: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2225: k=kmax;
2226: }
2227: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2228: k=kmax; l=lmax*10.;
2229: }
2230: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2231: delts=delt;
2232: }
2233: }
2234: }
2235: delti[theta]=delts;
2236: return res;
2237:
2238: }
2239:
2240: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2241: {
2242: int i;
2243: int l=1, l1, lmax=20;
2244: double k1,k2,k3,k4,res,fx;
2245: double p2[MAXPARM+1];
2246: int k;
2247:
2248: fx=func(x);
2249: for (k=1; k<=2; k++) {
2250: for (i=1;i<=npar;i++) p2[i]=x[i];
2251: p2[thetai]=x[thetai]+delti[thetai]/k;
2252: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2253: k1=func(p2)-fx;
2254:
2255: p2[thetai]=x[thetai]+delti[thetai]/k;
2256: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2257: k2=func(p2)-fx;
2258:
2259: p2[thetai]=x[thetai]-delti[thetai]/k;
2260: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2261: k3=func(p2)-fx;
2262:
2263: p2[thetai]=x[thetai]-delti[thetai]/k;
2264: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2265: k4=func(p2)-fx;
2266: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2267: #ifdef DEBUG
2268: 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);
2269: 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);
2270: #endif
2271: }
2272: return res;
2273: }
2274:
2275: /************** Inverse of matrix **************/
2276: void ludcmp(double **a, int n, int *indx, double *d)
2277: {
2278: int i,imax,j,k;
2279: double big,dum,sum,temp;
2280: double *vv;
2281:
2282: vv=vector(1,n);
2283: *d=1.0;
2284: for (i=1;i<=n;i++) {
2285: big=0.0;
2286: for (j=1;j<=n;j++)
2287: if ((temp=fabs(a[i][j])) > big) big=temp;
2288: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2289: vv[i]=1.0/big;
2290: }
2291: for (j=1;j<=n;j++) {
2292: for (i=1;i<j;i++) {
2293: sum=a[i][j];
2294: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2295: a[i][j]=sum;
2296: }
2297: big=0.0;
2298: for (i=j;i<=n;i++) {
2299: sum=a[i][j];
2300: for (k=1;k<j;k++)
2301: sum -= a[i][k]*a[k][j];
2302: a[i][j]=sum;
2303: if ( (dum=vv[i]*fabs(sum)) >= big) {
2304: big=dum;
2305: imax=i;
2306: }
2307: }
2308: if (j != imax) {
2309: for (k=1;k<=n;k++) {
2310: dum=a[imax][k];
2311: a[imax][k]=a[j][k];
2312: a[j][k]=dum;
2313: }
2314: *d = -(*d);
2315: vv[imax]=vv[j];
2316: }
2317: indx[j]=imax;
2318: if (a[j][j] == 0.0) a[j][j]=TINY;
2319: if (j != n) {
2320: dum=1.0/(a[j][j]);
2321: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2322: }
2323: }
2324: free_vector(vv,1,n); /* Doesn't work */
2325: ;
2326: }
2327:
2328: void lubksb(double **a, int n, int *indx, double b[])
2329: {
2330: int i,ii=0,ip,j;
2331: double sum;
2332:
2333: for (i=1;i<=n;i++) {
2334: ip=indx[i];
2335: sum=b[ip];
2336: b[ip]=b[i];
2337: if (ii)
2338: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2339: else if (sum) ii=i;
2340: b[i]=sum;
2341: }
2342: for (i=n;i>=1;i--) {
2343: sum=b[i];
2344: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2345: b[i]=sum/a[i][i];
2346: }
2347: }
2348:
2349: void pstamp(FILE *fichier)
2350: {
2351: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2352: }
2353:
2354: /************ Frequencies ********************/
2355: 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[])
2356: { /* Some frequencies */
2357:
2358: int i, m, jk, k1,i1, j1, bool, z1,j;
2359: int first;
2360: double ***freq; /* Frequencies */
2361: double *pp, **prop;
2362: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2363: char fileresp[FILENAMELENGTH];
2364:
2365: pp=vector(1,nlstate);
2366: prop=matrix(1,nlstate,iagemin,iagemax+3);
2367: strcpy(fileresp,"p");
2368: strcat(fileresp,fileres);
2369: if((ficresp=fopen(fileresp,"w"))==NULL) {
2370: printf("Problem with prevalence resultfile: %s\n", fileresp);
2371: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2372: exit(0);
2373: }
2374: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2375: j1=0;
2376:
2377: j=cptcoveff;
2378: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2379:
2380: first=1;
2381:
2382: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2383: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2384: /* j1++;
2385: */
2386: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2387: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2388: scanf("%d", i);*/
2389: for (i=-5; i<=nlstate+ndeath; i++)
2390: for (jk=-5; jk<=nlstate+ndeath; jk++)
2391: for(m=iagemin; m <= iagemax+3; m++)
2392: freq[i][jk][m]=0;
2393:
2394: for (i=1; i<=nlstate; i++)
2395: for(m=iagemin; m <= iagemax+3; m++)
2396: prop[i][m]=0;
2397:
2398: dateintsum=0;
2399: k2cpt=0;
2400: for (i=1; i<=imx; i++) {
2401: bool=1;
2402: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2403: for (z1=1; z1<=cptcoveff; z1++)
2404: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2405: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2406: bool=0;
2407: /* 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",
2408: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2409: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2410: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2411: }
2412: }
2413:
2414: if (bool==1){
2415: for(m=firstpass; m<=lastpass; m++){
2416: k2=anint[m][i]+(mint[m][i]/12.);
2417: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2418: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2419: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2420: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2421: if (m<lastpass) {
2422: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2423: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2424: }
2425:
2426: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2427: dateintsum=dateintsum+k2;
2428: k2cpt++;
2429: }
2430: /*}*/
2431: }
2432: }
2433: } /* end i */
2434:
2435: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2436: pstamp(ficresp);
2437: if (cptcovn>0) {
2438: fprintf(ficresp, "\n#********** Variable ");
2439: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2440: fprintf(ficresp, "**********\n#");
2441: fprintf(ficlog, "\n#********** Variable ");
2442: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2443: fprintf(ficlog, "**********\n#");
2444: }
2445: for(i=1; i<=nlstate;i++)
2446: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2447: fprintf(ficresp, "\n");
2448:
2449: for(i=iagemin; i <= iagemax+3; i++){
2450: if(i==iagemax+3){
2451: fprintf(ficlog,"Total");
2452: }else{
2453: if(first==1){
2454: first=0;
2455: printf("See log file for details...\n");
2456: }
2457: fprintf(ficlog,"Age %d", i);
2458: }
2459: for(jk=1; jk <=nlstate ; jk++){
2460: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2461: pp[jk] += freq[jk][m][i];
2462: }
2463: for(jk=1; jk <=nlstate ; jk++){
2464: for(m=-1, pos=0; m <=0 ; m++)
2465: pos += freq[jk][m][i];
2466: if(pp[jk]>=1.e-10){
2467: if(first==1){
2468: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2469: }
2470: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2471: }else{
2472: if(first==1)
2473: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2474: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2475: }
2476: }
2477:
2478: for(jk=1; jk <=nlstate ; jk++){
2479: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2480: pp[jk] += freq[jk][m][i];
2481: }
2482: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2483: pos += pp[jk];
2484: posprop += prop[jk][i];
2485: }
2486: for(jk=1; jk <=nlstate ; jk++){
2487: if(pos>=1.e-5){
2488: if(first==1)
2489: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2490: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2491: }else{
2492: if(first==1)
2493: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2494: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2495: }
2496: if( i <= iagemax){
2497: if(pos>=1.e-5){
2498: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2499: /*probs[i][jk][j1]= pp[jk]/pos;*/
2500: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2501: }
2502: else
2503: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2504: }
2505: }
2506:
2507: for(jk=-1; jk <=nlstate+ndeath; jk++)
2508: for(m=-1; m <=nlstate+ndeath; m++)
2509: if(freq[jk][m][i] !=0 ) {
2510: if(first==1)
2511: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2512: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2513: }
2514: if(i <= iagemax)
2515: fprintf(ficresp,"\n");
2516: if(first==1)
2517: printf("Others in log...\n");
2518: fprintf(ficlog,"\n");
2519: }
2520: /*}*/
2521: }
2522: dateintmean=dateintsum/k2cpt;
2523:
2524: fclose(ficresp);
2525: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2526: free_vector(pp,1,nlstate);
2527: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2528: /* End of Freq */
2529: }
2530:
2531: /************ Prevalence ********************/
2532: 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)
2533: {
2534: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2535: in each health status at the date of interview (if between dateprev1 and dateprev2).
2536: We still use firstpass and lastpass as another selection.
2537: */
2538:
2539: int i, m, jk, k1, i1, j1, bool, z1,j;
2540: double ***freq; /* Frequencies */
2541: double *pp, **prop;
2542: double pos,posprop;
2543: double y2; /* in fractional years */
2544: int iagemin, iagemax;
2545: int first; /** to stop verbosity which is redirected to log file */
2546:
2547: iagemin= (int) agemin;
2548: iagemax= (int) agemax;
2549: /*pp=vector(1,nlstate);*/
2550: prop=matrix(1,nlstate,iagemin,iagemax+3);
2551: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2552: j1=0;
2553:
2554: /*j=cptcoveff;*/
2555: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2556:
2557: first=1;
2558: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2559: /*for(i1=1; i1<=ncodemax[k1];i1++){
2560: j1++;*/
2561:
2562: for (i=1; i<=nlstate; i++)
2563: for(m=iagemin; m <= iagemax+3; m++)
2564: prop[i][m]=0.0;
2565:
2566: for (i=1; i<=imx; i++) { /* Each individual */
2567: bool=1;
2568: if (cptcovn>0) {
2569: for (z1=1; z1<=cptcoveff; z1++)
2570: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2571: bool=0;
2572: }
2573: if (bool==1) {
2574: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2575: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2576: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2577: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2578: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2579: 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);
2580: if (s[m][i]>0 && s[m][i]<=nlstate) {
2581: /*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]]);*/
2582: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2583: prop[s[m][i]][iagemax+3] += weight[i];
2584: }
2585: }
2586: } /* end selection of waves */
2587: }
2588: }
2589: for(i=iagemin; i <= iagemax+3; i++){
2590: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2591: posprop += prop[jk][i];
2592: }
2593:
2594: for(jk=1; jk <=nlstate ; jk++){
2595: if( i <= iagemax){
2596: if(posprop>=1.e-5){
2597: probs[i][jk][j1]= prop[jk][i]/posprop;
2598: } else{
2599: if(first==1){
2600: first=0;
2601: 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]);
2602: }
2603: }
2604: }
2605: }/* end jk */
2606: }/* end i */
2607: /*} *//* end i1 */
2608: } /* end j1 */
2609:
2610: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2611: /*free_vector(pp,1,nlstate);*/
2612: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2613: } /* End of prevalence */
2614:
2615: /************* Waves Concatenation ***************/
2616:
2617: 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)
2618: {
2619: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2620: Death is a valid wave (if date is known).
2621: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2622: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2623: and mw[mi+1][i]. dh depends on stepm.
2624: */
2625:
2626: int i, mi, m;
2627: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2628: double sum=0., jmean=0.;*/
2629: int first;
2630: int j, k=0,jk, ju, jl;
2631: double sum=0.;
2632: first=0;
2633: jmin=1e+5;
2634: jmax=-1;
2635: jmean=0.;
2636: for(i=1; i<=imx; i++){
2637: mi=0;
2638: m=firstpass;
2639: while(s[m][i] <= nlstate){
2640: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2641: mw[++mi][i]=m;
2642: if(m >=lastpass)
2643: break;
2644: else
2645: m++;
2646: }/* end while */
2647: if (s[m][i] > nlstate){
2648: mi++; /* Death is another wave */
2649: /* if(mi==0) never been interviewed correctly before death */
2650: /* Only death is a correct wave */
2651: mw[mi][i]=m;
2652: }
2653:
2654: wav[i]=mi;
2655: if(mi==0){
2656: nbwarn++;
2657: if(first==0){
2658: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2659: first=1;
2660: }
2661: if(first==1){
2662: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2663: }
2664: } /* end mi==0 */
2665: } /* End individuals */
2666:
2667: for(i=1; i<=imx; i++){
2668: for(mi=1; mi<wav[i];mi++){
2669: if (stepm <=0)
2670: dh[mi][i]=1;
2671: else{
2672: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2673: if (agedc[i] < 2*AGESUP) {
2674: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2675: if(j==0) j=1; /* Survives at least one month after exam */
2676: else if(j<0){
2677: nberr++;
2678: 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]);
2679: j=1; /* Temporary Dangerous patch */
2680: 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);
2681: 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]);
2682: 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);
2683: }
2684: k=k+1;
2685: if (j >= jmax){
2686: jmax=j;
2687: ijmax=i;
2688: }
2689: if (j <= jmin){
2690: jmin=j;
2691: ijmin=i;
2692: }
2693: sum=sum+j;
2694: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2695: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2696: }
2697: }
2698: else{
2699: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2700: /* 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]); */
2701:
2702: k=k+1;
2703: if (j >= jmax) {
2704: jmax=j;
2705: ijmax=i;
2706: }
2707: else if (j <= jmin){
2708: jmin=j;
2709: ijmin=i;
2710: }
2711: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2712: /*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]);*/
2713: if(j<0){
2714: nberr++;
2715: 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]);
2716: 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]);
2717: }
2718: sum=sum+j;
2719: }
2720: jk= j/stepm;
2721: jl= j -jk*stepm;
2722: ju= j -(jk+1)*stepm;
2723: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2724: if(jl==0){
2725: dh[mi][i]=jk;
2726: bh[mi][i]=0;
2727: }else{ /* We want a negative bias in order to only have interpolation ie
2728: * to avoid the price of an extra matrix product in likelihood */
2729: dh[mi][i]=jk+1;
2730: bh[mi][i]=ju;
2731: }
2732: }else{
2733: if(jl <= -ju){
2734: dh[mi][i]=jk;
2735: bh[mi][i]=jl; /* bias is positive if real duration
2736: * is higher than the multiple of stepm and negative otherwise.
2737: */
2738: }
2739: else{
2740: dh[mi][i]=jk+1;
2741: bh[mi][i]=ju;
2742: }
2743: if(dh[mi][i]==0){
2744: dh[mi][i]=1; /* At least one step */
2745: bh[mi][i]=ju; /* At least one step */
2746: /* 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);*/
2747: }
2748: } /* end if mle */
2749: }
2750: } /* end wave */
2751: }
2752: jmean=sum/k;
2753: 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);
2754: 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);
2755: }
2756:
2757: /*********** Tricode ****************************/
2758: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2759: {
2760: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2761: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2762: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
2763: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2764: /* nbcode[Tvar[j]][1]=
2765: */
2766:
2767: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2768: int modmaxcovj=0; /* Modality max of covariates j */
2769: int cptcode=0; /* Modality max of covariates j */
2770: int modmincovj=0; /* Modality min of covariates j */
2771:
2772:
2773: cptcoveff=0;
2774:
2775: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2776: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2777:
2778: /* Loop on covariates without age and products */
2779: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2780: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2781: modality of this covariate Vj*/
2782: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2783: * If product of Vn*Vm, still boolean *:
2784: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2785: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2786: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2787: modality of the nth covariate of individual i. */
2788: if (ij > modmaxcovj)
2789: modmaxcovj=ij;
2790: else if (ij < modmincovj)
2791: modmincovj=ij;
2792: if ((ij < -1) && (ij > NCOVMAX)){
2793: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2794: exit(1);
2795: }else
2796: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2797: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2798: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2799: /* getting the maximum value of the modality of the covariate
2800: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2801: female is 1, then modmaxcovj=1.*/
2802: }
2803: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2804: cptcode=modmaxcovj;
2805: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2806: /*for (i=0; i<=cptcode; i++) {*/
2807: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2808: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2809: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2810: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2811: }
2812: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2813: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2814: } /* Ndum[-1] number of undefined modalities */
2815:
2816: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2817: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2818: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2819: modmincovj=3; modmaxcovj = 7;
2820: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2821: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2822: variables V1_1 and V1_2.
2823: nbcode[Tvar[j]][ij]=k;
2824: nbcode[Tvar[j]][1]=0;
2825: nbcode[Tvar[j]][2]=1;
2826: nbcode[Tvar[j]][3]=2;
2827: */
2828: ij=1; /* ij is similar to i but can jumps over null modalities */
2829: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2830: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2831: /*recode from 0 */
2832: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2833: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2834: k is a modality. If we have model=V1+V1*sex
2835: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2836: ij++;
2837: }
2838: if (ij > ncodemax[j]) break;
2839: } /* end of loop on */
2840: } /* end of loop on modality */
2841: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2842:
2843: for (k=-1; k< maxncov; k++) Ndum[k]=0;
2844:
2845: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2846: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2847: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2848: Ndum[ij]++;
2849: }
2850:
2851: ij=1;
2852: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2853: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
2854: if((Ndum[i]!=0) && (i<=ncovcol)){
2855: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2856: Tvaraff[ij]=i; /*For printing (unclear) */
2857: ij++;
2858: }else
2859: Tvaraff[ij]=0;
2860: }
2861: ij--;
2862: cptcoveff=ij; /*Number of total covariates*/
2863:
2864: }
2865:
2866:
2867: /*********** Health Expectancies ****************/
2868:
2869: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2870:
2871: {
2872: /* Health expectancies, no variances */
2873: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2874: int nhstepma, nstepma; /* Decreasing with age */
2875: double age, agelim, hf;
2876: double ***p3mat;
2877: double eip;
2878:
2879: pstamp(ficreseij);
2880: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2881: fprintf(ficreseij,"# Age");
2882: for(i=1; i<=nlstate;i++){
2883: for(j=1; j<=nlstate;j++){
2884: fprintf(ficreseij," e%1d%1d ",i,j);
2885: }
2886: fprintf(ficreseij," e%1d. ",i);
2887: }
2888: fprintf(ficreseij,"\n");
2889:
2890:
2891: if(estepm < stepm){
2892: printf ("Problem %d lower than %d\n",estepm, stepm);
2893: }
2894: else hstepm=estepm;
2895: /* We compute the life expectancy from trapezoids spaced every estepm months
2896: * This is mainly to measure the difference between two models: for example
2897: * if stepm=24 months pijx are given only every 2 years and by summing them
2898: * we are calculating an estimate of the Life Expectancy assuming a linear
2899: * progression in between and thus overestimating or underestimating according
2900: * to the curvature of the survival function. If, for the same date, we
2901: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2902: * to compare the new estimate of Life expectancy with the same linear
2903: * hypothesis. A more precise result, taking into account a more precise
2904: * curvature will be obtained if estepm is as small as stepm. */
2905:
2906: /* For example we decided to compute the life expectancy with the smallest unit */
2907: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2908: nhstepm is the number of hstepm from age to agelim
2909: nstepm is the number of stepm from age to agelin.
2910: Look at hpijx to understand the reason of that which relies in memory size
2911: and note for a fixed period like estepm months */
2912: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2913: survival function given by stepm (the optimization length). Unfortunately it
2914: means that if the survival funtion is printed only each two years of age and if
2915: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2916: results. So we changed our mind and took the option of the best precision.
2917: */
2918: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2919:
2920: agelim=AGESUP;
2921: /* If stepm=6 months */
2922: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2923: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2924:
2925: /* nhstepm age range expressed in number of stepm */
2926: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2927: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2928: /* if (stepm >= YEARM) hstepm=1;*/
2929: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2930: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2931:
2932: for (age=bage; age<=fage; age ++){
2933: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2934: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2935: /* if (stepm >= YEARM) hstepm=1;*/
2936: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2937:
2938: /* If stepm=6 months */
2939: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2940: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2941:
2942: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2943:
2944: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2945:
2946: printf("%d|",(int)age);fflush(stdout);
2947: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2948:
2949: /* Computing expectancies */
2950: for(i=1; i<=nlstate;i++)
2951: for(j=1; j<=nlstate;j++)
2952: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2953: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2954:
2955: /* 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]);*/
2956:
2957: }
2958:
2959: fprintf(ficreseij,"%3.0f",age );
2960: for(i=1; i<=nlstate;i++){
2961: eip=0;
2962: for(j=1; j<=nlstate;j++){
2963: eip +=eij[i][j][(int)age];
2964: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2965: }
2966: fprintf(ficreseij,"%9.4f", eip );
2967: }
2968: fprintf(ficreseij,"\n");
2969:
2970: }
2971: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2972: printf("\n");
2973: fprintf(ficlog,"\n");
2974:
2975: }
2976:
2977: 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[] )
2978:
2979: {
2980: /* Covariances of health expectancies eij and of total life expectancies according
2981: to initial status i, ei. .
2982: */
2983: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2984: int nhstepma, nstepma; /* Decreasing with age */
2985: double age, agelim, hf;
2986: double ***p3matp, ***p3matm, ***varhe;
2987: double **dnewm,**doldm;
2988: double *xp, *xm;
2989: double **gp, **gm;
2990: double ***gradg, ***trgradg;
2991: int theta;
2992:
2993: double eip, vip;
2994:
2995: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2996: xp=vector(1,npar);
2997: xm=vector(1,npar);
2998: dnewm=matrix(1,nlstate*nlstate,1,npar);
2999: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3000:
3001: pstamp(ficresstdeij);
3002: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3003: fprintf(ficresstdeij,"# Age");
3004: for(i=1; i<=nlstate;i++){
3005: for(j=1; j<=nlstate;j++)
3006: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3007: fprintf(ficresstdeij," e%1d. ",i);
3008: }
3009: fprintf(ficresstdeij,"\n");
3010:
3011: pstamp(ficrescveij);
3012: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3013: fprintf(ficrescveij,"# Age");
3014: for(i=1; i<=nlstate;i++)
3015: for(j=1; j<=nlstate;j++){
3016: cptj= (j-1)*nlstate+i;
3017: for(i2=1; i2<=nlstate;i2++)
3018: for(j2=1; j2<=nlstate;j2++){
3019: cptj2= (j2-1)*nlstate+i2;
3020: if(cptj2 <= cptj)
3021: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3022: }
3023: }
3024: fprintf(ficrescveij,"\n");
3025:
3026: if(estepm < stepm){
3027: printf ("Problem %d lower than %d\n",estepm, stepm);
3028: }
3029: else hstepm=estepm;
3030: /* We compute the life expectancy from trapezoids spaced every estepm months
3031: * This is mainly to measure the difference between two models: for example
3032: * if stepm=24 months pijx are given only every 2 years and by summing them
3033: * we are calculating an estimate of the Life Expectancy assuming a linear
3034: * progression in between and thus overestimating or underestimating according
3035: * to the curvature of the survival function. If, for the same date, we
3036: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3037: * to compare the new estimate of Life expectancy with the same linear
3038: * hypothesis. A more precise result, taking into account a more precise
3039: * curvature will be obtained if estepm is as small as stepm. */
3040:
3041: /* For example we decided to compute the life expectancy with the smallest unit */
3042: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3043: nhstepm is the number of hstepm from age to agelim
3044: nstepm is the number of stepm from age to agelin.
3045: Look at hpijx to understand the reason of that which relies in memory size
3046: and note for a fixed period like estepm months */
3047: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3048: survival function given by stepm (the optimization length). Unfortunately it
3049: means that if the survival funtion is printed only each two years of age and if
3050: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3051: results. So we changed our mind and took the option of the best precision.
3052: */
3053: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3054:
3055: /* If stepm=6 months */
3056: /* nhstepm age range expressed in number of stepm */
3057: agelim=AGESUP;
3058: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3059: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3060: /* if (stepm >= YEARM) hstepm=1;*/
3061: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3062:
3063: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3064: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3065: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3066: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3067: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3068: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3069:
3070: for (age=bage; age<=fage; age ++){
3071: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3072: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3073: /* if (stepm >= YEARM) hstepm=1;*/
3074: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3075:
3076: /* If stepm=6 months */
3077: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3078: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3079:
3080: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3081:
3082: /* Computing Variances of health expectancies */
3083: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3084: decrease memory allocation */
3085: for(theta=1; theta <=npar; theta++){
3086: for(i=1; i<=npar; i++){
3087: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3088: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3089: }
3090: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3091: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3092:
3093: for(j=1; j<= nlstate; j++){
3094: for(i=1; i<=nlstate; i++){
3095: for(h=0; h<=nhstepm-1; h++){
3096: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3097: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3098: }
3099: }
3100: }
3101:
3102: for(ij=1; ij<= nlstate*nlstate; ij++)
3103: for(h=0; h<=nhstepm-1; h++){
3104: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3105: }
3106: }/* End theta */
3107:
3108:
3109: for(h=0; h<=nhstepm-1; h++)
3110: for(j=1; j<=nlstate*nlstate;j++)
3111: for(theta=1; theta <=npar; theta++)
3112: trgradg[h][j][theta]=gradg[h][theta][j];
3113:
3114:
3115: for(ij=1;ij<=nlstate*nlstate;ij++)
3116: for(ji=1;ji<=nlstate*nlstate;ji++)
3117: varhe[ij][ji][(int)age] =0.;
3118:
3119: printf("%d|",(int)age);fflush(stdout);
3120: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3121: for(h=0;h<=nhstepm-1;h++){
3122: for(k=0;k<=nhstepm-1;k++){
3123: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3124: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3125: for(ij=1;ij<=nlstate*nlstate;ij++)
3126: for(ji=1;ji<=nlstate*nlstate;ji++)
3127: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3128: }
3129: }
3130:
3131: /* Computing expectancies */
3132: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3133: for(i=1; i<=nlstate;i++)
3134: for(j=1; j<=nlstate;j++)
3135: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3136: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3137:
3138: /* 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]);*/
3139:
3140: }
3141:
3142: fprintf(ficresstdeij,"%3.0f",age );
3143: for(i=1; i<=nlstate;i++){
3144: eip=0.;
3145: vip=0.;
3146: for(j=1; j<=nlstate;j++){
3147: eip += eij[i][j][(int)age];
3148: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3149: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3150: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3151: }
3152: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3153: }
3154: fprintf(ficresstdeij,"\n");
3155:
3156: fprintf(ficrescveij,"%3.0f",age );
3157: for(i=1; i<=nlstate;i++)
3158: for(j=1; j<=nlstate;j++){
3159: cptj= (j-1)*nlstate+i;
3160: for(i2=1; i2<=nlstate;i2++)
3161: for(j2=1; j2<=nlstate;j2++){
3162: cptj2= (j2-1)*nlstate+i2;
3163: if(cptj2 <= cptj)
3164: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3165: }
3166: }
3167: fprintf(ficrescveij,"\n");
3168:
3169: }
3170: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3171: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3172: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3173: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3174: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3175: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3176: printf("\n");
3177: fprintf(ficlog,"\n");
3178:
3179: free_vector(xm,1,npar);
3180: free_vector(xp,1,npar);
3181: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3182: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3183: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3184: }
3185:
3186: /************ Variance ******************/
3187: 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[])
3188: {
3189: /* Variance of health expectancies */
3190: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3191: /* double **newm;*/
3192: double **dnewm,**doldm;
3193: double **dnewmp,**doldmp;
3194: int i, j, nhstepm, hstepm, h, nstepm ;
3195: int k, cptcode;
3196: double *xp;
3197: double **gp, **gm; /* for var eij */
3198: double ***gradg, ***trgradg; /*for var eij */
3199: double **gradgp, **trgradgp; /* for var p point j */
3200: double *gpp, *gmp; /* for var p point j */
3201: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3202: double ***p3mat;
3203: double age,agelim, hf;
3204: double ***mobaverage;
3205: int theta;
3206: char digit[4];
3207: char digitp[25];
3208:
3209: char fileresprobmorprev[FILENAMELENGTH];
3210:
3211: if(popbased==1){
3212: if(mobilav!=0)
3213: strcpy(digitp,"-populbased-mobilav-");
3214: else strcpy(digitp,"-populbased-nomobil-");
3215: }
3216: else
3217: strcpy(digitp,"-stablbased-");
3218:
3219: if (mobilav!=0) {
3220: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3221: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3222: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3223: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3224: }
3225: }
3226:
3227: strcpy(fileresprobmorprev,"prmorprev");
3228: sprintf(digit,"%-d",ij);
3229: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3230: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3231: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3232: strcat(fileresprobmorprev,fileres);
3233: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3234: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3235: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3236: }
3237: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3238:
3239: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3240: pstamp(ficresprobmorprev);
3241: 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);
3242: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3243: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3244: fprintf(ficresprobmorprev," p.%-d SE",j);
3245: for(i=1; i<=nlstate;i++)
3246: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3247: }
3248: fprintf(ficresprobmorprev,"\n");
3249: fprintf(ficgp,"\n# Routine varevsij");
3250: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3251: 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");
3252: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3253: /* } */
3254: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3255: pstamp(ficresvij);
3256: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3257: if(popbased==1)
3258: 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);
3259: else
3260: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3261: fprintf(ficresvij,"# Age");
3262: for(i=1; i<=nlstate;i++)
3263: for(j=1; j<=nlstate;j++)
3264: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3265: fprintf(ficresvij,"\n");
3266:
3267: xp=vector(1,npar);
3268: dnewm=matrix(1,nlstate,1,npar);
3269: doldm=matrix(1,nlstate,1,nlstate);
3270: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3271: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3272:
3273: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3274: gpp=vector(nlstate+1,nlstate+ndeath);
3275: gmp=vector(nlstate+1,nlstate+ndeath);
3276: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3277:
3278: if(estepm < stepm){
3279: printf ("Problem %d lower than %d\n",estepm, stepm);
3280: }
3281: else hstepm=estepm;
3282: /* For example we decided to compute the life expectancy with the smallest unit */
3283: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3284: nhstepm is the number of hstepm from age to agelim
3285: nstepm is the number of stepm from age to agelin.
3286: Look at function hpijx to understand why (it is linked to memory size questions) */
3287: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3288: survival function given by stepm (the optimization length). Unfortunately it
3289: means that if the survival funtion is printed every two years of age and if
3290: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3291: results. So we changed our mind and took the option of the best precision.
3292: */
3293: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3294: agelim = AGESUP;
3295: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3296: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3297: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3298: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3299: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3300: gp=matrix(0,nhstepm,1,nlstate);
3301: gm=matrix(0,nhstepm,1,nlstate);
3302:
3303:
3304: for(theta=1; theta <=npar; theta++){
3305: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3306: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3307: }
3308: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3309: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3310:
3311: if (popbased==1) {
3312: if(mobilav ==0){
3313: for(i=1; i<=nlstate;i++)
3314: prlim[i][i]=probs[(int)age][i][ij];
3315: }else{ /* mobilav */
3316: for(i=1; i<=nlstate;i++)
3317: prlim[i][i]=mobaverage[(int)age][i][ij];
3318: }
3319: }
3320:
3321: for(j=1; j<= nlstate; j++){
3322: for(h=0; h<=nhstepm; h++){
3323: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3324: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3325: }
3326: }
3327: /* This for computing probability of death (h=1 means
3328: computed over hstepm matrices product = hstepm*stepm months)
3329: as a weighted average of prlim.
3330: */
3331: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3332: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3333: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3334: }
3335: /* end probability of death */
3336:
3337: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3338: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3339: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3340: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3341:
3342: if (popbased==1) {
3343: if(mobilav ==0){
3344: for(i=1; i<=nlstate;i++)
3345: prlim[i][i]=probs[(int)age][i][ij];
3346: }else{ /* mobilav */
3347: for(i=1; i<=nlstate;i++)
3348: prlim[i][i]=mobaverage[(int)age][i][ij];
3349: }
3350: }
3351:
3352: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3353: for(h=0; h<=nhstepm; h++){
3354: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3355: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3356: }
3357: }
3358: /* This for computing probability of death (h=1 means
3359: computed over hstepm matrices product = hstepm*stepm months)
3360: as a weighted average of prlim.
3361: */
3362: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3363: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3364: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3365: }
3366: /* end probability of death */
3367:
3368: for(j=1; j<= nlstate; j++) /* vareij */
3369: for(h=0; h<=nhstepm; h++){
3370: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3371: }
3372:
3373: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3374: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3375: }
3376:
3377: } /* End theta */
3378:
3379: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3380:
3381: for(h=0; h<=nhstepm; h++) /* veij */
3382: for(j=1; j<=nlstate;j++)
3383: for(theta=1; theta <=npar; theta++)
3384: trgradg[h][j][theta]=gradg[h][theta][j];
3385:
3386: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3387: for(theta=1; theta <=npar; theta++)
3388: trgradgp[j][theta]=gradgp[theta][j];
3389:
3390:
3391: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3392: for(i=1;i<=nlstate;i++)
3393: for(j=1;j<=nlstate;j++)
3394: vareij[i][j][(int)age] =0.;
3395:
3396: for(h=0;h<=nhstepm;h++){
3397: for(k=0;k<=nhstepm;k++){
3398: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3399: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3400: for(i=1;i<=nlstate;i++)
3401: for(j=1;j<=nlstate;j++)
3402: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3403: }
3404: }
3405:
3406: /* pptj */
3407: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3408: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3409: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3410: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3411: varppt[j][i]=doldmp[j][i];
3412: /* end ppptj */
3413: /* x centered again */
3414: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3415: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3416:
3417: if (popbased==1) {
3418: if(mobilav ==0){
3419: for(i=1; i<=nlstate;i++)
3420: prlim[i][i]=probs[(int)age][i][ij];
3421: }else{ /* mobilav */
3422: for(i=1; i<=nlstate;i++)
3423: prlim[i][i]=mobaverage[(int)age][i][ij];
3424: }
3425: }
3426:
3427: /* This for computing probability of death (h=1 means
3428: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3429: as a weighted average of prlim.
3430: */
3431: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3432: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3433: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3434: }
3435: /* end probability of death */
3436:
3437: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3438: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3439: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3440: for(i=1; i<=nlstate;i++){
3441: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3442: }
3443: }
3444: fprintf(ficresprobmorprev,"\n");
3445:
3446: fprintf(ficresvij,"%.0f ",age );
3447: for(i=1; i<=nlstate;i++)
3448: for(j=1; j<=nlstate;j++){
3449: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3450: }
3451: fprintf(ficresvij,"\n");
3452: free_matrix(gp,0,nhstepm,1,nlstate);
3453: free_matrix(gm,0,nhstepm,1,nlstate);
3454: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3455: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3456: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3457: } /* End age */
3458: free_vector(gpp,nlstate+1,nlstate+ndeath);
3459: free_vector(gmp,nlstate+1,nlstate+ndeath);
3460: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3461: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3462: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3463: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3464: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3465: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3466: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3467: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3468: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3469: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3470: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3471: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3472: 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);
3473: /* 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);
3474: */
3475: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3476: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3477:
3478: free_vector(xp,1,npar);
3479: free_matrix(doldm,1,nlstate,1,nlstate);
3480: free_matrix(dnewm,1,nlstate,1,npar);
3481: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3482: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3483: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3484: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3485: fclose(ficresprobmorprev);
3486: fflush(ficgp);
3487: fflush(fichtm);
3488: } /* end varevsij */
3489:
3490: /************ Variance of prevlim ******************/
3491: 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[])
3492: {
3493: /* Variance of prevalence limit */
3494: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3495: double **newm;
3496: double **dnewm,**doldm;
3497: int i, j, nhstepm, hstepm;
3498: int k, cptcode;
3499: double *xp;
3500: double *gp, *gm;
3501: double **gradg, **trgradg;
3502: double age,agelim;
3503: int theta;
3504:
3505: pstamp(ficresvpl);
3506: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3507: fprintf(ficresvpl,"# Age");
3508: for(i=1; i<=nlstate;i++)
3509: fprintf(ficresvpl," %1d-%1d",i,i);
3510: fprintf(ficresvpl,"\n");
3511:
3512: xp=vector(1,npar);
3513: dnewm=matrix(1,nlstate,1,npar);
3514: doldm=matrix(1,nlstate,1,nlstate);
3515:
3516: hstepm=1*YEARM; /* Every year of age */
3517: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3518: agelim = AGESUP;
3519: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3520: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3521: if (stepm >= YEARM) hstepm=1;
3522: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3523: gradg=matrix(1,npar,1,nlstate);
3524: gp=vector(1,nlstate);
3525: gm=vector(1,nlstate);
3526:
3527: for(theta=1; theta <=npar; theta++){
3528: for(i=1; i<=npar; i++){ /* Computes gradient */
3529: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3530: }
3531: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3532: for(i=1;i<=nlstate;i++)
3533: gp[i] = prlim[i][i];
3534:
3535: for(i=1; i<=npar; i++) /* Computes gradient */
3536: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3537: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3538: for(i=1;i<=nlstate;i++)
3539: gm[i] = prlim[i][i];
3540:
3541: for(i=1;i<=nlstate;i++)
3542: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3543: } /* End theta */
3544:
3545: trgradg =matrix(1,nlstate,1,npar);
3546:
3547: for(j=1; j<=nlstate;j++)
3548: for(theta=1; theta <=npar; theta++)
3549: trgradg[j][theta]=gradg[theta][j];
3550:
3551: for(i=1;i<=nlstate;i++)
3552: varpl[i][(int)age] =0.;
3553: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3554: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3555: for(i=1;i<=nlstate;i++)
3556: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3557:
3558: fprintf(ficresvpl,"%.0f ",age );
3559: for(i=1; i<=nlstate;i++)
3560: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3561: fprintf(ficresvpl,"\n");
3562: free_vector(gp,1,nlstate);
3563: free_vector(gm,1,nlstate);
3564: free_matrix(gradg,1,npar,1,nlstate);
3565: free_matrix(trgradg,1,nlstate,1,npar);
3566: } /* End age */
3567:
3568: free_vector(xp,1,npar);
3569: free_matrix(doldm,1,nlstate,1,npar);
3570: free_matrix(dnewm,1,nlstate,1,nlstate);
3571:
3572: }
3573:
3574: /************ Variance of one-step probabilities ******************/
3575: 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[])
3576: {
3577: int i, j=0, i1, k1, l1, t, tj;
3578: int k2, l2, j1, z1;
3579: int k=0,l, cptcode;
3580: int first=1, first1, first2;
3581: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3582: double **dnewm,**doldm;
3583: double *xp;
3584: double *gp, *gm;
3585: double **gradg, **trgradg;
3586: double **mu;
3587: double age,agelim, cov[NCOVMAX+1];
3588: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3589: int theta;
3590: char fileresprob[FILENAMELENGTH];
3591: char fileresprobcov[FILENAMELENGTH];
3592: char fileresprobcor[FILENAMELENGTH];
3593: double ***varpij;
3594:
3595: strcpy(fileresprob,"prob");
3596: strcat(fileresprob,fileres);
3597: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3598: printf("Problem with resultfile: %s\n", fileresprob);
3599: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3600: }
3601: strcpy(fileresprobcov,"probcov");
3602: strcat(fileresprobcov,fileres);
3603: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3604: printf("Problem with resultfile: %s\n", fileresprobcov);
3605: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3606: }
3607: strcpy(fileresprobcor,"probcor");
3608: strcat(fileresprobcor,fileres);
3609: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3610: printf("Problem with resultfile: %s\n", fileresprobcor);
3611: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3612: }
3613: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3614: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3615: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3616: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3617: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3618: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3619: pstamp(ficresprob);
3620: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3621: fprintf(ficresprob,"# Age");
3622: pstamp(ficresprobcov);
3623: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3624: fprintf(ficresprobcov,"# Age");
3625: pstamp(ficresprobcor);
3626: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3627: fprintf(ficresprobcor,"# Age");
3628:
3629:
3630: for(i=1; i<=nlstate;i++)
3631: for(j=1; j<=(nlstate+ndeath);j++){
3632: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3633: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3634: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3635: }
3636: /* fprintf(ficresprob,"\n");
3637: fprintf(ficresprobcov,"\n");
3638: fprintf(ficresprobcor,"\n");
3639: */
3640: xp=vector(1,npar);
3641: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3642: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3643: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3644: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3645: first=1;
3646: fprintf(ficgp,"\n# Routine varprob");
3647: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3648: fprintf(fichtm,"\n");
3649:
3650: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3651: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3652: file %s<br>\n",optionfilehtmcov);
3653: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3654: and drawn. It helps understanding how is the covariance between two incidences.\
3655: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3656: 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. \
3657: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3658: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3659: standard deviations wide on each axis. <br>\
3660: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3661: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3662: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3663:
3664: cov[1]=1;
3665: /* tj=cptcoveff; */
3666: tj = (int) pow(2,cptcoveff);
3667: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3668: j1=0;
3669: for(j1=1; j1<=tj;j1++){
3670: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3671: /*j1++;*/
3672: if (cptcovn>0) {
3673: fprintf(ficresprob, "\n#********** Variable ");
3674: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3675: fprintf(ficresprob, "**********\n#\n");
3676: fprintf(ficresprobcov, "\n#********** Variable ");
3677: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3678: fprintf(ficresprobcov, "**********\n#\n");
3679:
3680: fprintf(ficgp, "\n#********** Variable ");
3681: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3682: fprintf(ficgp, "**********\n#\n");
3683:
3684:
3685: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3686: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3687: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3688:
3689: fprintf(ficresprobcor, "\n#********** Variable ");
3690: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3691: fprintf(ficresprobcor, "**********\n#");
3692: }
3693:
3694: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3695: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3696: gp=vector(1,(nlstate)*(nlstate+ndeath));
3697: gm=vector(1,(nlstate)*(nlstate+ndeath));
3698: for (age=bage; age<=fage; age ++){
3699: cov[2]=age;
3700: for (k=1; k<=cptcovn;k++) {
3701: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3702: * 1 1 1 1 1
3703: * 2 2 1 1 1
3704: * 3 1 2 1 1
3705: */
3706: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3707: }
3708: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3709: for (k=1; k<=cptcovprod;k++)
3710: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3711:
3712:
3713: for(theta=1; theta <=npar; theta++){
3714: for(i=1; i<=npar; i++)
3715: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3716:
3717: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3718:
3719: k=0;
3720: for(i=1; i<= (nlstate); i++){
3721: for(j=1; j<=(nlstate+ndeath);j++){
3722: k=k+1;
3723: gp[k]=pmmij[i][j];
3724: }
3725: }
3726:
3727: for(i=1; i<=npar; i++)
3728: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3729:
3730: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3731: k=0;
3732: for(i=1; i<=(nlstate); i++){
3733: for(j=1; j<=(nlstate+ndeath);j++){
3734: k=k+1;
3735: gm[k]=pmmij[i][j];
3736: }
3737: }
3738:
3739: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3740: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3741: }
3742:
3743: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3744: for(theta=1; theta <=npar; theta++)
3745: trgradg[j][theta]=gradg[theta][j];
3746:
3747: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3748: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3749:
3750: pmij(pmmij,cov,ncovmodel,x,nlstate);
3751:
3752: k=0;
3753: for(i=1; i<=(nlstate); i++){
3754: for(j=1; j<=(nlstate+ndeath);j++){
3755: k=k+1;
3756: mu[k][(int) age]=pmmij[i][j];
3757: }
3758: }
3759: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3760: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3761: varpij[i][j][(int)age] = doldm[i][j];
3762:
3763: /*printf("\n%d ",(int)age);
3764: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3765: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3766: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3767: }*/
3768:
3769: fprintf(ficresprob,"\n%d ",(int)age);
3770: fprintf(ficresprobcov,"\n%d ",(int)age);
3771: fprintf(ficresprobcor,"\n%d ",(int)age);
3772:
3773: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3774: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3775: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3776: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3777: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3778: }
3779: i=0;
3780: for (k=1; k<=(nlstate);k++){
3781: for (l=1; l<=(nlstate+ndeath);l++){
3782: i++;
3783: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3784: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3785: for (j=1; j<=i;j++){
3786: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3787: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3788: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3789: }
3790: }
3791: }/* end of loop for state */
3792: } /* end of loop for age */
3793: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3794: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3795: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3796: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3797:
3798: /* Confidence intervalle of pij */
3799: /*
3800: fprintf(ficgp,"\nunset parametric;unset label");
3801: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3802: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3803: 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);
3804: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3805: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3806: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3807: */
3808:
3809: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3810: first1=1;first2=2;
3811: for (k2=1; k2<=(nlstate);k2++){
3812: for (l2=1; l2<=(nlstate+ndeath);l2++){
3813: if(l2==k2) continue;
3814: j=(k2-1)*(nlstate+ndeath)+l2;
3815: for (k1=1; k1<=(nlstate);k1++){
3816: for (l1=1; l1<=(nlstate+ndeath);l1++){
3817: if(l1==k1) continue;
3818: i=(k1-1)*(nlstate+ndeath)+l1;
3819: if(i<=j) continue;
3820: for (age=bage; age<=fage; age ++){
3821: if ((int)age %5==0){
3822: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3823: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3824: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3825: mu1=mu[i][(int) age]/stepm*YEARM ;
3826: mu2=mu[j][(int) age]/stepm*YEARM;
3827: c12=cv12/sqrt(v1*v2);
3828: /* Computing eigen value of matrix of covariance */
3829: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3830: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3831: if ((lc2 <0) || (lc1 <0) ){
3832: if(first2==1){
3833: first1=0;
3834: 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);
3835: }
3836: 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);
3837: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3838: /* lc2=fabs(lc2); */
3839: }
3840:
3841: /* Eigen vectors */
3842: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3843: /*v21=sqrt(1.-v11*v11); *//* error */
3844: v21=(lc1-v1)/cv12*v11;
3845: v12=-v21;
3846: v22=v11;
3847: tnalp=v21/v11;
3848: if(first1==1){
3849: first1=0;
3850: 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);
3851: }
3852: 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);
3853: /*printf(fignu*/
3854: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3855: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3856: if(first==1){
3857: first=0;
3858: fprintf(ficgp,"\nset parametric;unset label");
3859: 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);
3860: fprintf(ficgp,"\nset ter png small size 320, 240");
3861: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3862: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3863: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3864: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3865: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3866: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3867: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3868: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3869: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3870: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3871: 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",\
3872: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3873: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3874: }else{
3875: first=0;
3876: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3877: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3878: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3879: 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",\
3880: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3881: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3882: }/* if first */
3883: } /* age mod 5 */
3884: } /* end loop age */
3885: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3886: first=1;
3887: } /*l12 */
3888: } /* k12 */
3889: } /*l1 */
3890: }/* k1 */
3891: /* } /* loop covariates */
3892: }
3893: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3894: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3895: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3896: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3897: free_vector(xp,1,npar);
3898: fclose(ficresprob);
3899: fclose(ficresprobcov);
3900: fclose(ficresprobcor);
3901: fflush(ficgp);
3902: fflush(fichtmcov);
3903: }
3904:
3905:
3906: /******************* Printing html file ***********/
3907: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3908: int lastpass, int stepm, int weightopt, char model[],\
3909: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3910: int popforecast, int estepm ,\
3911: double jprev1, double mprev1,double anprev1, \
3912: double jprev2, double mprev2,double anprev2){
3913: int jj1, k1, i1, cpt;
3914:
3915: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3916: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3917: </ul>");
3918: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3919: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3920: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3921: fprintf(fichtm,"\
3922: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3923: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3924: fprintf(fichtm,"\
3925: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3926: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3927: fprintf(fichtm,"\
3928: - (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): \
3929: <a href=\"%s\">%s</a> <br>\n",
3930: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3931: fprintf(fichtm,"\
3932: - Population projections by age and states: \
3933: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3934:
3935: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3936:
3937: m=pow(2,cptcoveff);
3938: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3939:
3940: jj1=0;
3941: for(k1=1; k1<=m;k1++){
3942: for(i1=1; i1<=ncodemax[k1];i1++){
3943: jj1++;
3944: if (cptcovn > 0) {
3945: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3946: for (cpt=1; cpt<=cptcoveff;cpt++)
3947: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3948: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3949: }
3950: /* Pij */
3951: 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> \
3952: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3953: /* Quasi-incidences */
3954: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3955: 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> \
3956: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3957: /* Period (stable) prevalence in each health state */
3958: for(cpt=1; cpt<=nlstate;cpt++){
3959: fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3960: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3961: }
3962: for(cpt=1; cpt<=nlstate;cpt++) {
3963: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3964: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3965: }
3966: } /* end i1 */
3967: }/* End k1 */
3968: fprintf(fichtm,"</ul>");
3969:
3970:
3971: fprintf(fichtm,"\
3972: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3973: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3974:
3975: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3976: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3977: fprintf(fichtm,"\
3978: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3979: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3980:
3981: fprintf(fichtm,"\
3982: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3983: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3984: fprintf(fichtm,"\
3985: - 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): \
3986: <a href=\"%s\">%s</a> <br>\n</li>",
3987: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3988: fprintf(fichtm,"\
3989: - (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): \
3990: <a href=\"%s\">%s</a> <br>\n</li>",
3991: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3992: fprintf(fichtm,"\
3993: - 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",
3994: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3995: fprintf(fichtm,"\
3996: - 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",
3997: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3998: fprintf(fichtm,"\
3999: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4000: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4001:
4002: /* if(popforecast==1) fprintf(fichtm,"\n */
4003: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4004: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4005: /* <br>",fileres,fileres,fileres,fileres); */
4006: /* else */
4007: /* 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); */
4008: fflush(fichtm);
4009: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4010:
4011: m=pow(2,cptcoveff);
4012: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4013:
4014: jj1=0;
4015: for(k1=1; k1<=m;k1++){
4016: for(i1=1; i1<=ncodemax[k1];i1++){
4017: jj1++;
4018: if (cptcovn > 0) {
4019: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4020: for (cpt=1; cpt<=cptcoveff;cpt++)
4021: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4022: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4023: }
4024: for(cpt=1; cpt<=nlstate;cpt++) {
4025: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4026: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4027: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4028: }
4029: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4030: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4031: true period expectancies (those weighted with period prevalences are also\
4032: drawn in addition to the population based expectancies computed using\
4033: observed and cahotic prevalences: %s%d.png<br>\
4034: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4035: } /* end i1 */
4036: }/* End k1 */
4037: fprintf(fichtm,"</ul>");
4038: fflush(fichtm);
4039: }
4040:
4041: /******************* Gnuplot file **************/
4042: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4043:
4044: char dirfileres[132],optfileres[132];
4045: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4046: int ng=0;
4047: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4048: /* printf("Problem with file %s",optionfilegnuplot); */
4049: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4050: /* } */
4051:
4052: /*#ifdef windows */
4053: fprintf(ficgp,"cd \"%s\" \n",pathc);
4054: /*#endif */
4055: m=pow(2,cptcoveff);
4056:
4057: strcpy(dirfileres,optionfilefiname);
4058: strcpy(optfileres,"vpl");
4059: /* 1eme*/
4060: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4061: for (cpt=1; cpt<= nlstate ; cpt ++) {
4062: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4063: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4064: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4065: fprintf(ficgp,"set xlabel \"Age\" \n\
4066: set ylabel \"Probability\" \n\
4067: set ter png small size 320, 240\n\
4068: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4069:
4070: for (i=1; i<= nlstate ; i ++) {
4071: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4072: else fprintf(ficgp," \%%*lf (\%%*lf)");
4073: }
4074: 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);
4075: for (i=1; i<= nlstate ; i ++) {
4076: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4077: else fprintf(ficgp," \%%*lf (\%%*lf)");
4078: }
4079: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4080: for (i=1; i<= nlstate ; i ++) {
4081: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4082: else fprintf(ficgp," \%%*lf (\%%*lf)");
4083: }
4084: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4085: }
4086: }
4087: /*2 eme*/
4088: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4089: for (k1=1; k1<= m ; k1 ++) {
4090: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4091: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4092:
4093: for (i=1; i<= nlstate+1 ; i ++) {
4094: k=2*i;
4095: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4096: for (j=1; j<= nlstate+1 ; j ++) {
4097: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4098: else fprintf(ficgp," \%%*lf (\%%*lf)");
4099: }
4100: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4101: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4102: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4103: for (j=1; j<= nlstate+1 ; j ++) {
4104: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4105: else fprintf(ficgp," \%%*lf (\%%*lf)");
4106: }
4107: fprintf(ficgp,"\" t\"\" w l lt 0,");
4108: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4109: for (j=1; j<= nlstate+1 ; j ++) {
4110: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4111: else fprintf(ficgp," \%%*lf (\%%*lf)");
4112: }
4113: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4114: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4115: }
4116: }
4117:
4118: /*3eme*/
4119:
4120: for (k1=1; k1<= m ; k1 ++) {
4121: for (cpt=1; cpt<= nlstate ; cpt ++) {
4122: /* k=2+nlstate*(2*cpt-2); */
4123: k=2+(nlstate+1)*(cpt-1);
4124: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4125: fprintf(ficgp,"set ter png small size 320, 240\n\
4126: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4127: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4128: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4129: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4130: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4131: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4132: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4133:
4134: */
4135: for (i=1; i< nlstate ; i ++) {
4136: 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);
4137: /* 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);*/
4138:
4139: }
4140: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4141: }
4142: }
4143:
4144: /* CV preval stable (period) */
4145: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4146: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4147: k=3;
4148: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4149: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4150: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4151: set ter png small size 320, 240\n\
4152: unset log y\n\
4153: plot [%.f:%.f] ", ageminpar, agemaxpar);
4154: for (i=1; i<= nlstate ; i ++){
4155: if(i==1)
4156: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4157: else
4158: fprintf(ficgp,", '' ");
4159: l=(nlstate+ndeath)*(i-1)+1;
4160: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4161: for (j=1; j<= (nlstate-1) ; j ++)
4162: fprintf(ficgp,"+$%d",k+l+j);
4163: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4164: } /* nlstate */
4165: fprintf(ficgp,"\n");
4166: } /* end cpt state*/
4167: } /* end covariate */
4168:
4169: /* proba elementaires */
4170: for(i=1,jk=1; i <=nlstate; i++){
4171: for(k=1; k <=(nlstate+ndeath); k++){
4172: if (k != i) {
4173: for(j=1; j <=ncovmodel; j++){
4174: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4175: jk++;
4176: fprintf(ficgp,"\n");
4177: }
4178: }
4179: }
4180: }
4181: /*goto avoid;*/
4182: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4183: for(jk=1; jk <=m; jk++) {
4184: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4185: if (ng==2)
4186: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4187: else
4188: fprintf(ficgp,"\nset title \"Probability\"\n");
4189: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4190: i=1;
4191: for(k2=1; k2<=nlstate; k2++) {
4192: k3=i;
4193: for(k=1; k<=(nlstate+ndeath); k++) {
4194: if (k != k2){
4195: if(ng==2)
4196: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4197: else
4198: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4199: ij=1;/* To be checked else nbcode[0][0] wrong */
4200: for(j=3; j <=ncovmodel; j++) {
4201: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4202: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4203: /* ij++; */
4204: /* } */
4205: /* else */
4206: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4207: }
4208: fprintf(ficgp,")/(1");
4209:
4210: for(k1=1; k1 <=nlstate; k1++){
4211: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4212: ij=1;
4213: for(j=3; j <=ncovmodel; j++){
4214: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4215: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4216: /* ij++; */
4217: /* } */
4218: /* else */
4219: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4220: }
4221: fprintf(ficgp,")");
4222: }
4223: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4224: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4225: i=i+ncovmodel;
4226: }
4227: } /* end k */
4228: } /* end k2 */
4229: } /* end jk */
4230: } /* end ng */
4231: avoid:
4232: fflush(ficgp);
4233: } /* end gnuplot */
4234:
4235:
4236: /*************** Moving average **************/
4237: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4238:
4239: int i, cpt, cptcod;
4240: int modcovmax =1;
4241: int mobilavrange, mob;
4242: double age;
4243:
4244: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4245: a covariate has 2 modalities */
4246: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4247:
4248: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4249: if(mobilav==1) mobilavrange=5; /* default */
4250: else mobilavrange=mobilav;
4251: for (age=bage; age<=fage; age++)
4252: for (i=1; i<=nlstate;i++)
4253: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4254: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4255: /* We keep the original values on the extreme ages bage, fage and for
4256: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4257: we use a 5 terms etc. until the borders are no more concerned.
4258: */
4259: for (mob=3;mob <=mobilavrange;mob=mob+2){
4260: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4261: for (i=1; i<=nlstate;i++){
4262: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4263: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4264: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4265: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4266: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4267: }
4268: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4269: }
4270: }
4271: }/* end age */
4272: }/* end mob */
4273: }else return -1;
4274: return 0;
4275: }/* End movingaverage */
4276:
4277:
4278: /************** Forecasting ******************/
4279: 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){
4280: /* proj1, year, month, day of starting projection
4281: agemin, agemax range of age
4282: dateprev1 dateprev2 range of dates during which prevalence is computed
4283: anproj2 year of en of projection (same day and month as proj1).
4284: */
4285: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4286: int *popage;
4287: double agec; /* generic age */
4288: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4289: double *popeffectif,*popcount;
4290: double ***p3mat;
4291: double ***mobaverage;
4292: char fileresf[FILENAMELENGTH];
4293:
4294: agelim=AGESUP;
4295: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4296:
4297: strcpy(fileresf,"f");
4298: strcat(fileresf,fileres);
4299: if((ficresf=fopen(fileresf,"w"))==NULL) {
4300: printf("Problem with forecast resultfile: %s\n", fileresf);
4301: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4302: }
4303: printf("Computing forecasting: result on file '%s' \n", fileresf);
4304: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4305:
4306: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4307:
4308: if (mobilav!=0) {
4309: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4310: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4311: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4312: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4313: }
4314: }
4315:
4316: stepsize=(int) (stepm+YEARM-1)/YEARM;
4317: if (stepm<=12) stepsize=1;
4318: if(estepm < stepm){
4319: printf ("Problem %d lower than %d\n",estepm, stepm);
4320: }
4321: else hstepm=estepm;
4322:
4323: hstepm=hstepm/stepm;
4324: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4325: fractional in yp1 */
4326: anprojmean=yp;
4327: yp2=modf((yp1*12),&yp);
4328: mprojmean=yp;
4329: yp1=modf((yp2*30.5),&yp);
4330: jprojmean=yp;
4331: if(jprojmean==0) jprojmean=1;
4332: if(mprojmean==0) jprojmean=1;
4333:
4334: i1=cptcoveff;
4335: if (cptcovn < 1){i1=1;}
4336:
4337: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4338:
4339: fprintf(ficresf,"#****** Routine prevforecast **\n");
4340:
4341: /* if (h==(int)(YEARM*yearp)){ */
4342: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4343: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4344: k=k+1;
4345: fprintf(ficresf,"\n#******");
4346: for(j=1;j<=cptcoveff;j++) {
4347: 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]]);
4348: }
4349: fprintf(ficresf,"******\n");
4350: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4351: for(j=1; j<=nlstate+ndeath;j++){
4352: for(i=1; i<=nlstate;i++)
4353: fprintf(ficresf," p%d%d",i,j);
4354: fprintf(ficresf," p.%d",j);
4355: }
4356: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4357: fprintf(ficresf,"\n");
4358: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4359:
4360: for (agec=fage; agec>=(ageminpar-1); agec--){
4361: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4362: nhstepm = nhstepm/hstepm;
4363: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4364: oldm=oldms;savm=savms;
4365: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4366:
4367: for (h=0; h<=nhstepm; h++){
4368: if (h*hstepm/YEARM*stepm ==yearp) {
4369: fprintf(ficresf,"\n");
4370: for(j=1;j<=cptcoveff;j++)
4371: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4372: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4373: }
4374: for(j=1; j<=nlstate+ndeath;j++) {
4375: ppij=0.;
4376: for(i=1; i<=nlstate;i++) {
4377: if (mobilav==1)
4378: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4379: else {
4380: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4381: }
4382: if (h*hstepm/YEARM*stepm== yearp) {
4383: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4384: }
4385: } /* end i */
4386: if (h*hstepm/YEARM*stepm==yearp) {
4387: fprintf(ficresf," %.3f", ppij);
4388: }
4389: }/* end j */
4390: } /* end h */
4391: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4392: } /* end agec */
4393: } /* end yearp */
4394: } /* end cptcod */
4395: } /* end cptcov */
4396:
4397: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4398:
4399: fclose(ficresf);
4400: }
4401:
4402: /************** Forecasting *****not tested NB*************/
4403: 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){
4404:
4405: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4406: int *popage;
4407: double calagedatem, agelim, kk1, kk2;
4408: double *popeffectif,*popcount;
4409: double ***p3mat,***tabpop,***tabpopprev;
4410: double ***mobaverage;
4411: char filerespop[FILENAMELENGTH];
4412:
4413: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4414: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4415: agelim=AGESUP;
4416: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4417:
4418: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4419:
4420:
4421: strcpy(filerespop,"pop");
4422: strcat(filerespop,fileres);
4423: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4424: printf("Problem with forecast resultfile: %s\n", filerespop);
4425: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4426: }
4427: printf("Computing forecasting: result on file '%s' \n", filerespop);
4428: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4429:
4430: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4431:
4432: if (mobilav!=0) {
4433: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4434: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4435: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4436: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4437: }
4438: }
4439:
4440: stepsize=(int) (stepm+YEARM-1)/YEARM;
4441: if (stepm<=12) stepsize=1;
4442:
4443: agelim=AGESUP;
4444:
4445: hstepm=1;
4446: hstepm=hstepm/stepm;
4447:
4448: if (popforecast==1) {
4449: if((ficpop=fopen(popfile,"r"))==NULL) {
4450: printf("Problem with population file : %s\n",popfile);exit(0);
4451: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4452: }
4453: popage=ivector(0,AGESUP);
4454: popeffectif=vector(0,AGESUP);
4455: popcount=vector(0,AGESUP);
4456:
4457: i=1;
4458: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4459:
4460: imx=i;
4461: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4462: }
4463:
4464: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4465: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4466: k=k+1;
4467: fprintf(ficrespop,"\n#******");
4468: for(j=1;j<=cptcoveff;j++) {
4469: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4470: }
4471: fprintf(ficrespop,"******\n");
4472: fprintf(ficrespop,"# Age");
4473: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4474: if (popforecast==1) fprintf(ficrespop," [Population]");
4475:
4476: for (cpt=0; cpt<=0;cpt++) {
4477: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4478:
4479: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4480: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4481: nhstepm = nhstepm/hstepm;
4482:
4483: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4484: oldm=oldms;savm=savms;
4485: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4486:
4487: for (h=0; h<=nhstepm; h++){
4488: if (h==(int) (calagedatem+YEARM*cpt)) {
4489: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4490: }
4491: for(j=1; j<=nlstate+ndeath;j++) {
4492: kk1=0.;kk2=0;
4493: for(i=1; i<=nlstate;i++) {
4494: if (mobilav==1)
4495: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4496: else {
4497: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4498: }
4499: }
4500: if (h==(int)(calagedatem+12*cpt)){
4501: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4502: /*fprintf(ficrespop," %.3f", kk1);
4503: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4504: }
4505: }
4506: for(i=1; i<=nlstate;i++){
4507: kk1=0.;
4508: for(j=1; j<=nlstate;j++){
4509: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4510: }
4511: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4512: }
4513:
4514: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4515: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4516: }
4517: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4518: }
4519: }
4520:
4521: /******/
4522:
4523: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4524: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4525: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4526: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4527: nhstepm = nhstepm/hstepm;
4528:
4529: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4530: oldm=oldms;savm=savms;
4531: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4532: for (h=0; h<=nhstepm; h++){
4533: if (h==(int) (calagedatem+YEARM*cpt)) {
4534: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4535: }
4536: for(j=1; j<=nlstate+ndeath;j++) {
4537: kk1=0.;kk2=0;
4538: for(i=1; i<=nlstate;i++) {
4539: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4540: }
4541: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4542: }
4543: }
4544: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4545: }
4546: }
4547: }
4548: }
4549:
4550: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4551:
4552: if (popforecast==1) {
4553: free_ivector(popage,0,AGESUP);
4554: free_vector(popeffectif,0,AGESUP);
4555: free_vector(popcount,0,AGESUP);
4556: }
4557: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4558: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4559: fclose(ficrespop);
4560: } /* End of popforecast */
4561:
4562: int fileappend(FILE *fichier, char *optionfich)
4563: {
4564: if((fichier=fopen(optionfich,"a"))==NULL) {
4565: printf("Problem with file: %s\n", optionfich);
4566: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4567: return (0);
4568: }
4569: fflush(fichier);
4570: return (1);
4571: }
4572:
4573:
4574: /**************** function prwizard **********************/
4575: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4576: {
4577:
4578: /* Wizard to print covariance matrix template */
4579:
4580: char ca[32], cb[32], cc[32];
4581: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4582: int numlinepar;
4583:
4584: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4585: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4586: for(i=1; i <=nlstate; i++){
4587: jj=0;
4588: for(j=1; j <=nlstate+ndeath; j++){
4589: if(j==i) continue;
4590: jj++;
4591: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4592: printf("%1d%1d",i,j);
4593: fprintf(ficparo,"%1d%1d",i,j);
4594: for(k=1; k<=ncovmodel;k++){
4595: /* printf(" %lf",param[i][j][k]); */
4596: /* fprintf(ficparo," %lf",param[i][j][k]); */
4597: printf(" 0.");
4598: fprintf(ficparo," 0.");
4599: }
4600: printf("\n");
4601: fprintf(ficparo,"\n");
4602: }
4603: }
4604: printf("# Scales (for hessian or gradient estimation)\n");
4605: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4606: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4607: for(i=1; i <=nlstate; i++){
4608: jj=0;
4609: for(j=1; j <=nlstate+ndeath; j++){
4610: if(j==i) continue;
4611: jj++;
4612: fprintf(ficparo,"%1d%1d",i,j);
4613: printf("%1d%1d",i,j);
4614: fflush(stdout);
4615: for(k=1; k<=ncovmodel;k++){
4616: /* printf(" %le",delti3[i][j][k]); */
4617: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4618: printf(" 0.");
4619: fprintf(ficparo," 0.");
4620: }
4621: numlinepar++;
4622: printf("\n");
4623: fprintf(ficparo,"\n");
4624: }
4625: }
4626: printf("# Covariance matrix\n");
4627: /* # 121 Var(a12)\n\ */
4628: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4629: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4630: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4631: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4632: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4633: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4634: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4635: fflush(stdout);
4636: fprintf(ficparo,"# Covariance matrix\n");
4637: /* # 121 Var(a12)\n\ */
4638: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4639: /* # ...\n\ */
4640: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4641:
4642: for(itimes=1;itimes<=2;itimes++){
4643: jj=0;
4644: for(i=1; i <=nlstate; i++){
4645: for(j=1; j <=nlstate+ndeath; j++){
4646: if(j==i) continue;
4647: for(k=1; k<=ncovmodel;k++){
4648: jj++;
4649: ca[0]= k+'a'-1;ca[1]='\0';
4650: if(itimes==1){
4651: printf("#%1d%1d%d",i,j,k);
4652: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4653: }else{
4654: printf("%1d%1d%d",i,j,k);
4655: fprintf(ficparo,"%1d%1d%d",i,j,k);
4656: /* printf(" %.5le",matcov[i][j]); */
4657: }
4658: ll=0;
4659: for(li=1;li <=nlstate; li++){
4660: for(lj=1;lj <=nlstate+ndeath; lj++){
4661: if(lj==li) continue;
4662: for(lk=1;lk<=ncovmodel;lk++){
4663: ll++;
4664: if(ll<=jj){
4665: cb[0]= lk +'a'-1;cb[1]='\0';
4666: if(ll<jj){
4667: if(itimes==1){
4668: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4669: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4670: }else{
4671: printf(" 0.");
4672: fprintf(ficparo," 0.");
4673: }
4674: }else{
4675: if(itimes==1){
4676: printf(" Var(%s%1d%1d)",ca,i,j);
4677: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4678: }else{
4679: printf(" 0.");
4680: fprintf(ficparo," 0.");
4681: }
4682: }
4683: }
4684: } /* end lk */
4685: } /* end lj */
4686: } /* end li */
4687: printf("\n");
4688: fprintf(ficparo,"\n");
4689: numlinepar++;
4690: } /* end k*/
4691: } /*end j */
4692: } /* end i */
4693: } /* end itimes */
4694:
4695: } /* end of prwizard */
4696: /******************* Gompertz Likelihood ******************************/
4697: double gompertz(double x[])
4698: {
4699: double A,B,L=0.0,sump=0.,num=0.;
4700: int i,n=0; /* n is the size of the sample */
4701:
4702: for (i=0;i<=imx-1 ; i++) {
4703: sump=sump+weight[i];
4704: /* sump=sump+1;*/
4705: num=num+1;
4706: }
4707:
4708:
4709: /* for (i=0; i<=imx; i++)
4710: 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]);*/
4711:
4712: for (i=1;i<=imx ; i++)
4713: {
4714: if (cens[i] == 1 && wav[i]>1)
4715: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4716:
4717: if (cens[i] == 0 && wav[i]>1)
4718: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4719: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4720:
4721: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4722: if (wav[i] > 1 ) { /* ??? */
4723: L=L+A*weight[i];
4724: /* 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]);*/
4725: }
4726: }
4727:
4728: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4729:
4730: return -2*L*num/sump;
4731: }
4732:
4733: #ifdef GSL
4734: /******************* Gompertz_f Likelihood ******************************/
4735: double gompertz_f(const gsl_vector *v, void *params)
4736: {
4737: double A,B,LL=0.0,sump=0.,num=0.;
4738: double *x= (double *) v->data;
4739: int i,n=0; /* n is the size of the sample */
4740:
4741: for (i=0;i<=imx-1 ; i++) {
4742: sump=sump+weight[i];
4743: /* sump=sump+1;*/
4744: num=num+1;
4745: }
4746:
4747:
4748: /* for (i=0; i<=imx; i++)
4749: 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]);*/
4750: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4751: for (i=1;i<=imx ; i++)
4752: {
4753: if (cens[i] == 1 && wav[i]>1)
4754: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4755:
4756: if (cens[i] == 0 && wav[i]>1)
4757: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4758: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4759:
4760: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4761: if (wav[i] > 1 ) { /* ??? */
4762: LL=LL+A*weight[i];
4763: /* 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]);*/
4764: }
4765: }
4766:
4767: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4768: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4769:
4770: return -2*LL*num/sump;
4771: }
4772: #endif
4773:
4774: /******************* Printing html file ***********/
4775: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4776: int lastpass, int stepm, int weightopt, char model[],\
4777: int imx, double p[],double **matcov,double agemortsup){
4778: int i,k;
4779:
4780: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4781: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4782: for (i=1;i<=2;i++)
4783: 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]));
4784: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4785: fprintf(fichtm,"</ul>");
4786:
4787: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4788:
4789: 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>");
4790:
4791: for (k=agegomp;k<(agemortsup-2);k++)
4792: 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]);
4793:
4794:
4795: fflush(fichtm);
4796: }
4797:
4798: /******************* Gnuplot file **************/
4799: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4800:
4801: char dirfileres[132],optfileres[132];
4802: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4803: int ng;
4804:
4805:
4806: /*#ifdef windows */
4807: fprintf(ficgp,"cd \"%s\" \n",pathc);
4808: /*#endif */
4809:
4810:
4811: strcpy(dirfileres,optionfilefiname);
4812: strcpy(optfileres,"vpl");
4813: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4814: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4815: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4816: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4817: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4818:
4819: }
4820:
4821: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4822: {
4823:
4824: /*-------- data file ----------*/
4825: FILE *fic;
4826: char dummy[]=" ";
4827: int i, j, n;
4828: int linei, month, year,iout;
4829: char line[MAXLINE], linetmp[MAXLINE];
4830: char stra[80], strb[80];
4831: char *stratrunc;
4832: int lstra;
4833:
4834:
4835: if((fic=fopen(datafile,"r"))==NULL) {
4836: printf("Problem while opening datafile: %s\n", datafile);return 1;
4837: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4838: }
4839:
4840: i=1;
4841: linei=0;
4842: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4843: linei=linei+1;
4844: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4845: if(line[j] == '\t')
4846: line[j] = ' ';
4847: }
4848: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4849: ;
4850: };
4851: line[j+1]=0; /* Trims blanks at end of line */
4852: if(line[0]=='#'){
4853: fprintf(ficlog,"Comment line\n%s\n",line);
4854: printf("Comment line\n%s\n",line);
4855: continue;
4856: }
4857: trimbb(linetmp,line); /* Trims multiple blanks in line */
4858: for (j=0; line[j]!='\0';j++){
4859: line[j]=linetmp[j];
4860: }
4861:
4862:
4863: for (j=maxwav;j>=1;j--){
4864: cutv(stra, strb, line, ' ');
4865: if(strb[0]=='.') { /* Missing status */
4866: lval=-1;
4867: }else{
4868: errno=0;
4869: lval=strtol(strb,&endptr,10);
4870: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4871: if( strb[0]=='\0' || (*endptr != '\0')){
4872: 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);
4873: 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);
4874: return 1;
4875: }
4876: }
4877: s[j][i]=lval;
4878:
4879: strcpy(line,stra);
4880: cutv(stra, strb,line,' ');
4881: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4882: }
4883: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4884: month=99;
4885: year=9999;
4886: }else{
4887: 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);
4888: 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);
4889: return 1;
4890: }
4891: anint[j][i]= (double) year;
4892: mint[j][i]= (double)month;
4893: strcpy(line,stra);
4894: } /* ENd Waves */
4895:
4896: cutv(stra, strb,line,' ');
4897: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4898: }
4899: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4900: month=99;
4901: year=9999;
4902: }else{
4903: 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);
4904: 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);
4905: return 1;
4906: }
4907: andc[i]=(double) year;
4908: moisdc[i]=(double) month;
4909: strcpy(line,stra);
4910:
4911: cutv(stra, strb,line,' ');
4912: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4913: }
4914: else if(iout=sscanf(strb,"%s.", dummy) != 0){
4915: month=99;
4916: year=9999;
4917: }else{
4918: 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);
4919: 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);
4920: return 1;
4921: }
4922: if (year==9999) {
4923: 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);
4924: 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);
4925: return 1;
4926:
4927: }
4928: annais[i]=(double)(year);
4929: moisnais[i]=(double)(month);
4930: strcpy(line,stra);
4931:
4932: cutv(stra, strb,line,' ');
4933: errno=0;
4934: dval=strtod(strb,&endptr);
4935: if( strb[0]=='\0' || (*endptr != '\0')){
4936: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4937: 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);
4938: fflush(ficlog);
4939: return 1;
4940: }
4941: weight[i]=dval;
4942: strcpy(line,stra);
4943:
4944: for (j=ncovcol;j>=1;j--){
4945: cutv(stra, strb,line,' ');
4946: if(strb[0]=='.') { /* Missing status */
4947: lval=-1;
4948: }else{
4949: errno=0;
4950: lval=strtol(strb,&endptr,10);
4951: if( strb[0]=='\0' || (*endptr != '\0')){
4952: 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);
4953: 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);
4954: return 1;
4955: }
4956: }
4957: if(lval <-1 || lval >1){
4958: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4959: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4960: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4961: For example, for multinomial values like 1, 2 and 3,\n \
4962: build V1=0 V2=0 for the reference value (1),\n \
4963: V1=1 V2=0 for (2) \n \
4964: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4965: output of IMaCh is often meaningless.\n \
4966: Exiting.\n",lval,linei, i,line,j);
4967: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
4968: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4969: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4970: For example, for multinomial values like 1, 2 and 3,\n \
4971: build V1=0 V2=0 for the reference value (1),\n \
4972: V1=1 V2=0 for (2) \n \
4973: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4974: output of IMaCh is often meaningless.\n \
4975: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4976: return 1;
4977: }
4978: covar[j][i]=(double)(lval);
4979: strcpy(line,stra);
4980: }
4981: lstra=strlen(stra);
4982:
4983: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4984: stratrunc = &(stra[lstra-9]);
4985: num[i]=atol(stratrunc);
4986: }
4987: else
4988: num[i]=atol(stra);
4989: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4990: 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;}*/
4991:
4992: i=i+1;
4993: } /* End loop reading data */
4994:
4995: *imax=i-1; /* Number of individuals */
4996: fclose(fic);
4997:
4998: return (0);
4999: endread:
5000: printf("Exiting readdata: ");
5001: fclose(fic);
5002: return (1);
5003:
5004:
5005:
5006: }
5007: void removespace(char *str) {
5008: char *p1 = str, *p2 = str;
5009: do
5010: while (*p2 == ' ')
5011: p2++;
5012: while (*p1++ = *p2++);
5013: }
5014:
5015: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5016: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5017: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5018: * - cptcovn or number of covariates k of the models excluding age*products =6
5019: * - cptcovage number of covariates with age*products =2
5020: * - cptcovs number of simple covariates
5021: * - 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
5022: * which is a new column after the 9 (ncovcol) variables.
5023: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5024: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5025: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5026: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5027: */
5028: {
5029: int i, j, k, ks;
5030: int i1, j1, k1, k2;
5031: char modelsav[80];
5032: char stra[80], strb[80], strc[80], strd[80],stre[80];
5033:
5034: /*removespace(model);*/
5035: if (strlen(model) >1){ /* If there is at least 1 covariate */
5036: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5037: j=nbocc(model,'+'); /**< j=Number of '+' */
5038: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5039: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5040: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5041: /* including age products which are counted in cptcovage.
5042: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5043: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5044: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5045: strcpy(modelsav,model);
5046: if (strstr(model,"AGE") !=0){
5047: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5048: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5049: return 1;
5050: }
5051: if (strstr(model,"v") !=0){
5052: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5053: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5054: return 1;
5055: }
5056:
5057: /* Design
5058: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5059: * < ncovcol=8 >
5060: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5061: * k= 1 2 3 4 5 6 7 8
5062: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5063: * covar[k,i], value of kth covariate if not including age for individual i:
5064: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5065: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5066: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5067: * Tage[++cptcovage]=k
5068: * if products, new covar are created after ncovcol with k1
5069: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5070: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5071: * 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
5072: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5073: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5074: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5075: * < ncovcol=8 >
5076: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5077: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5078: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5079: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5080: * p Tprod[1]@2={ 6, 5}
5081: *p Tvard[1][1]@4= {7, 8, 5, 6}
5082: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5083: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5084: *How to reorganize?
5085: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5086: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5087: * {2, 1, 4, 8, 5, 6, 3, 7}
5088: * Struct []
5089: */
5090:
5091: /* This loop fills the array Tvar from the string 'model'.*/
5092: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5093: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5094: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5095: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5096: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5097: /* k=1 Tvar[1]=2 (from V2) */
5098: /* k=5 Tvar[5] */
5099: /* for (k=1; k<=cptcovn;k++) { */
5100: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5101: /* } */
5102: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5103: /*
5104: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5105: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5106: Tvar[k]=0;
5107: cptcovage=0;
5108: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5109: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5110: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5111: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5112: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5113: /*scanf("%d",i);*/
5114: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5115: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5116: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5117: /* covar is not filled and then is empty */
5118: cptcovprod--;
5119: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5120: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5121: cptcovage++; /* Sums the number of covariates which include age as a product */
5122: Tage[cptcovage]=k; /* Tage[1] = 4 */
5123: /*printf("stre=%s ", stre);*/
5124: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5125: cptcovprod--;
5126: cutl(stre,strb,strc,'V');
5127: Tvar[k]=atoi(stre);
5128: cptcovage++;
5129: Tage[cptcovage]=k;
5130: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5131: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5132: cptcovn++;
5133: cptcovprodnoage++;k1++;
5134: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5135: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5136: because this model-covariate is a construction we invent a new column
5137: ncovcol + k1
5138: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5139: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5140: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5141: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5142: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5143: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5144: k2=k2+2;
5145: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5146: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5147: for (i=1; i<=lastobs;i++){
5148: /* Computes the new covariate which is a product of
5149: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5150: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5151: }
5152: } /* End age is not in the model */
5153: } /* End if model includes a product */
5154: else { /* no more sum */
5155: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5156: /* scanf("%d",i);*/
5157: cutl(strd,strc,strb,'V');
5158: ks++; /**< Number of simple covariates */
5159: cptcovn++;
5160: Tvar[k]=atoi(strd);
5161: }
5162: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5163: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5164: scanf("%d",i);*/
5165: } /* end of loop + */
5166: } /* end model */
5167:
5168: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5169: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5170:
5171: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5172: printf("cptcovprod=%d ", cptcovprod);
5173: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5174:
5175: scanf("%d ",i);*/
5176:
5177:
5178: return (0); /* with covar[new additional covariate if product] and Tage if age */
5179: endread:
5180: printf("Exiting decodemodel: ");
5181: return (1);
5182: }
5183:
5184: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5185: {
5186: int i, m;
5187:
5188: for (i=1; i<=imx; i++) {
5189: for(m=2; (m<= maxwav); m++) {
5190: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5191: anint[m][i]=9999;
5192: s[m][i]=-1;
5193: }
5194: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5195: *nberr++;
5196: 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);
5197: 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);
5198: s[m][i]=-1;
5199: }
5200: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5201: *nberr++;
5202: 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]);
5203: 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]);
5204: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5205: }
5206: }
5207: }
5208:
5209: for (i=1; i<=imx; i++) {
5210: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5211: for(m=firstpass; (m<= lastpass); m++){
5212: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5213: if (s[m][i] >= nlstate+1) {
5214: if(agedc[i]>0)
5215: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5216: agev[m][i]=agedc[i];
5217: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5218: else {
5219: if ((int)andc[i]!=9999){
5220: nbwarn++;
5221: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5222: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5223: agev[m][i]=-1;
5224: }
5225: }
5226: }
5227: else if(s[m][i] !=9){ /* Standard case, age in fractional
5228: years but with the precision of a month */
5229: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5230: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5231: agev[m][i]=1;
5232: else if(agev[m][i] < *agemin){
5233: *agemin=agev[m][i];
5234: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5235: }
5236: else if(agev[m][i] >*agemax){
5237: *agemax=agev[m][i];
5238: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5239: }
5240: /*agev[m][i]=anint[m][i]-annais[i];*/
5241: /* agev[m][i] = age[i]+2*m;*/
5242: }
5243: else { /* =9 */
5244: agev[m][i]=1;
5245: s[m][i]=-1;
5246: }
5247: }
5248: else /*= 0 Unknown */
5249: agev[m][i]=1;
5250: }
5251:
5252: }
5253: for (i=1; i<=imx; i++) {
5254: for(m=firstpass; (m<=lastpass); m++){
5255: if (s[m][i] > (nlstate+ndeath)) {
5256: *nberr++;
5257: 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);
5258: 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);
5259: return 1;
5260: }
5261: }
5262: }
5263:
5264: /*for (i=1; i<=imx; i++){
5265: for (m=firstpass; (m<lastpass); m++){
5266: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5267: }
5268:
5269: }*/
5270:
5271:
5272: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5273: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5274:
5275: return (0);
5276: endread:
5277: printf("Exiting calandcheckages: ");
5278: return (1);
5279: }
5280:
5281:
5282: /***********************************************/
5283: /**************** Main Program *****************/
5284: /***********************************************/
5285:
5286: int main(int argc, char *argv[])
5287: {
5288: #ifdef GSL
5289: const gsl_multimin_fminimizer_type *T;
5290: size_t iteri = 0, it;
5291: int rval = GSL_CONTINUE;
5292: int status = GSL_SUCCESS;
5293: double ssval;
5294: #endif
5295: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5296: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5297: int linei, month, year,iout;
5298: int jj, ll, li, lj, lk, imk;
5299: int numlinepar=0; /* Current linenumber of parameter file */
5300: int itimes;
5301: int NDIM=2;
5302: int vpopbased=0;
5303:
5304: char ca[32], cb[32], cc[32];
5305: /* FILE *fichtm; *//* Html File */
5306: /* FILE *ficgp;*/ /*Gnuplot File */
5307: struct stat info;
5308: double agedeb, agefin,hf;
5309: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5310:
5311: double fret;
5312: double **xi,tmp,delta;
5313:
5314: double dum; /* Dummy variable */
5315: double ***p3mat;
5316: double ***mobaverage;
5317: int *indx;
5318: char line[MAXLINE], linepar[MAXLINE];
5319: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5320: char pathr[MAXLINE], pathimach[MAXLINE];
5321: char **bp, *tok, *val; /* pathtot */
5322: int firstobs=1, lastobs=10;
5323: int sdeb, sfin; /* Status at beginning and end */
5324: int c, h , cpt,l;
5325: int ju,jl, mi;
5326: int i1,j1, jk,aa,bb, stepsize, ij;
5327: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5328: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5329: int mobilav=0,popforecast=0;
5330: int hstepm, nhstepm;
5331: int agemortsup;
5332: float sumlpop=0.;
5333: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5334: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5335:
5336: double bage, fage, age, agelim, agebase;
5337: double ftolpl=FTOL;
5338: double **prlim;
5339: double ***param; /* Matrix of parameters */
5340: double *p;
5341: double **matcov; /* Matrix of covariance */
5342: double ***delti3; /* Scale */
5343: double *delti; /* Scale */
5344: double ***eij, ***vareij;
5345: double **varpl; /* Variances of prevalence limits by age */
5346: double *epj, vepp;
5347: double kk1, kk2;
5348: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5349: double **ximort;
5350: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5351: int *dcwave;
5352:
5353: char z[1]="c", occ;
5354:
5355: /*char *strt;*/
5356: char strtend[80];
5357:
5358: long total_usecs;
5359:
5360: /* setlocale (LC_ALL, ""); */
5361: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5362: /* textdomain (PACKAGE); */
5363: /* setlocale (LC_CTYPE, ""); */
5364: /* setlocale (LC_MESSAGES, ""); */
5365:
5366: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5367: rstart_time = time(NULL);
5368: /* (void) gettimeofday(&start_time,&tzp);*/
5369: start_time = *localtime(&rstart_time);
5370: curr_time=start_time;
5371: /*tml = *localtime(&start_time.tm_sec);*/
5372: /* strcpy(strstart,asctime(&tml)); */
5373: strcpy(strstart,asctime(&start_time));
5374:
5375: /* printf("Localtime (at start)=%s",strstart); */
5376: /* tp.tm_sec = tp.tm_sec +86400; */
5377: /* tm = *localtime(&start_time.tm_sec); */
5378: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5379: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5380: /* tmg.tm_hour=tmg.tm_hour + 1; */
5381: /* tp.tm_sec = mktime(&tmg); */
5382: /* strt=asctime(&tmg); */
5383: /* printf("Time(after) =%s",strstart); */
5384: /* (void) time (&time_value);
5385: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5386: * tm = *localtime(&time_value);
5387: * strstart=asctime(&tm);
5388: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5389: */
5390:
5391: nberr=0; /* Number of errors and warnings */
5392: nbwarn=0;
5393: getcwd(pathcd, size);
5394:
5395: printf("\n%s\n%s",version,fullversion);
5396: if(argc <=1){
5397: printf("\nEnter the parameter file name: ");
5398: fgets(pathr,FILENAMELENGTH,stdin);
5399: i=strlen(pathr);
5400: if(pathr[i-1]=='\n')
5401: pathr[i-1]='\0';
5402: i=strlen(pathr);
5403: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5404: pathr[i-1]='\0';
5405: for (tok = pathr; tok != NULL; ){
5406: printf("Pathr |%s|\n",pathr);
5407: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5408: printf("val= |%s| pathr=%s\n",val,pathr);
5409: strcpy (pathtot, val);
5410: if(pathr[0] == '\0') break; /* Dirty */
5411: }
5412: }
5413: else{
5414: strcpy(pathtot,argv[1]);
5415: }
5416: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5417: /*cygwin_split_path(pathtot,path,optionfile);
5418: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5419: /* cutv(path,optionfile,pathtot,'\\');*/
5420:
5421: /* Split argv[0], imach program to get pathimach */
5422: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5423: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5424: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5425: /* strcpy(pathimach,argv[0]); */
5426: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5427: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5428: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5429: chdir(path); /* Can be a relative path */
5430: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5431: printf("Current directory %s!\n",pathcd);
5432: strcpy(command,"mkdir ");
5433: strcat(command,optionfilefiname);
5434: if((outcmd=system(command)) != 0){
5435: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5436: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5437: /* fclose(ficlog); */
5438: /* exit(1); */
5439: }
5440: /* if((imk=mkdir(optionfilefiname))<0){ */
5441: /* perror("mkdir"); */
5442: /* } */
5443:
5444: /*-------- arguments in the command line --------*/
5445:
5446: /* Log file */
5447: strcat(filelog, optionfilefiname);
5448: strcat(filelog,".log"); /* */
5449: if((ficlog=fopen(filelog,"w"))==NULL) {
5450: printf("Problem with logfile %s\n",filelog);
5451: goto end;
5452: }
5453: fprintf(ficlog,"Log filename:%s\n",filelog);
5454: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5455: fprintf(ficlog,"\nEnter the parameter file name: \n");
5456: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5457: path=%s \n\
5458: optionfile=%s\n\
5459: optionfilext=%s\n\
5460: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5461:
5462: printf("Local time (at start):%s",strstart);
5463: fprintf(ficlog,"Local time (at start): %s",strstart);
5464: fflush(ficlog);
5465: /* (void) gettimeofday(&curr_time,&tzp); */
5466: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5467:
5468: /* */
5469: strcpy(fileres,"r");
5470: strcat(fileres, optionfilefiname);
5471: strcat(fileres,".txt"); /* Other files have txt extension */
5472:
5473: /*---------arguments file --------*/
5474:
5475: if((ficpar=fopen(optionfile,"r"))==NULL) {
5476: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5477: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5478: fflush(ficlog);
5479: /* goto end; */
5480: exit(70);
5481: }
5482:
5483:
5484:
5485: strcpy(filereso,"o");
5486: strcat(filereso,fileres);
5487: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5488: printf("Problem with Output resultfile: %s\n", filereso);
5489: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5490: fflush(ficlog);
5491: goto end;
5492: }
5493:
5494: /* Reads comments: lines beginning with '#' */
5495: numlinepar=0;
5496: while((c=getc(ficpar))=='#' && c!= EOF){
5497: ungetc(c,ficpar);
5498: fgets(line, MAXLINE, ficpar);
5499: numlinepar++;
5500: fputs(line,stdout);
5501: fputs(line,ficparo);
5502: fputs(line,ficlog);
5503: }
5504: ungetc(c,ficpar);
5505:
5506: 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);
5507: numlinepar++;
5508: 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);
5509: 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);
5510: 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);
5511: fflush(ficlog);
5512: while((c=getc(ficpar))=='#' && c!= EOF){
5513: ungetc(c,ficpar);
5514: fgets(line, MAXLINE, ficpar);
5515: numlinepar++;
5516: fputs(line, stdout);
5517: //puts(line);
5518: fputs(line,ficparo);
5519: fputs(line,ficlog);
5520: }
5521: ungetc(c,ficpar);
5522:
5523:
5524: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5525: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5526: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5527: v1+v2*age+v2*v3 makes cptcovn = 3
5528: */
5529: if (strlen(model)>1)
5530: 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*/
5531: else
5532: ncovmodel=2;
5533: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5534: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5535: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5536: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5537: 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);
5538: 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);
5539: fflush(stdout);
5540: fclose (ficlog);
5541: goto end;
5542: }
5543: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5544: delti=delti3[1][1];
5545: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5546: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5547: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5548: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5549: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5550: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5551: fclose (ficparo);
5552: fclose (ficlog);
5553: goto end;
5554: exit(0);
5555: }
5556: else if(mle==-3) {
5557: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5558: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5559: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5560: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5561: matcov=matrix(1,npar,1,npar);
5562: }
5563: else{
5564: /* Read guessed parameters */
5565: /* Reads comments: lines beginning with '#' */
5566: while((c=getc(ficpar))=='#' && c!= EOF){
5567: ungetc(c,ficpar);
5568: fgets(line, MAXLINE, ficpar);
5569: numlinepar++;
5570: fputs(line,stdout);
5571: fputs(line,ficparo);
5572: fputs(line,ficlog);
5573: }
5574: ungetc(c,ficpar);
5575:
5576: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5577: for(i=1; i <=nlstate; i++){
5578: j=0;
5579: for(jj=1; jj <=nlstate+ndeath; jj++){
5580: if(jj==i) continue;
5581: j++;
5582: fscanf(ficpar,"%1d%1d",&i1,&j1);
5583: if ((i1 != i) && (j1 != j)){
5584: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5585: It might be a problem of design; if ncovcol and the model are correct\n \
5586: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5587: exit(1);
5588: }
5589: fprintf(ficparo,"%1d%1d",i1,j1);
5590: if(mle==1)
5591: printf("%1d%1d",i,j);
5592: fprintf(ficlog,"%1d%1d",i,j);
5593: for(k=1; k<=ncovmodel;k++){
5594: fscanf(ficpar," %lf",¶m[i][j][k]);
5595: if(mle==1){
5596: printf(" %lf",param[i][j][k]);
5597: fprintf(ficlog," %lf",param[i][j][k]);
5598: }
5599: else
5600: fprintf(ficlog," %lf",param[i][j][k]);
5601: fprintf(ficparo," %lf",param[i][j][k]);
5602: }
5603: fscanf(ficpar,"\n");
5604: numlinepar++;
5605: if(mle==1)
5606: printf("\n");
5607: fprintf(ficlog,"\n");
5608: fprintf(ficparo,"\n");
5609: }
5610: }
5611: fflush(ficlog);
5612:
5613: /* Reads scales values */
5614: p=param[1][1];
5615:
5616: /* Reads comments: lines beginning with '#' */
5617: while((c=getc(ficpar))=='#' && c!= EOF){
5618: ungetc(c,ficpar);
5619: fgets(line, MAXLINE, ficpar);
5620: numlinepar++;
5621: fputs(line,stdout);
5622: fputs(line,ficparo);
5623: fputs(line,ficlog);
5624: }
5625: ungetc(c,ficpar);
5626:
5627: for(i=1; i <=nlstate; i++){
5628: for(j=1; j <=nlstate+ndeath-1; j++){
5629: fscanf(ficpar,"%1d%1d",&i1,&j1);
5630: if ((i1-i)*(j1-j)!=0){
5631: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5632: exit(1);
5633: }
5634: printf("%1d%1d",i,j);
5635: fprintf(ficparo,"%1d%1d",i1,j1);
5636: fprintf(ficlog,"%1d%1d",i1,j1);
5637: for(k=1; k<=ncovmodel;k++){
5638: fscanf(ficpar,"%le",&delti3[i][j][k]);
5639: printf(" %le",delti3[i][j][k]);
5640: fprintf(ficparo," %le",delti3[i][j][k]);
5641: fprintf(ficlog," %le",delti3[i][j][k]);
5642: }
5643: fscanf(ficpar,"\n");
5644: numlinepar++;
5645: printf("\n");
5646: fprintf(ficparo,"\n");
5647: fprintf(ficlog,"\n");
5648: }
5649: }
5650: fflush(ficlog);
5651:
5652: /* Reads covariance matrix */
5653: delti=delti3[1][1];
5654:
5655:
5656: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5657:
5658: /* Reads comments: lines beginning with '#' */
5659: while((c=getc(ficpar))=='#' && c!= EOF){
5660: ungetc(c,ficpar);
5661: fgets(line, MAXLINE, ficpar);
5662: numlinepar++;
5663: fputs(line,stdout);
5664: fputs(line,ficparo);
5665: fputs(line,ficlog);
5666: }
5667: ungetc(c,ficpar);
5668:
5669: matcov=matrix(1,npar,1,npar);
5670: for(i=1; i <=npar; i++)
5671: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5672:
5673: for(i=1; i <=npar; i++){
5674: fscanf(ficpar,"%s",str);
5675: if(mle==1)
5676: printf("%s",str);
5677: fprintf(ficlog,"%s",str);
5678: fprintf(ficparo,"%s",str);
5679: for(j=1; j <=i; j++){
5680: fscanf(ficpar," %le",&matcov[i][j]);
5681: if(mle==1){
5682: printf(" %.5le",matcov[i][j]);
5683: }
5684: fprintf(ficlog," %.5le",matcov[i][j]);
5685: fprintf(ficparo," %.5le",matcov[i][j]);
5686: }
5687: fscanf(ficpar,"\n");
5688: numlinepar++;
5689: if(mle==1)
5690: printf("\n");
5691: fprintf(ficlog,"\n");
5692: fprintf(ficparo,"\n");
5693: }
5694: for(i=1; i <=npar; i++)
5695: for(j=i+1;j<=npar;j++)
5696: matcov[i][j]=matcov[j][i];
5697:
5698: if(mle==1)
5699: printf("\n");
5700: fprintf(ficlog,"\n");
5701:
5702: fflush(ficlog);
5703:
5704: /*-------- Rewriting parameter file ----------*/
5705: strcpy(rfileres,"r"); /* "Rparameterfile */
5706: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5707: strcat(rfileres,"."); /* */
5708: strcat(rfileres,optionfilext); /* Other files have txt extension */
5709: if((ficres =fopen(rfileres,"w"))==NULL) {
5710: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5711: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5712: }
5713: fprintf(ficres,"#%s\n",version);
5714: } /* End of mle != -3 */
5715:
5716:
5717: n= lastobs;
5718: num=lvector(1,n);
5719: moisnais=vector(1,n);
5720: annais=vector(1,n);
5721: moisdc=vector(1,n);
5722: andc=vector(1,n);
5723: agedc=vector(1,n);
5724: cod=ivector(1,n);
5725: weight=vector(1,n);
5726: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5727: mint=matrix(1,maxwav,1,n);
5728: anint=matrix(1,maxwav,1,n);
5729: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5730: tab=ivector(1,NCOVMAX);
5731: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5732:
5733: /* Reads data from file datafile */
5734: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5735: goto end;
5736:
5737: /* Calculation of the number of parameters from char model */
5738: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5739: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5740: k=3 V4 Tvar[k=3]= 4 (from V4)
5741: k=2 V1 Tvar[k=2]= 1 (from V1)
5742: k=1 Tvar[1]=2 (from V2)
5743: */
5744: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5745: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5746: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5747: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5748: */
5749: /* For model-covariate k tells which data-covariate to use but
5750: because this model-covariate is a construction we invent a new column
5751: ncovcol + k1
5752: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5753: Tvar[3=V1*V4]=4+1 etc */
5754: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
5755: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5756: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5757: */
5758: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5759: 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
5760: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5761: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
5762: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
5763: 4 covariates (3 plus signs)
5764: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5765: */
5766:
5767: if(decodemodel(model, lastobs) == 1)
5768: goto end;
5769:
5770: if((double)(lastobs-imx)/(double)imx > 1.10){
5771: nbwarn++;
5772: 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);
5773: 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);
5774: }
5775: /* if(mle==1){*/
5776: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5777: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
5778: }
5779:
5780: /*-calculation of age at interview from date of interview and age at death -*/
5781: agev=matrix(1,maxwav,1,imx);
5782:
5783: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5784: goto end;
5785:
5786:
5787: agegomp=(int)agemin;
5788: free_vector(moisnais,1,n);
5789: free_vector(annais,1,n);
5790: /* free_matrix(mint,1,maxwav,1,n);
5791: free_matrix(anint,1,maxwav,1,n);*/
5792: free_vector(moisdc,1,n);
5793: free_vector(andc,1,n);
5794: /* */
5795:
5796: wav=ivector(1,imx);
5797: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5798: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5799: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5800:
5801: /* Concatenates waves */
5802: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5803: /* */
5804:
5805: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5806:
5807: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5808: ncodemax[1]=1;
5809: Ndum =ivector(-1,NCOVMAX);
5810: if (ncovmodel > 2)
5811: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5812:
5813: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5814: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5815: h=0;
5816:
5817:
5818: /*if (cptcovn > 0) */
5819:
5820:
5821: m=pow(2,cptcoveff);
5822:
5823: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5824: 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 */
5825: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5826: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5827: h++;
5828: if (h>m)
5829: h=1;
5830: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
5831: * h 1 2 3 4
5832: *______________________________
5833: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5834: * 2 2 1 1 1
5835: * 3 i=2 1 2 1 1
5836: * 4 2 2 1 1
5837: * 5 i=3 1 i=2 1 2 1
5838: * 6 2 1 2 1
5839: * 7 i=4 1 2 2 1
5840: * 8 2 2 2 1
5841: * 9 i=5 1 i=3 1 i=2 1 1
5842: * 10 2 1 1 1
5843: * 11 i=6 1 2 1 1
5844: * 12 2 2 1 1
5845: * 13 i=7 1 i=4 1 2 1
5846: * 14 2 1 2 1
5847: * 15 i=8 1 2 2 1
5848: * 16 2 2 2 1
5849: */
5850: codtab[h][k]=j;
5851: /*codtab[h][Tvar[k]]=j;*/
5852: 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]]);
5853: }
5854: }
5855: }
5856: }
5857: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5858: codtab[1][2]=1;codtab[2][2]=2; */
5859: /* for(i=1; i <=m ;i++){
5860: for(k=1; k <=cptcovn; k++){
5861: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5862: }
5863: printf("\n");
5864: }
5865: scanf("%d",i);*/
5866:
5867: free_ivector(Ndum,-1,NCOVMAX);
5868:
5869:
5870:
5871: /*------------ gnuplot -------------*/
5872: strcpy(optionfilegnuplot,optionfilefiname);
5873: if(mle==-3)
5874: strcat(optionfilegnuplot,"-mort");
5875: strcat(optionfilegnuplot,".gp");
5876:
5877: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5878: printf("Problem with file %s",optionfilegnuplot);
5879: }
5880: else{
5881: fprintf(ficgp,"\n# %s\n", version);
5882: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5883: //fprintf(ficgp,"set missing 'NaNq'\n");
5884: fprintf(ficgp,"set datafile missing 'NaNq'\n");
5885: }
5886: /* fclose(ficgp);*/
5887: /*--------- index.htm --------*/
5888:
5889: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5890: if(mle==-3)
5891: strcat(optionfilehtm,"-mort");
5892: strcat(optionfilehtm,".htm");
5893: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5894: printf("Problem with %s \n",optionfilehtm);
5895: exit(0);
5896: }
5897:
5898: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5899: strcat(optionfilehtmcov,"-cov.htm");
5900: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5901: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5902: }
5903: else{
5904: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5905: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5906: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5907: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5908: }
5909:
5910: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5911: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5912: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5913: \n\
5914: <hr size=\"2\" color=\"#EC5E5E\">\
5915: <ul><li><h4>Parameter files</h4>\n\
5916: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5917: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5918: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5919: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5920: - Date and time at start: %s</ul>\n",\
5921: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5922: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5923: fileres,fileres,\
5924: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5925: fflush(fichtm);
5926:
5927: strcpy(pathr,path);
5928: strcat(pathr,optionfilefiname);
5929: chdir(optionfilefiname); /* Move to directory named optionfile */
5930:
5931: /* Calculates basic frequencies. Computes observed prevalence at single age
5932: and prints on file fileres'p'. */
5933: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5934:
5935: fprintf(fichtm,"\n");
5936: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5937: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5938: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5939: imx,agemin,agemax,jmin,jmax,jmean);
5940: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5941: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5942: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5943: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5944: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5945:
5946:
5947: /* For Powell, parameters are in a vector p[] starting at p[1]
5948: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5949: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5950:
5951: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5952:
5953: if (mle==-3){
5954: ximort=matrix(1,NDIM,1,NDIM);
5955: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
5956: cens=ivector(1,n);
5957: ageexmed=vector(1,n);
5958: agecens=vector(1,n);
5959: dcwave=ivector(1,n);
5960:
5961: for (i=1; i<=imx; i++){
5962: dcwave[i]=-1;
5963: for (m=firstpass; m<=lastpass; m++)
5964: if (s[m][i]>nlstate) {
5965: dcwave[i]=m;
5966: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5967: break;
5968: }
5969: }
5970:
5971: for (i=1; i<=imx; i++) {
5972: if (wav[i]>0){
5973: ageexmed[i]=agev[mw[1][i]][i];
5974: j=wav[i];
5975: agecens[i]=1.;
5976:
5977: if (ageexmed[i]> 1 && wav[i] > 0){
5978: agecens[i]=agev[mw[j][i]][i];
5979: cens[i]= 1;
5980: }else if (ageexmed[i]< 1)
5981: cens[i]= -1;
5982: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5983: cens[i]=0 ;
5984: }
5985: else cens[i]=-1;
5986: }
5987:
5988: for (i=1;i<=NDIM;i++) {
5989: for (j=1;j<=NDIM;j++)
5990: ximort[i][j]=(i == j ? 1.0 : 0.0);
5991: }
5992:
5993: /*p[1]=0.0268; p[NDIM]=0.083;*/
5994: /*printf("%lf %lf", p[1], p[2]);*/
5995:
5996:
5997: #ifdef GSL
5998: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5999: #elsedef
6000: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6001: #endif
6002: strcpy(filerespow,"pow-mort");
6003: strcat(filerespow,fileres);
6004: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6005: printf("Problem with resultfile: %s\n", filerespow);
6006: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6007: }
6008: #ifdef GSL
6009: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6010: #elsedef
6011: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6012: #endif
6013: /* for (i=1;i<=nlstate;i++)
6014: for(j=1;j<=nlstate+ndeath;j++)
6015: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6016: */
6017: fprintf(ficrespow,"\n");
6018: #ifdef GSL
6019: /* gsl starts here */
6020: T = gsl_multimin_fminimizer_nmsimplex;
6021: gsl_multimin_fminimizer *sfm = NULL;
6022: gsl_vector *ss, *x;
6023: gsl_multimin_function minex_func;
6024:
6025: /* Initial vertex size vector */
6026: ss = gsl_vector_alloc (NDIM);
6027:
6028: if (ss == NULL){
6029: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6030: }
6031: /* Set all step sizes to 1 */
6032: gsl_vector_set_all (ss, 0.001);
6033:
6034: /* Starting point */
6035:
6036: x = gsl_vector_alloc (NDIM);
6037:
6038: if (x == NULL){
6039: gsl_vector_free(ss);
6040: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6041: }
6042:
6043: /* Initialize method and iterate */
6044: /* p[1]=0.0268; p[NDIM]=0.083; */
6045: /* gsl_vector_set(x, 0, 0.0268); */
6046: /* gsl_vector_set(x, 1, 0.083); */
6047: gsl_vector_set(x, 0, p[1]);
6048: gsl_vector_set(x, 1, p[2]);
6049:
6050: minex_func.f = &gompertz_f;
6051: minex_func.n = NDIM;
6052: minex_func.params = (void *)&p; /* ??? */
6053:
6054: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6055: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6056:
6057: printf("Iterations beginning .....\n\n");
6058: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6059:
6060: iteri=0;
6061: while (rval == GSL_CONTINUE){
6062: iteri++;
6063: status = gsl_multimin_fminimizer_iterate(sfm);
6064:
6065: if (status) printf("error: %s\n", gsl_strerror (status));
6066: fflush(0);
6067:
6068: if (status)
6069: break;
6070:
6071: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6072: ssval = gsl_multimin_fminimizer_size (sfm);
6073:
6074: if (rval == GSL_SUCCESS)
6075: printf ("converged to a local maximum at\n");
6076:
6077: printf("%5d ", iteri);
6078: for (it = 0; it < NDIM; it++){
6079: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6080: }
6081: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6082: }
6083:
6084: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6085:
6086: gsl_vector_free(x); /* initial values */
6087: gsl_vector_free(ss); /* inital step size */
6088: for (it=0; it<NDIM; it++){
6089: p[it+1]=gsl_vector_get(sfm->x,it);
6090: fprintf(ficrespow," %.12lf", p[it]);
6091: }
6092: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6093: #endif
6094: #ifdef POWELL
6095: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6096: #endif
6097: fclose(ficrespow);
6098:
6099: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6100:
6101: for(i=1; i <=NDIM; i++)
6102: for(j=i+1;j<=NDIM;j++)
6103: matcov[i][j]=matcov[j][i];
6104:
6105: printf("\nCovariance matrix\n ");
6106: for(i=1; i <=NDIM; i++) {
6107: for(j=1;j<=NDIM;j++){
6108: printf("%f ",matcov[i][j]);
6109: }
6110: printf("\n ");
6111: }
6112:
6113: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6114: for (i=1;i<=NDIM;i++)
6115: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6116:
6117: lsurv=vector(1,AGESUP);
6118: lpop=vector(1,AGESUP);
6119: tpop=vector(1,AGESUP);
6120: lsurv[agegomp]=100000;
6121:
6122: for (k=agegomp;k<=AGESUP;k++) {
6123: agemortsup=k;
6124: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6125: }
6126:
6127: for (k=agegomp;k<agemortsup;k++)
6128: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6129:
6130: for (k=agegomp;k<agemortsup;k++){
6131: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6132: sumlpop=sumlpop+lpop[k];
6133: }
6134:
6135: tpop[agegomp]=sumlpop;
6136: for (k=agegomp;k<(agemortsup-3);k++){
6137: /* tpop[k+1]=2;*/
6138: tpop[k+1]=tpop[k]-lpop[k];
6139: }
6140:
6141:
6142: printf("\nAge lx qx dx Lx Tx e(x)\n");
6143: for (k=agegomp;k<(agemortsup-2);k++)
6144: 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]);
6145:
6146:
6147: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6148: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6149:
6150: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6151: stepm, weightopt,\
6152: model,imx,p,matcov,agemortsup);
6153:
6154: free_vector(lsurv,1,AGESUP);
6155: free_vector(lpop,1,AGESUP);
6156: free_vector(tpop,1,AGESUP);
6157: #ifdef GSL
6158: free_ivector(cens,1,n);
6159: free_vector(agecens,1,n);
6160: free_ivector(dcwave,1,n);
6161: free_matrix(ximort,1,NDIM,1,NDIM);
6162: #endif
6163: } /* Endof if mle==-3 */
6164:
6165: else{ /* For mle >=1 */
6166: globpr=0;/* debug */
6167: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6168: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6169: for (k=1; k<=npar;k++)
6170: printf(" %d %8.5f",k,p[k]);
6171: printf("\n");
6172: globpr=1; /* to print the contributions */
6173: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6174: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6175: for (k=1; k<=npar;k++)
6176: printf(" %d %8.5f",k,p[k]);
6177: printf("\n");
6178: if(mle>=1){ /* Could be 1 or 2 */
6179: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6180: }
6181:
6182: /*--------- results files --------------*/
6183: 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);
6184:
6185:
6186: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6187: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6188: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6189: for(i=1,jk=1; i <=nlstate; i++){
6190: for(k=1; k <=(nlstate+ndeath); k++){
6191: if (k != i) {
6192: printf("%d%d ",i,k);
6193: fprintf(ficlog,"%d%d ",i,k);
6194: fprintf(ficres,"%1d%1d ",i,k);
6195: for(j=1; j <=ncovmodel; j++){
6196: printf("%lf ",p[jk]);
6197: fprintf(ficlog,"%lf ",p[jk]);
6198: fprintf(ficres,"%lf ",p[jk]);
6199: jk++;
6200: }
6201: printf("\n");
6202: fprintf(ficlog,"\n");
6203: fprintf(ficres,"\n");
6204: }
6205: }
6206: }
6207: if(mle!=0){
6208: /* Computing hessian and covariance matrix */
6209: ftolhess=ftol; /* Usually correct */
6210: hesscov(matcov, p, npar, delti, ftolhess, func);
6211: }
6212: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6213: printf("# Scales (for hessian or gradient estimation)\n");
6214: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6215: for(i=1,jk=1; i <=nlstate; i++){
6216: for(j=1; j <=nlstate+ndeath; j++){
6217: if (j!=i) {
6218: fprintf(ficres,"%1d%1d",i,j);
6219: printf("%1d%1d",i,j);
6220: fprintf(ficlog,"%1d%1d",i,j);
6221: for(k=1; k<=ncovmodel;k++){
6222: printf(" %.5e",delti[jk]);
6223: fprintf(ficlog," %.5e",delti[jk]);
6224: fprintf(ficres," %.5e",delti[jk]);
6225: jk++;
6226: }
6227: printf("\n");
6228: fprintf(ficlog,"\n");
6229: fprintf(ficres,"\n");
6230: }
6231: }
6232: }
6233:
6234: 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");
6235: if(mle>=1)
6236: 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");
6237: 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");
6238: /* # 121 Var(a12)\n\ */
6239: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6240: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6241: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6242: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6243: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6244: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6245: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6246:
6247:
6248: /* Just to have a covariance matrix which will be more understandable
6249: even is we still don't want to manage dictionary of variables
6250: */
6251: for(itimes=1;itimes<=2;itimes++){
6252: jj=0;
6253: for(i=1; i <=nlstate; i++){
6254: for(j=1; j <=nlstate+ndeath; j++){
6255: if(j==i) continue;
6256: for(k=1; k<=ncovmodel;k++){
6257: jj++;
6258: ca[0]= k+'a'-1;ca[1]='\0';
6259: if(itimes==1){
6260: if(mle>=1)
6261: printf("#%1d%1d%d",i,j,k);
6262: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6263: fprintf(ficres,"#%1d%1d%d",i,j,k);
6264: }else{
6265: if(mle>=1)
6266: printf("%1d%1d%d",i,j,k);
6267: fprintf(ficlog,"%1d%1d%d",i,j,k);
6268: fprintf(ficres,"%1d%1d%d",i,j,k);
6269: }
6270: ll=0;
6271: for(li=1;li <=nlstate; li++){
6272: for(lj=1;lj <=nlstate+ndeath; lj++){
6273: if(lj==li) continue;
6274: for(lk=1;lk<=ncovmodel;lk++){
6275: ll++;
6276: if(ll<=jj){
6277: cb[0]= lk +'a'-1;cb[1]='\0';
6278: if(ll<jj){
6279: if(itimes==1){
6280: if(mle>=1)
6281: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6282: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6283: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6284: }else{
6285: if(mle>=1)
6286: printf(" %.5e",matcov[jj][ll]);
6287: fprintf(ficlog," %.5e",matcov[jj][ll]);
6288: fprintf(ficres," %.5e",matcov[jj][ll]);
6289: }
6290: }else{
6291: if(itimes==1){
6292: if(mle>=1)
6293: printf(" Var(%s%1d%1d)",ca,i,j);
6294: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6295: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6296: }else{
6297: if(mle>=1)
6298: printf(" %.5e",matcov[jj][ll]);
6299: fprintf(ficlog," %.5e",matcov[jj][ll]);
6300: fprintf(ficres," %.5e",matcov[jj][ll]);
6301: }
6302: }
6303: }
6304: } /* end lk */
6305: } /* end lj */
6306: } /* end li */
6307: if(mle>=1)
6308: printf("\n");
6309: fprintf(ficlog,"\n");
6310: fprintf(ficres,"\n");
6311: numlinepar++;
6312: } /* end k*/
6313: } /*end j */
6314: } /* end i */
6315: } /* end itimes */
6316:
6317: fflush(ficlog);
6318: fflush(ficres);
6319:
6320: while((c=getc(ficpar))=='#' && c!= EOF){
6321: ungetc(c,ficpar);
6322: fgets(line, MAXLINE, ficpar);
6323: fputs(line,stdout);
6324: fputs(line,ficparo);
6325: }
6326: ungetc(c,ficpar);
6327:
6328: estepm=0;
6329: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6330: if (estepm==0 || estepm < stepm) estepm=stepm;
6331: if (fage <= 2) {
6332: bage = ageminpar;
6333: fage = agemaxpar;
6334: }
6335:
6336: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6337: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6338: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6339:
6340: while((c=getc(ficpar))=='#' && c!= EOF){
6341: ungetc(c,ficpar);
6342: fgets(line, MAXLINE, ficpar);
6343: fputs(line,stdout);
6344: fputs(line,ficparo);
6345: }
6346: ungetc(c,ficpar);
6347:
6348: 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);
6349: 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);
6350: 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);
6351: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6352: 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);
6353:
6354: while((c=getc(ficpar))=='#' && c!= EOF){
6355: ungetc(c,ficpar);
6356: fgets(line, MAXLINE, ficpar);
6357: fputs(line,stdout);
6358: fputs(line,ficparo);
6359: }
6360: ungetc(c,ficpar);
6361:
6362:
6363: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6364: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6365:
6366: fscanf(ficpar,"pop_based=%d\n",&popbased);
6367: fprintf(ficparo,"pop_based=%d\n",popbased);
6368: fprintf(ficres,"pop_based=%d\n",popbased);
6369:
6370: while((c=getc(ficpar))=='#' && c!= EOF){
6371: ungetc(c,ficpar);
6372: fgets(line, MAXLINE, ficpar);
6373: fputs(line,stdout);
6374: fputs(line,ficparo);
6375: }
6376: ungetc(c,ficpar);
6377:
6378: 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);
6379: 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);
6380: 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);
6381: 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);
6382: 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);
6383: /* day and month of proj2 are not used but only year anproj2.*/
6384:
6385:
6386:
6387: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6388: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6389:
6390: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6391: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6392:
6393: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6394: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6395: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6396:
6397: /*------------ free_vector -------------*/
6398: /* chdir(path); */
6399:
6400: free_ivector(wav,1,imx);
6401: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6402: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6403: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6404: free_lvector(num,1,n);
6405: free_vector(agedc,1,n);
6406: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6407: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6408: fclose(ficparo);
6409: fclose(ficres);
6410:
6411:
6412: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6413: #include "prevlim.h" /* Use ficrespl, ficlog */
6414: fclose(ficrespl);
6415:
6416: #ifdef FREEEXIT2
6417: #include "freeexit2.h"
6418: #endif
6419:
6420: /*------------- h Pij x at various ages ------------*/
6421: #include "hpijx.h"
6422: fclose(ficrespij);
6423:
6424: /*-------------- Variance of one-step probabilities---*/
6425: k=1;
6426: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6427:
6428:
6429: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6430: for(i=1;i<=AGESUP;i++)
6431: for(j=1;j<=NCOVMAX;j++)
6432: for(k=1;k<=NCOVMAX;k++)
6433: probs[i][j][k]=0.;
6434:
6435: /*---------- Forecasting ------------------*/
6436: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6437: if(prevfcast==1){
6438: /* if(stepm ==1){*/
6439: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6440: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6441: /* } */
6442: /* else{ */
6443: /* erreur=108; */
6444: /* 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); */
6445: /* 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); */
6446: /* } */
6447: }
6448:
6449:
6450: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6451:
6452: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6453: /* 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",\
6454: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6455: */
6456:
6457: if (mobilav!=0) {
6458: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6459: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6460: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6461: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6462: }
6463: }
6464:
6465:
6466: /*---------- Health expectancies, no variances ------------*/
6467:
6468: strcpy(filerese,"e");
6469: strcat(filerese,fileres);
6470: if((ficreseij=fopen(filerese,"w"))==NULL) {
6471: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6472: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6473: }
6474: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6475: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6476: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6477: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6478:
6479: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6480: fprintf(ficreseij,"\n#****** ");
6481: for(j=1;j<=cptcoveff;j++) {
6482: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6483: }
6484: fprintf(ficreseij,"******\n");
6485:
6486: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6487: oldm=oldms;savm=savms;
6488: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6489:
6490: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6491: /*}*/
6492: }
6493: fclose(ficreseij);
6494:
6495:
6496: /*---------- Health expectancies and variances ------------*/
6497:
6498:
6499: strcpy(filerest,"t");
6500: strcat(filerest,fileres);
6501: if((ficrest=fopen(filerest,"w"))==NULL) {
6502: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6503: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6504: }
6505: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6506: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6507:
6508:
6509: strcpy(fileresstde,"stde");
6510: strcat(fileresstde,fileres);
6511: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6512: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6513: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6514: }
6515: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6516: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6517:
6518: strcpy(filerescve,"cve");
6519: strcat(filerescve,fileres);
6520: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6521: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6522: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6523: }
6524: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6525: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6526:
6527: strcpy(fileresv,"v");
6528: strcat(fileresv,fileres);
6529: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6530: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6531: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6532: }
6533: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6534: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6535:
6536: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6537: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6538:
6539: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6540: fprintf(ficrest,"\n#****** ");
6541: for(j=1;j<=cptcoveff;j++)
6542: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6543: fprintf(ficrest,"******\n");
6544:
6545: fprintf(ficresstdeij,"\n#****** ");
6546: fprintf(ficrescveij,"\n#****** ");
6547: for(j=1;j<=cptcoveff;j++) {
6548: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6549: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6550: }
6551: fprintf(ficresstdeij,"******\n");
6552: fprintf(ficrescveij,"******\n");
6553:
6554: fprintf(ficresvij,"\n#****** ");
6555: for(j=1;j<=cptcoveff;j++)
6556: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6557: fprintf(ficresvij,"******\n");
6558:
6559: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6560: oldm=oldms;savm=savms;
6561: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6562: /*
6563: */
6564: /* goto endfree; */
6565:
6566: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6567: pstamp(ficrest);
6568:
6569:
6570: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6571: oldm=oldms;savm=savms; /* Segmentation fault */
6572: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6573: 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 ");
6574: if(vpopbased==1)
6575: 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);
6576: else
6577: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6578: fprintf(ficrest,"# Age e.. (std) ");
6579: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6580: fprintf(ficrest,"\n");
6581:
6582: epj=vector(1,nlstate+1);
6583: for(age=bage; age <=fage ;age++){
6584: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6585: if (vpopbased==1) {
6586: if(mobilav ==0){
6587: for(i=1; i<=nlstate;i++)
6588: prlim[i][i]=probs[(int)age][i][k];
6589: }else{ /* mobilav */
6590: for(i=1; i<=nlstate;i++)
6591: prlim[i][i]=mobaverage[(int)age][i][k];
6592: }
6593: }
6594:
6595: fprintf(ficrest," %4.0f",age);
6596: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6597: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6598: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6599: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6600: }
6601: epj[nlstate+1] +=epj[j];
6602: }
6603:
6604: for(i=1, vepp=0.;i <=nlstate;i++)
6605: for(j=1;j <=nlstate;j++)
6606: vepp += vareij[i][j][(int)age];
6607: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6608: for(j=1;j <=nlstate;j++){
6609: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6610: }
6611: fprintf(ficrest,"\n");
6612: }
6613: }
6614: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6615: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6616: free_vector(epj,1,nlstate+1);
6617: /*}*/
6618: }
6619: free_vector(weight,1,n);
6620: free_imatrix(Tvard,1,NCOVMAX,1,2);
6621: free_imatrix(s,1,maxwav+1,1,n);
6622: free_matrix(anint,1,maxwav,1,n);
6623: free_matrix(mint,1,maxwav,1,n);
6624: free_ivector(cod,1,n);
6625: free_ivector(tab,1,NCOVMAX);
6626: fclose(ficresstdeij);
6627: fclose(ficrescveij);
6628: fclose(ficresvij);
6629: fclose(ficrest);
6630: fclose(ficpar);
6631:
6632: /*------- Variance of period (stable) prevalence------*/
6633:
6634: strcpy(fileresvpl,"vpl");
6635: strcat(fileresvpl,fileres);
6636: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6637: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6638: exit(0);
6639: }
6640: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6641:
6642: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6643: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6644:
6645: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6646: fprintf(ficresvpl,"\n#****** ");
6647: for(j=1;j<=cptcoveff;j++)
6648: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6649: fprintf(ficresvpl,"******\n");
6650:
6651: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6652: oldm=oldms;savm=savms;
6653: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6654: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6655: /*}*/
6656: }
6657:
6658: fclose(ficresvpl);
6659:
6660: /*---------- End : free ----------------*/
6661: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6662: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6663: } /* mle==-3 arrives here for freeing */
6664: endfree:
6665: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6666: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6667: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6668: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6669: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6670: free_matrix(covar,0,NCOVMAX,1,n);
6671: free_matrix(matcov,1,npar,1,npar);
6672: /*free_vector(delti,1,npar);*/
6673: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6674: free_matrix(agev,1,maxwav,1,imx);
6675: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6676:
6677: free_ivector(ncodemax,1,NCOVMAX);
6678: free_ivector(Tvar,1,NCOVMAX);
6679: free_ivector(Tprod,1,NCOVMAX);
6680: free_ivector(Tvaraff,1,NCOVMAX);
6681: free_ivector(Tage,1,NCOVMAX);
6682:
6683: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6684: free_imatrix(codtab,1,100,1,10);
6685: fflush(fichtm);
6686: fflush(ficgp);
6687:
6688:
6689: if((nberr >0) || (nbwarn>0)){
6690: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6691: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6692: }else{
6693: printf("End of Imach\n");
6694: fprintf(ficlog,"End of Imach\n");
6695: }
6696: printf("See log file on %s\n",filelog);
6697: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6698: /*(void) gettimeofday(&end_time,&tzp);*/
6699: rend_time = time(NULL);
6700: end_time = *localtime(&rend_time);
6701: /* tml = *localtime(&end_time.tm_sec); */
6702: strcpy(strtend,asctime(&end_time));
6703: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6704: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6705: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6706:
6707: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6708: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6709: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6710: /* printf("Total time was %d uSec.\n", total_usecs);*/
6711: /* if(fileappend(fichtm,optionfilehtm)){ */
6712: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6713: fclose(fichtm);
6714: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6715: fclose(fichtmcov);
6716: fclose(ficgp);
6717: fclose(ficlog);
6718: /*------ End -----------*/
6719:
6720:
6721: printf("Before Current directory %s!\n",pathcd);
6722: if(chdir(pathcd) != 0)
6723: printf("Can't move to directory %s!\n",path);
6724: if(getcwd(pathcd,MAXLINE) > 0)
6725: printf("Current directory %s!\n",pathcd);
6726: /*strcat(plotcmd,CHARSEPARATOR);*/
6727: sprintf(plotcmd,"gnuplot");
6728: #ifdef _WIN32
6729: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6730: #endif
6731: if(!stat(plotcmd,&info)){
6732: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6733: if(!stat(getenv("GNUPLOTBIN"),&info)){
6734: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6735: }else
6736: strcpy(pplotcmd,plotcmd);
6737: #ifdef __unix
6738: strcpy(plotcmd,GNUPLOTPROGRAM);
6739: if(!stat(plotcmd,&info)){
6740: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6741: }else
6742: strcpy(pplotcmd,plotcmd);
6743: #endif
6744: }else
6745: strcpy(pplotcmd,plotcmd);
6746:
6747: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6748: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
6749:
6750: if((outcmd=system(plotcmd)) != 0){
6751: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
6752: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
6753: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
6754: if((outcmd=system(plotcmd)) != 0)
6755: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
6756: }
6757: printf(" Successful, please wait...");
6758: while (z[0] != 'q') {
6759: /* chdir(path); */
6760: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
6761: scanf("%s",z);
6762: /* if (z[0] == 'c') system("./imach"); */
6763: if (z[0] == 'e') {
6764: #ifdef __APPLE__
6765: sprintf(pplotcmd, "open %s", optionfilehtm);
6766: #elif __linux
6767: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
6768: #else
6769: sprintf(pplotcmd, "%s", optionfilehtm);
6770: #endif
6771: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6772: system(pplotcmd);
6773: }
6774: else if (z[0] == 'g') system(plotcmd);
6775: else if (z[0] == 'q') exit(0);
6776: }
6777: end:
6778: while (z[0] != 'q') {
6779: printf("\nType q for exiting: ");
6780: scanf("%s",z);
6781: }
6782: }
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